From 3cd136861c68b8c24cc653c903c620d55be4b294 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 2 Apr 2012 09:18:14 +0200 Subject: Remove PC descriptor --- application.rb | 48 - java/Acme/IntHashtable.class | Bin 3135 -> 0 bytes java/Acme/IntHashtableEntry.class | Bin 420 -> 0 bytes java/Acme/IntHashtableEnumerator.class | Bin 879 -> 0 bytes java/Acme/JPM/Encoders/GifEncoder.class | Bin 6055 -> 0 bytes java/Acme/JPM/Encoders/GifEncoderHashitem.class | Bin 300 -> 0 bytes java/Acme/JPM/Encoders/GrayJPEG.class | Bin 9093 -> 0 bytes java/Acme/JPM/Encoders/ImageEncoder.class | Bin 2918 -> 0 bytes java/Acme/JPM/Encoders/PpmEncoder.class | Bin 1207 -> 0 bytes java/Jmol.jar | Bin 3422261 -> 0 bytes java/JoelibFc.class | Bin 2069 -> 0 bytes java/ant.jar | Bin 999966 -> 0 bytes java/bin2hex.pl | 35 - java/cformat/PrintfFormat$DecDouble.class | Bin 1481 -> 0 bytes java/cformat/PrintfFormat$OutBuffer.class | Bin 1048 -> 0 bytes java/cformat/PrintfFormat.class | Bin 7388 -> 0 bytes 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java/joelib2/feature/result/IntMatrixResult.class | Bin 3982 -> 0 bytes java/joelib2/feature/result/IntResult.class | Bin 3167 -> 0 bytes java/joelib2/feature/result/SMILESResult.class | Bin 2435 -> 0 bytes .../joelib2/feature/result/StringArrayResult.class | Bin 3971 -> 0 bytes java/joelib2/feature/result/StringResult.class | Bin 1977 -> 0 bytes .../feature/result/StringVectorResult.class | Bin 3539 -> 0 bytes .../feature/types/APropertyDistanceMatrix.class | Bin 4253 -> 0 bytes java/joelib2/feature/types/Autocorrelation.class | Bin 5603 -> 0 bytes java/joelib2/feature/types/BCUT.class | Bin 4716 -> 0 bytes java/joelib2/feature/types/BurdenEigenvalues.class | Bin 6571 -> 0 bytes .../feature/types/BurdenModifiedEigenvalues.class | Bin 4778 -> 0 bytes .../feature/types/CharacteristicPolynomial.class | Bin 5802 -> 0 bytes .../CharacteristicPolynomialCoefficients.class | Bin 5957 -> 0 bytes .../feature/types/ConjElectroTopolState.class | Bin 6033 -> 0 bytes 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java/joelib2/feature/types/KierShape1.class | Bin 2589 -> 0 bytes java/joelib2/feature/types/KierShape2.class | Bin 2598 -> 0 bytes java/joelib2/feature/types/KierShape3.class | Bin 2706 -> 0 bytes java/joelib2/feature/types/LogP.class | Bin 2318 -> 0 bytes java/joelib2/feature/types/MolarRefractivity.class | Bin 2328 -> 0 bytes java/joelib2/feature/types/MolecularWeight.class | Bin 2306 -> 0 bytes java/joelib2/feature/types/MoleculeHashcode.class | Bin 2639 -> 0 bytes java/joelib2/feature/types/PolarSurfaceArea.class | Bin 2329 -> 0 bytes .../feature/types/RadialDistributionFunction.class | Bin 8152 -> 0 bytes java/joelib2/feature/types/RotatableBonds.class | Bin 2495 -> 0 bytes java/joelib2/feature/types/SMILESMolecule.class | Bin 3445 -> 0 bytes java/joelib2/feature/types/SSKey3DS.class | Bin 9920 -> 0 bytes .../feature/types/TopologicalDiameter.class | Bin 2798 -> 0 bytes java/joelib2/feature/types/TopologicalRadius.class | Bin 2792 -> 0 bytes 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.../joelib2/feature/types/atomlabel/AtomMass.class | Bin 2620 -> 0 bytes .../types/atomlabel/AtomPartialCharge.class | Bin 3400 -> 0 bytes .../joelib2/feature/types/atomlabel/AtomType.class | Bin 3395 -> 0 bytes .../feature/types/atomlabel/AtomValence.class | Bin 2534 -> 0 bytes .../feature/types/atomlabel/AtomValenceSum.class | Bin 2949 -> 0 bytes .../types/atomlabel/AtomVanDerWaalsVolume.class | Bin 2664 -> 0 bytes java/joelib2/feature/types/atompair/AtomPair.class | Bin 3129 -> 0 bytes .../feature/types/atompair/AtomPairAtomType.class | Bin 2465 -> 0 bytes .../feature/types/atompair/AtomPairResult.class | Bin 4639 -> 0 bytes .../types/atompair/AtomPairTypeComparator.class | Bin 1002 -> 0 bytes .../types/atompair/AtomPairTypeHolder.class | Bin 1483 -> 0 bytes .../feature/types/atompair/AtomTypePair.class | Bin 798 -> 0 bytes .../types/atompair/BasicAPDistanceMetric.class | Bin 1419 -> 0 bytes .../types/atompair/TopologicalAtomPair.class | Bin 6574 -> 0 bytes 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.../gui/render3D/molecule/ViewerBonds.class | Bin 775 -> 0 bytes .../gui/render3D/molecule/ViewerMolecule.class | Bin 7050 -> 0 bytes java/joelib2/gui/render3D/usage.txt | 11 - .../gui/render3D/util/CentralDisplayAdapter.class | Bin 713 -> 0 bytes java/joelib2/gui/render3D/util/CentralLookup.class | Bin 831 -> 0 bytes java/joelib2/gui/render3D/util/Java3DHelper.class | Bin 702 -> 0 bytes .../joelib2/gui/render3D/util/MolViewerEvent.class | Bin 805 -> 0 bytes .../gui/render3D/util/MolViewerEventAdapter.class | Bin 3350 -> 0 bytes .../gui/render3D/util/MolViewerEventListener.class | Bin 252 -> 0 bytes .../gui/util/JEditorPaneAndPagePrinter.class | Bin 1190 -> 0 bytes java/joelib2/gui/util/JLog4JPanel$LogWriter.class | Bin 743 -> 0 bytes java/joelib2/gui/util/JLog4JPanel.class | Bin 2488 -> 0 bytes java/joelib2/gui/util/MolFileChooser.class | Bin 2374 -> 0 bytes java/joelib2/gui/util/MolFileFilter.class | Bin 2851 -> 0 bytes java/joelib2/gui/util/ToolTipInfo.class | Bin 168 -> 0 bytes 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Create PC descriptors -# -# @param [String] pc_type -# @return [text/uri-list] Task ID -get '/:id/pcdesc' do -algorithm = OpenTox::Algorithm::Generic.new(url_for('/dataset/id/pcdesc',:full)) - algorithm.metadata = { - DC.title => 'Physico-chemical (PC) descriptor calculation', - DC.creator => "andreas@maunz.de, vorgrimmlerdavid@gmx.de", - RDF.type => [OT.Algorithm,OTA.PatternMiningSupervised], - OT.parameters => [ - { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" }, - { DC.description => "PC type", OT.paramScope => "mandatory", DC.title => "pc_type" }, - ] - } - case request.env['HTTP_ACCEPT'] - when /text\/html/ - content_type "text/html" - OpenTox.text_to_html algorithm.to_yaml - when /application\/x-yaml/ - content_type "application/x-yaml" - algorithm.to_yaml - else - response['Content-Type'] = 'application/rdf+xml' - algorithm.to_rdfxml - end -end - - - -post '/:id/pcdesc' do - response['Content-Type'] = 'text/uri-list' - raise "No PC type given" unless params["pc_type"] - - task = OpenTox::Task.create("PC descriptor calculation for dataset ", @uri) do |task| - types = params[:pc_type].split(",") - if types.include?("joelib") - Rjb.load(nil,["-Xmx64m"]) - s = Rjb::import('JoelibFc') - end - OpenTox::Algorithm.pc_descriptors( { :dataset_uri => @uri, :pc_type => params[:pc_type], :rjb => s, :task => task } ) - end - raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled" - halt 202,task.uri.to_s+"\n" -end - - - # Deletes datasets that have been created by a crossvalidatoin that does not exist anymore # (This can happen if a crossvalidation fails unexpectedly) delete '/cleanup' do diff --git a/java/Acme/IntHashtable.class b/java/Acme/IntHashtable.class deleted file mode 100644 index d589d5e..0000000 Binary files a/java/Acme/IntHashtable.class and /dev/null differ diff --git a/java/Acme/IntHashtableEntry.class b/java/Acme/IntHashtableEntry.class deleted file mode 100644 index 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/dev/null @@ -1,35 +0,0 @@ -o = lo0; //Zeiger auf die Elemente unterhalb des partitionElement - int hi = hi0; //Zeiger auf die Elemente oberhalb des partitionElement - double pElem; //partitionElement. It divide the data array in two parts. - int noRecPar = 20; //Ist der zu sortierende Teilbereich kleiner als (hier:20) x Elemente, so ueberspringe - //die Rekursion. Am Ende aller (mit QuickSort) vorsortierten Elemente wird nun - //InsertSoert angewendet. Man koennte auch die einzelnen Teilbereiche mit InsertSort - //sortieren, jedoch ist die Anwendung auf das gesamte vorsortierte Array effektiver. - - if ( (hi0 - lo0) >= noRecPar) - { - - //nimmt einfach das mittlere Element als teilendes Element. - pElem = xy.x[ ( lo0 + hi0 ) / 2 ]; - - //wiederholt die Schleife bis sich die Zeiger schneiden. - while( lo <= hi ) - { - //suche das erste Element, das groeSer oder gleich dem teilenden Element (partitionElement) - //ist, beginnend mit dem kleinsten Index (Zeiger). - while( ( lo < hi0 ) && ( xy.x[lo] < pElem )) ++lo; - - //suche das erste Element, das kleiner oder gleich dem teilenden Element (partitionElement) - //ist, beginnend mit dem groeStem Index (Zeiger). - while( ( hi > lo0 ) && ( xy.x[hi] > pElem )) --hi; - - // vertausche die gefundenen Werte, wenn die Zeiger noch nicht vertauscht sind. - if( lo <= hi ) - { - xy.swap(lo, hi); - ++lo; - --hi; - } - } - - //Wenn \ No newline at end of file diff --git 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Descriptor

Valence

Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).

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Breadth First Search (BFS)

The BFS method performs a breadth-first search [clr98] of a graph. -A breadth-first search visits vertices that are closer to the -source before visiting vertices that are further away. In this -context `distance' is defined as the number of edges in the -shortest path from the source vertex. -

Figure 1. Pseudocode for the BFS algorithm

paint all vertices white;
-paint the source grey, set its distance to 0 and enqueue it;
-repeat
-  dequeue vertex v;
-  if v is the target, we're done - exit this algorithm;
-  paint v black;
-  for each white neighbor w of v
-	paint w grey;
-	set distance w to (distance v + 1);
-	set parent w to v;
-	enqueue w
-until the queue is empty
-if we haven't yet exited, we didn't find the target
-The time complexity is [clr98].

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Depth First Search (DFS)

The DFS method performs a depth--first search [clr98] of a graph. -A depth--first search visits vertices that are further to the -source before visiting vertices that are closer away. In this -context `distance' is defined as the number of edges in the -shortest path from the source vertex. -

Figure 1. Pseudocode for the DFS algorithm

DFS(G)
-  {
-    For each v in V,
-    {
-      color[v]=white;
-      pred[u]=NULL
-    }
-
-    time=0;
-    For each u in V
-      If (color[u]=white) DFSVISIT(u)
-  }
-
-
-  DFSVISIT(u)
-  {
-    color[u]=gray;
-    d[u] = ++time;
-
-    For each v in Adj(u)  do
-      If (color[v] = white)
-      {
-        pred[v] = u;
-        DFSVISIT(v);
-      }
-
-    color[u] = black; f[u]=++time;
-  }
-The time complexity is [clr98].

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Topological distance matrix

Calculates the topological distances between all atom pairs. -Here a simple Breadth First Search (BFS ) -is used to calculate these distances, which causes a running time of -O(A3), where -A is the number of atoms.

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Geometrical distance matrix

The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.

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Morgan: Unique atom numbering

Algorithm to get a unique numbering for molecules (graphs) [mor65]. -

Figure 1. Pseudocode for the Morgan labeling algorithm

label each atom with its degree;
-labels=count the number of different labels;
-hasNTchanged=5;
-for all time
-  label each atom with sum of label+all neighbor labels;
-  actLabels=count the number of different labels;
-  if actLabels equal labels then
-    decrement hasNTchanged;
-    if hasNTchanged is zero break loop;
-  fi
-rof
-The sloppy breaking criteria is necessary, because it's possible that the number of different labels can be -constant for only two iterations. But that's not so interesting, let's continue with the -renumbering part of the Morgan algorithm. As you can see, it's possible, that 'symmetric' atoms in the -molecule will have same labels. Is there now a possibility to solve these 'labeling/renumbering' ties ? -Yes, additional informations, like bond order and element number can be used for resolving renumbering ties -or the suggested Jochum-Gasteiger canonical renumbering [tc00] informations can be used. -

Figure 2. Pseudocode for the Morgan renumbering algorithm

calculate the morgan atom labels;
-start breadth first search from this atom;
-choose node with the highest label and set new atom index to 1;
-repeat
-  build deque i of atoms with same BFS traversing number i;
-  if deque i contains no equal labels
-    renumber atoms in order of decreasing atom labels.
-  fi
-  else
-    try to resolve renumbering tie for the equal labels:
-      1. prefer atom with higher bond order for renumbering
-      2. prefer atom with higher element number for renumbering
-      3. ...
-    if tie solved
-      renumber atoms in order of decreasing atom labels.
-    fi
-    else
-      show renumbering tie warning;
-    esle
-  esle
-  increment i;
-until all atoms are numbered
-The uniquely renumbered molecule can be used to calculate molecule -hashcodes and canonical/unique SMILES representations (see ).

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Bibliography

[bmv84] P. Broto, G. Moreau, and C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies, Eur. J. Med. Chem., 19, 66-70, 1984.

[bs93] B. L. Bush and R. P. Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases, J. Chem. Inf. Comput. Sci., 33, 756-762, 1993.

[clr98] T. Cormen, C. Leiserson, and R. L. Rivest, 0-262-03141-8, MIT-Press, Introduction to Algorithms, 1998.

[dl93] A. N. Davies and P. Lampen, JCAMP-DX for NMR, Appl. Spec., 47, 1093-1099, 1993.

[dw88] R. S. Mc Donald and P. A. Wilks, JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form, Appl. Spec., 42, 151-162, 1988.

[ers00] P. Ertl, B. Rohde, and P. Selzer, Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties, J. Med. Chem., 43, 3714-3717, 2000.

[fig96] J. Figueras, Ring Perception Using Breadth-First Search, J. Chem. Inf. Comput. Sci., 36, 986-991, 1996.

[gas95] J. Gasteiger, Keyword Reference Manual for Gasteiger Clear Text Files.

[gbt02] A. Golbraikh, D. Bonchev, and A. Tropsha, Novel Z/E-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis, J. Chem. Inf. Comput. Sci., 42, 769-787, 2002.

[ghhjs91] J. Gasteiger, B. M. Hendriks, P. Hoever, C. Jochum, and H. Somberg, JCAMP-CS: A Standard Format for Chemical Structure Information in Computer Readable Form, Appl. Spec., 45, 4-11, 1991.

[gm78] J. Gasteiger and M. Marsili, A New Model for Calculating Atomic Charges in Molecules, Tetrahedron Lett., ?, 3181-3184, 1978.

[gt03] A. Golbraikh and A. Tropsha, QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology, J. Chem. Inf. Comput. Sci., 42, 144-154, 2003.

[gxsb00] L. Xue, F. L. Stahura, J. W. Godden, and J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling, Pac. Symp. Biocomput., 8, 566-575, 2000.

[lhdl94] P. Lampen, H. Hillig, A. N. Davies, and M. Linscheid, JCAMP-DX for Mass Spectrometry, Appl. Spec., 48, 1545-1552, 1994.

[mor65] H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service, J. Chem. Doc., 5, 107-113, 1965.

[mr99] P. Murray-Rust and H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles, J. Chem. Inf. Comput. Sci., 39, 928-942, 1999.

[mr01a] P. Murray-Rust and H. S. Rzepa, Chemical Markup, XML and the World-Wide Web. 2. Information Objects and the CMLDOM, J. Chem. Inf. Comput. Sci., 41, ?-?, 2001.

[mr01b] G. V. Gkoutos, P. Murray-Rust, H. S. Rzepa, and M. Wright, Chemical markup, XML, and the world-wide web. 3. toward a signed semantic chemical web of trust, J. Chem. Inf. Comput. Sci., 41, 1295-1300, 2001.

[sdf] Inc. MDL Information Systems, Structured Data File format.

[smarts] Inc. Daylight Chemical Information Systems, Smiles ARbitrary Target Specification (SMARTS).

[smiles] Inc. Daylight Chemical Information Systems, Simplified Molecular Input Line Entry System (SMILES).

[tc00] R. Todeschini and V. Consonni, 3-52-29913-0, Wiley-VCH, Handbook of Molecular Descriptors.

[wc99] S. A. Wildman and G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions, J. Chem. Inf. Comput. Sci., 39, 868-873, 1999.

[wei88] D. Weinenger, SMILES: a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules, J. Chem. Inf. Comput. Sci., 28, 31-36, 1988.

[wei89] D. Weinenger, SMILES 2: Algorithm for Generation of Unique SMILES Notation, J. Chem. Inf. Comput. Sci., 29, 97-101, 1989.

[wil01] E. L. Willighagen, Processing CML Conventions in Java, Internet Journal of Chemistry, 4, 4, 2001.

[wy96] W. P. Walters and S. H. Yalkowsky, ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology, J. Chem. Inf. Comput. Sci., 36, 1015-1017, 1996.

[zup89] J. Zupan, 0-471-92173-4, Wiley-VCH, Algorithms for Chemists.

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Descriptor

Atom property breadth first search

Breadth first search calculating the distance only between boolean atom properties (default: Atom in conjugated environment).

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Descriptor

Atom property distance matrix

Distance matrix calculating the distance only between boolean atom properties (default: Atom in conjugated environment).

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Descriptor

Number of acidic groups

Number of acidic groups.

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Descriptor

Number of aliphatic hydroxy groups

Number of aliphatic hydroxy groups.

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Descriptor

Number of aromatic bonds

Number of aromatic bonds.

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Descriptor

Number of Hydrogen Bond Donors (HBD)

Number of Hydrogen Bond Donors (HBD). The default SMARTS pattern is: [!#6;!H0].

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Descriptor

Atom in acceptor

Is this atom a hydrogen acceptor atom.

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Descriptor

Atom in conjugated environment

Atom in conjugated environment. -

Table 1. SMARTS definitions for assigning the conjugated atom property flag

SMARTSDescription
aAromatic atoms
*=,#*-,=*=,#*All butadien analogues
[N,P,O,S]=,#*-[*;!H0]alpha, beta unsaturated (pi effect)
*=,#*-[F,Cl,Br,I]alpha, beta unsaturated (sigma effect)
*=,#*-[N,P,O,S;!H0]alpha, beta unsaturated (pi effect, tautomer)

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Descriptor

Atom in donor or acceptor

Is this atom a hydrogen donor or acceptor atom.

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Descriptor

Atom in donor

Is this atom a hydrogen donor atom.

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Descriptor

Atom in ring

Is this atom a ring atom.

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\ No newline at end of file diff --git a/java/docs/feature/AtomInRingsCount.html b/java/docs/feature/AtomInRingsCount.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomInRingsCount.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomInTerminalCarbon.html b/java/docs/feature/AtomInTerminalCarbon.html deleted file mode 100644 index 23c8b41..0000000 --- a/java/docs/feature/AtomInTerminalCarbon.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Atom is terminal carbon

Is this atom a terminal carbon atom.

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Descriptor

Atom is negative

Is this atom a negative charged atom.

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Descriptor

Atom is positive

Is this atom a positive charged atom.

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\ No newline at end of file diff --git a/java/docs/feature/AtomIsSulfateOxygen.html b/java/docs/feature/AtomIsSulfateOxygen.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomIsSulfateOxygen.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomIsSulfur.html b/java/docs/feature/AtomIsSulfur.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomIsSulfur.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomIsUnsaturated.html b/java/docs/feature/AtomIsUnsaturated.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomIsUnsaturated.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomKekuleBondOrderSum.html b/java/docs/feature/AtomKekuleBondOrderSum.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomKekuleBondOrderSum.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomMass.html b/java/docs/feature/AtomMass.html deleted file mode 100644 index f1a2cde..0000000 --- a/java/docs/feature/AtomMass.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Atom masss

Atom mass.

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\ No newline at end of file diff --git a/java/docs/feature/AtomPartialCharge.html b/java/docs/feature/AtomPartialCharge.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomPartialCharge.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomType.html b/java/docs/feature/AtomType.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomType.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomValence.html b/java/docs/feature/AtomValence.html deleted file mode 100644 index dcd6db8..0000000 --- a/java/docs/feature/AtomValence.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Valence

Valence.

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\ No newline at end of file diff --git a/java/docs/feature/AtomValenceSum.html b/java/docs/feature/AtomValenceSum.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/AtomValenceSum.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/AtomVanDerWaalsVolume.html b/java/docs/feature/AtomVanDerWaalsVolume.html deleted file mode 100644 index bf76e72..0000000 --- a/java/docs/feature/AtomVanDerWaalsVolume.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Van der Waals volume

Van der Waals volume.

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Descriptor

Moreau-Broto topological autocorrelation

Moreau-Broto topological autocorrelation [bmv84]. -

Equation 1. Moreau-Broto autocorrelation

-where dij is the topological distance between the atoms -i and atom j, wi -and wj are the atom properties of the atoms i and -j.

It must be mentioned that the autocorrelation is only a special case of the radial distribution function ().

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\ No newline at end of file diff --git a/java/docs/feature/BCUT.html b/java/docs/feature/BCUT.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BCUT.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BasicGroups.html b/java/docs/feature/BasicGroups.html deleted file mode 100644 index 581d187..0000000 --- a/java/docs/feature/BasicGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of basic groups

Number of basic groups.

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\ No newline at end of file diff --git a/java/docs/feature/BondInAromaticSystem.html b/java/docs/feature/BondInAromaticSystem.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondInAromaticSystem.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondInRing.html b/java/docs/feature/BondInRing.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondInRing.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsAmide.html b/java/docs/feature/BondIsAmide.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsAmide.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsCarbonyl.html b/java/docs/feature/BondIsCarbonyl.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsCarbonyl.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsClosure.html b/java/docs/feature/BondIsClosure.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsClosure.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsEster.html b/java/docs/feature/BondIsEster.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsEster.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsPrimaryAmide.html b/java/docs/feature/BondIsPrimaryAmide.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsPrimaryAmide.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondIsRotor.html b/java/docs/feature/BondIsRotor.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondIsRotor.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BondKekuleType.html b/java/docs/feature/BondKekuleType.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BondKekuleType.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BurdenEigenvalues.html b/java/docs/feature/BurdenEigenvalues.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/BurdenEigenvalues.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/BurdenModifiedEigenvalues.html b/java/docs/feature/BurdenModifiedEigenvalues.html deleted file mode 100644 index dc6a83b..0000000 --- a/java/docs/feature/BurdenModifiedEigenvalues.html +++ /dev/null @@ -1,96 +0,0 @@ -

Descriptor

Burden modified eigenvalues

Burden modified eigenvalues [tc00].

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\ No newline at end of file diff --git a/java/docs/feature/CompressedFeatureMatrix.html b/java/docs/feature/CompressedFeatureMatrix.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/CompressedFeatureMatrix.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/ConjElectroTopolState.html b/java/docs/feature/ConjElectroTopolState.html deleted file mode 100644 index bc0369e..0000000 --- a/java/docs/feature/ConjElectroTopolState.html +++ /dev/null @@ -1,173 +0,0 @@ -

Descriptor

Conjugated electrotopological state

Conjugated electrotopological state [wz03,wfz04b]. -

Equation 1. Conjugated electrotopological state

-Ii is the intrinsic state of atom i () -and k the distance influence. The distance influence is reduced by the conjugated topological distance -

Equation 2. Conjugated topological distance

-where Ci is the conjugated atom i () -of the molecule.

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\ No newline at end of file diff --git a/java/docs/feature/ConjugatedTopologicalDistance.html b/java/docs/feature/ConjugatedTopologicalDistance.html deleted file mode 100644 index 6deea0d..0000000 --- a/java/docs/feature/ConjugatedTopologicalDistance.html +++ /dev/null @@ -1,117 +0,0 @@ -

Descriptor

Conjugated topological distance

Conjugated topological distance [wz03,wfz04b]. -

Equation 1. Conjugated topological distance

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\ No newline at end of file diff --git a/java/docs/feature/DistanceDistanceMatrix.html b/java/docs/feature/DistanceDistanceMatrix.html deleted file mode 100644 index 0d10a46..0000000 --- a/java/docs/feature/DistanceDistanceMatrix.html +++ /dev/null @@ -1,3 +0,0 @@ - -Dummy - \ No newline at end of file diff --git a/java/docs/feature/DistanceMatrix.html b/java/docs/feature/DistanceMatrix.html deleted file mode 100644 index ecd0533..0000000 --- a/java/docs/feature/DistanceMatrix.html +++ /dev/null @@ -1,111 +0,0 @@ -

Descriptor

Topological distance matrix

Calculates the topological distances between all atom pairs. -Here a simple BFS (see also ) -is used to calculate these distances, which causes a running time of -O(A3), where -A is the number of atoms.

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Descriptor

Electrogeometrical state

Electrogeometrical state [wz03,wfz04b]. -

Equation 1. Electrogeometrical state

-Ii is the intrinsic state of atom i () -and k the distance influence.

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\ No newline at end of file diff --git a/java/docs/feature/ElectrotopologicalState.html b/java/docs/feature/ElectrotopologicalState.html deleted file mode 100644 index 6de0bf2..0000000 --- a/java/docs/feature/ElectrotopologicalState.html +++ /dev/null @@ -1,139 +0,0 @@ -

Descriptor

Electrotopological state

Electrotopological state [tc00,wfz04b]. -

Equation 1. Electrotopological state

-Ii is the intrinsic state of atom i () -and k the distance influence.

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\ No newline at end of file diff --git a/java/docs/feature/FractionRotatableBonds.html b/java/docs/feature/FractionRotatableBonds.html deleted file mode 100644 index a34080c..0000000 --- a/java/docs/feature/FractionRotatableBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Fraction of rotatable bonds

Fraction of rotatable bonds.

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\ No newline at end of file diff --git a/java/docs/feature/GeomDistanceMatrix.html b/java/docs/feature/GeomDistanceMatrix.html deleted file mode 100644 index ff8cc05..0000000 --- a/java/docs/feature/GeomDistanceMatrix.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Geometrical distance matrix

The geometrical distance matrix calculates the euklidian distance between the 3D coordinates of all atom pairs.

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Descriptor

Geometrical diameter

Geometrical diameter.

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\ No newline at end of file diff --git a/java/docs/feature/GeometricalRadius.html b/java/docs/feature/GeometricalRadius.html deleted file mode 100644 index 76a2596..0000000 --- a/java/docs/feature/GeometricalRadius.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Geometrical radius

Geometrical radius.

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\ No newline at end of file diff --git a/java/docs/feature/GeometricalShapeCoefficient.html b/java/docs/feature/GeometricalShapeCoefficient.html deleted file mode 100644 index e1401be..0000000 --- a/java/docs/feature/GeometricalShapeCoefficient.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Geometrical shape coefficient

Geometrical shape coefficient.

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\ No newline at end of file diff --git a/java/docs/feature/GlobalTopologicalChargeIndex.html b/java/docs/feature/GlobalTopologicalChargeIndex.html deleted file mode 100644 index 63e2715..0000000 --- a/java/docs/feature/GlobalTopologicalChargeIndex.html +++ /dev/null @@ -1,96 +0,0 @@ -

Descriptor

Global topological charge

Global topological charge [tc00].

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\ No newline at end of file diff --git a/java/docs/feature/GraphPotentials.html b/java/docs/feature/GraphPotentials.html deleted file mode 100644 index a192e96..0000000 --- a/java/docs/feature/GraphPotentials.html +++ /dev/null @@ -1,131 +0,0 @@ -

Descriptor

Graph potentials

Graph potentials [wy96] or rotational symmetry descriptor. Only the connection table -is needed to calculate the external rotational symmetry, or topological equivalent atoms. -

Equation 1. Graph potentials

-where vi is the valence (vertex degree) of the atom -i.

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\ No newline at end of file diff --git a/java/docs/feature/GraphShapeCoefficient.html b/java/docs/feature/GraphShapeCoefficient.html deleted file mode 100644 index 735e913..0000000 --- a/java/docs/feature/GraphShapeCoefficient.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Graph shape coefficient

Graph shape coefficient.

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\ No newline at end of file diff --git a/java/docs/feature/HBA1.html b/java/docs/feature/HBA1.html deleted file mode 100644 index 6dcb012..0000000 --- a/java/docs/feature/HBA1.html +++ /dev/null @@ -1,94 +0,0 @@ -

Descriptor

Number of Hydrogen Bond Acceptors (HBA) 1

Number of Hydrogen Bond Acceptors (HBA) 1. -The default SMARTS pattern is: [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])].

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Descriptor

Number of Hydrogen Bond Acceptors (HBA) 2

Number of Hydrogen Bond Acceptors (HBA) 2. -The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].

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\ No newline at end of file diff --git a/java/docs/feature/HBD1.html b/java/docs/feature/HBD1.html deleted file mode 100644 index 58922cf..0000000 --- a/java/docs/feature/HBD1.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of Hydrogen Bond Donors (HBD) 1

Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].

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Descriptor

Number of Hydrogen Bond Donors (HBD) 2

Number of Hydrogen Bond Donors (HBD) 2. -The default SMARTS pattern is: [$([O;H1,-&!$(*-N=O)]),$([S;H1&X2,-&X1]),$([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]),$([#7;-])].

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\ No newline at end of file diff --git a/java/docs/feature/HeavyBonds.html b/java/docs/feature/HeavyBonds.html deleted file mode 100644 index c460fba..0000000 --- a/java/docs/feature/HeavyBonds.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of heavy bonds

Number of heavy bonds.

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\ No newline at end of file diff --git a/java/docs/feature/HeteroCycles.html b/java/docs/feature/HeteroCycles.html deleted file mode 100644 index d1e124f..0000000 --- a/java/docs/feature/HeteroCycles.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of heterocycles

Number of heterocycles.

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\ No newline at end of file diff --git a/java/docs/feature/HydrophobicGroups.html b/java/docs/feature/HydrophobicGroups.html deleted file mode 100644 index 020d78c..0000000 --- a/java/docs/feature/HydrophobicGroups.html +++ /dev/null @@ -1,93 +0,0 @@ -

Descriptor

Number of hydrophobic groups

Number of hydrophobic groups.

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\ No newline at end of file diff --git a/java/docs/feature/IntrinsicState.html b/java/docs/feature/IntrinsicState.html deleted file mode 100644 index 82c8c76..0000000 --- a/java/docs/feature/IntrinsicState.html +++ /dev/null @@ -1,145 +0,0 @@ -

Descriptor

Intrinsic topological state

Intrinsic topological state [tc00,wfz04b]. -

Equation 1. Intrinsic topological state

-where Li is the principal quantum number, - is the number of valence electrons, and - is the number of sigma electrons of the -ith atom ai.

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Descriptor

Kier Shape 1

The Kier shape - descriptor [tc00] -can be defined as :

Equation 1. Kier shape 1

Pmax is the maximum number of paths of length 1. -Pmin is the minimum number of paths of length 1 in a molecule graph of same -atom number. -P1 is the number of paths in the given molecule of length 1. -or:

Equation 2. Kier shape 1 (alternative formulation)

A means the number of nodes in the molecules graph. -P1 is the number of paths of length 1 in the given molecule.

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Descriptor

Kier shape 2

The Kier shape - descriptor [tc00] -can be defined as :

Equation 1. Kier shape 2

A means the number of nodes in the molecules graph. -P2 is the number of paths of length 2 in the given molecule.

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Descriptor

Kier shape 3

The Kier shape - descriptor [tc00] -can be defined as :

Equation 1. Kier shape 3

A means the number of nodes in the molecules graph. -P3 is the number of paths of length 3 in the given molecule.

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Descriptor

Octanol/Water partition coefficient (logP)

Octanol/Water partition coefficient (logP) or hydrophobicity [wc99].

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Descriptor

Molar refractivity (MR)

Molar refractivity (MR) [wc99].

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Descriptor

Molecular weight (MW)

Molecular weight (MW).

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Descriptor

Number of -NO2 groups

Number of -NO2 groups.

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Descriptor

Number of atoms

Number of atoms.

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Descriptor

Number of boron atoms

Number of boron atoms.

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Descriptor

Number of bonds

Number of bonds.

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Descriptor

Number of bromine atoms

Number of bromine atoms.

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Descriptor

Number of carbon atoms

Number of carbon atoms.

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Descriptor

Number of chlorine atoms

Number of chlorine atoms.

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Descriptor

Number of fluorine atoms

Number of fluorine atoms.

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Descriptor

Number of halogen atoms

Number of halogen atoms.

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Descriptor

Number of iodine atoms

Number of iodine atoms.

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Descriptor

Number of nitrogen atoms

Number of nitrogen atoms.

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Descriptor

Number of oxygen atoms

Number of oxygen atoms.

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Descriptor

Number of phosphorus atoms

Number of phosphorus atoms.

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Descriptor

Number of sulfur atoms

Number of sulfur atoms.

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Descriptor

Number of -OSO atoms

Number of -OSO atoms.

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Descriptor

Polar surface area (PSA)

Polar surface area (PSA) [ers00].

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Descriptor

Radial distribution function (RDF)

The radial distribution function (RDF) [msg99,wfz04b] can be interpreted as the probability distribution of finding an atom in a spherical volume of -radius r. -

Equation 1. Radial distribution function

-where rij is the geometrical distance between the atoms -i and atom j, wi -and wj are the atom properties of the atoms i and -j. B is the smoothing parameter -(fuzziness of the distance rij) for the interatomic distance and -f the scaling factor.

If B aims to infinity the RDF code approximates to the autocorrelation function () and the fuzziness -of the distance rij vanishes. So the RDF code can be treated as a generalized -autocorrelation function.

The RDF user parameters can be defined in the joelib.properties-file, otherwise the default parameters will be used:

jcompchem.joelib.desc.types.RadialDistributionFunction.minSphericalVolume = 0.2
-joelib.desc.types.RadialDistributionFunction.maxSphericalVolume = 10.0
-joelib.desc.types.RadialDistributionFunction.sphericalVolumeResolution = 0.2
-joelib.desc.types.RadialDistributionFunction.smoothingFactor = 25

Optional the RDF can be calculated with protonated molecules, but you must be sure that all available atom -properties are calculated with hydrogens also. Because this is not the standard, this option should be only used by developers.

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Descriptor

Number of rotatable bonds

Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp). -Additionally the bond is a non-ring-bond.

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Descriptor

Number of -SO2 atoms

Number of -SO2 atoms.

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Descriptor

Number of -SO groups

Number of -SO groups.

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Descriptor

Pharmacophore fingerprint

Pharmacophore fingerprint [gxsb00]. -

Table 1. Pharmacophore fingerprint definition

Bit positionSet when
1Fraction of rotatable bonds > 0.0
2Fraction of rotatable bonds > 0.1
3Fraction of rotatable bonds > 0.2
4Fraction of rotatable bonds > 0.3
5Fraction of rotatable bonds > 0.4
6Aromatic bonds in molecule > 2
7Aromatic bonds in molecule > 8
8Aromatic bonds in molecule > 16
9Aromatic bonds in molecule > 20
10Aromatic bonds in molecule > 26
11Aromatic bonds in molecule > 32
12Aromatic bonds in molecule > 38
13Molecule contains a heterocycle
14Molecule contains an aromatic hydroxy group
15Molecule contains an aliphatic hydroxy group
16Molecule contains an aliphatic secondary amine
17Molecule contains an aliphatic tertiary amine
18Molecule contains a phenyl ring
19Molecule contains a ring containing nitrogen
20Molecule contains a -SO2 group
21Molecule contains a -SO
22Molecule contains an ester
23Molecule contains an amide
24Molecule contains a 5-membered non-aromatic ring
25Molecule contains a 5-membered aromatic ring
26Molecule contains a 9-membered or larger (fused) ring
27Molecule contains a fused ring system
28Molecule contains a fused aromatic ring system
29Molecule contains a -OSO group
30Molecule contains a halogen atom
31Molecule contains a nitrogen atom attached to alpha-carbon of aromatic system
32Molecule contains a -NO2 group
33Molecule contains rings separated by 2-3 non-ring atoms
34Molecule contains rings separated by 4-5 non-ring atoms
35Molecule contains a NN group
36Molecule contains a carbon atom attached to 3 carbons and a hetero atom
37Molecule contains an oxygen atom separated by 2 atoms
38Molecule contains a methyl group attached to hetero atom
39Molecule contains a double bond
40Molecule contains a non-H atom linked to 3 heteroatoms
41Molecule contains a quaternary atom
42Molecule contains 2 methylenes separated by 2 atoms
43Molecule contains a non-ring oxygen atom attached to aromatic system
44Molecule contains 2 non-C,H atoms separated by 2 atoms
45Number of hydrogen bond acceptors >= 1
46Number of hydrogen bond acceptors >= 2
47Number of hydrogen bond acceptors >= 3
48Number of hydrogen bond acceptors >= 4
49Number of hydrogen bond acceptors >= 5
50Number of hydrogen bond acceptors >= 6
51Number of hydrogen bond acceptors >= 7
52Number of hydrogen bond acceptors >= 8
53Number of hydrogen bond acceptors >= 9
54Number of hydrogen bond acceptors >= 10

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Descriptor

Valence

Atom pair descriptor using topological distances.

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Descriptor

Topological diameter

Topological diameter.

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Descriptor

Topological radius

Topological radius.

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Descriptor

Weighted burden modified eigenvalues

Accepts six different weighted atom properties to calculate BCUT values.

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Descriptor

Zagreb index 1

Zagreb index 1 [tc00].

Equation 1. Zagreb index 1

where a are all atoms of the hydrogen depleted graph and - is the vertex degree.

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Descriptor

Zagreb index 2

Zagreb index 2 [tc00].

Equation 1. Zagreb index 2

where b are all bonds of the hydrogen depleted graph and - is the vertex degree. -i and j are the atom indices -of the atoms connected to the bond b.

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Zupan, Algorithms for Chemists , Wiley, 1989 , 102-142 . \ No newline at end of file diff --git a/java/docs/literature.tex b/java/docs/literature.tex deleted file mode 100644 index 1befd3f..0000000 --- a/java/docs/literature.tex +++ /dev/null @@ -1,34 +0,0 @@ -% -% Filename: $RCSfile: literature.tex,v $ -% Authors: Joerg Wegner -% Version: $Revision: 1.1.1.1 $ -% $Date: 2004/12/06 15:33:07 $ -% $Author: wegner $ -% Copyright (c) Joerg Wegner; CCC Computer Chemistry Center, Germany -% -% ------------------------------------------------------------------------ -% AMS-LaTeX Bibliography ************************************************* -% ------------------------------------------------------------------------ -\documentclass[11pt]{amsart} -\usepackage[inactive]{srcltx} -% **** ------------------------------------------------------------------- -\vfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc -\hfuzz1pc % Don't bother to report overfull boxes if over-edge is < 1pc - -%------------------------------------------------------------------------------------------- -% JUST FOR TTH USERS !;-) -%------------------------------------------------------------------------------------------- -%%tth:\begin{html}Literature JOELib, J.K. 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a/java/jmat/io/gui/plotTools/PlotAttributes.class b/java/jmat/io/gui/plotTools/PlotAttributes.class deleted file mode 100644 index 2bdc5c0..0000000 Binary files a/java/jmat/io/gui/plotTools/PlotAttributes.class and /dev/null differ diff --git a/java/jmat/test/Testjmat.class b/java/jmat/test/Testjmat.class deleted file mode 100644 index 4c9f53e..0000000 Binary files a/java/jmat/test/Testjmat.class and /dev/null differ diff --git a/java/joelib2.properties b/java/joelib2.properties deleted file mode 100644 index fdad7ff..0000000 --- a/java/joelib2.properties +++ /dev/null @@ -1,502 +0,0 @@ -############################################################################## -############################################################################## -############################################################################## -# -# JOELib2 properties -# -# \ slashes should be written as \\ -# spaces can be written as \ \, but white spaces are removed at the end of -# lines !!! -# Please use the Unicode expression \u0020 to encode white spaces !!! -# -############################################################################## -# -# Version: $Revision: 1.15 $ -# $Date: 2006/07/24 22:29:15 $ -# $Author: wegner $ -# -############################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -############################################################################## -############################################################################## - -############################################################################## -# resource locations of data files -############################################################################## -joelib2.data.BasicHybridisationTyper.resourceFile=joelib2/data/plain/hybridisation.txt -joelib2.data.BasicAromaticityTyper.resourceFile=joelib2/data/plain/aromatic.txt -joelib2.data.BasicAromaticityTyper.useAromaticityModel=true -joelib2.data.BasicImplicitValenceTyper.resourceFile=joelib2/data/plain/implicitValence.txt -joelib2.data.BasicAtomTyper.resourceFile=joelib2/data/plain/atomtype.txt -joelib2.data.BasicElementHolder.resourceFile=joelib2/data/plain/element.txt -joelib2.data.BasicIsotopeHolder.resourceFile=joelib2/data/plain/isotope.txt -joelib2.data.BasicProtonationModel.resourceFile=joelib2/data/plain/phmodel.txt - -joelib2.data.BasicGroupContributionHolder.resourceDir=joelib2/data/plain -joelib2.data.BasicGroupContributionHolder.contributionExtension=.contributions -joelib2.data.BasicGroupContributionHolder.models=LogP MR PSA - -joelib2.feature.ResultFactory.resourceFile=joelib2/data/plain/knownResults.txt -joelib2.process.types.DescriptorStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt -joelib2.process.types.DescriptorBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt - -############################################################################## -# Database -############################################################################## -wsi.ra.database.DatabaseConnection.location=jdbc:mysql://localhost/test -wsi.ra.database.DatabaseConnection.password= -wsi.ra.database.DatabaseConnection.username= -wsi.ra.database.DatabaseConnection.driver=org.gjt.mm.mysql.Driver - -############################################################################## -# 2D rendering options -############################################################################## -joelib2.gui.render2D.Renderer2DModel.bond.length=30.0 -joelib2.gui.render2D.Renderer2DModel.bond.distance=6.0 -joelib2.gui.render2D.Renderer2DModel.bond.width=2.0 -joelib2.gui.render2D.Renderer2DModel.drawNumbers=true -joelib2.gui.render2D.Renderer2DModel.useKekuleStructure=true -joelib2.gui.render2D.Renderer2DModel.showEndCarbons=true -joelib2.gui.render2D.Renderer2DModel.atomColoring=false -joelib2.gui.render2D.Renderer2DModel.drawCarbonAtoms=false -joelib2.gui.render2D.Renderer2DModel.orthoLineOffset=20 -joelib2.gui.render2D.Renderer2DModel.arrowOffset=10 -joelib2.gui.render2D.Renderer2DModel.arrowSize=5 - -joelib2.gui.render2D.Renderer2DModel.background.color.r=255 -joelib2.gui.render2D.Renderer2DModel.background.color.g=255 -joelib2.gui.render2D.Renderer2DModel.background.color.b=255 - -joelib2.gui.render2D.Renderer2DModel.foreground.color.r=0 -joelib2.gui.render2D.Renderer2DModel.foreground.color.g=0 -joelib2.gui.render2D.Renderer2DModel.foreground.color.b=0 - -joelib2.gui.render2D.Renderer2DModel.highlight.color.r=255 -joelib2.gui.render2D.Renderer2DModel.highlight.color.g=0 -joelib2.gui.render2D.Renderer2DModel.highlight.color.b=0 - -joelib2.gui.render2D.Renderer2DModel.number.color.r=0 -joelib2.gui.render2D.Renderer2DModel.number.color.g=0 -joelib2.gui.render2D.Renderer2DModel.number.color.b=255 - -joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.r=0 -joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.g=0 -joelib2.gui.render2D.Renderer2DModel.conjugatedRing.color.b=0 - -joelib2.gui.render2D.Renderer2DModel.arrow.color.r=0 -joelib2.gui.render2D.Renderer2DModel.arrow.color.g=255 -joelib2.gui.render2D.Renderer2DModel.arrow.color.b=0 - -joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.r=0 -joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.g=0 -joelib2.gui.render2D.Renderer2DModel.orthogonalLine.color.b=255 - -############################################################################## -# Smiles ARbitrary Target Specification (SMARTS) matcher parameters -############################################################################## -# '*' matches also explicite hydrogens when 'true' -# '*' matches only non-hydrogen (heavy weight) atoms when 'false' -joelib2.smarts.SMARTSParser.anyRecognizesExpliciteHydrogens=false - -############################################################################## -# Supported file types -############################################################################## -joelib2.filetypes.1.name = SDF -joelib2.filetypes.2.name = XYZ -joelib2.filetypes.3.name = SMILES -joelib2.filetypes.4.name = TINKER -joelib2.filetypes.5.name = CTX -joelib2.filetypes.6.name = CML -joelib2.filetypes.7.name = POV -joelib2.filetypes.8.name = MOL2 -joelib2.filetypes.9.name = PDB -joelib2.filetypes.10.name = MATLAB -joelib2.filetypes.11.name = FLAT -joelib2.filetypes.11.representation = joelib2.io.types.Flat -joelib2.filetypes.12.name = MOLCONNZ -joelib2.filetypes.12.representation = joelib2.io.types.MolconnZ -joelib2.filetypes.13.name = HIN -joelib2.filetypes.14.name = GAUSSIANCART -joelib2.filetypes.15.name = JPEG -joelib2.filetypes.16.name = GIF -joelib2.filetypes.17.name = PPM -# PNG requires another implementation or Marvin -#joelib2.filetypes.18.name = PNG -joelib2.filetypes.18.name = BMP -joelib2.filetypes.19.name = PDF -joelib2.filetypes.20.name = ZIP -joelib2.filetypes.21.name = PREP -joelib2.filetypes.22.name = MOPACOUT - -#joelib2.filetypes.16.name = GHEMICAL - -# if you want another loader/writer define one -#joelib2.filetypes.1.representation = joelib2.io.types.MDLSD -#joelib2.filetypes.2.representation = joelib2.io.types.XYZ -#joelib2.filetypes.3.representation = joelib2.io.types.Smiles - -############################################################################## -# filters -############################################################################## -joelib2.filter.1.name =NOTFilter -joelib2.filter.1.representation =joelib2.process.filter.NOTFilter -joelib2.filter.1.descriptionFile =docs/process/notFilter -joelib2.filter.2.name =ORFilter -joelib2.filter.2.representation =joelib2.process.filter.ORFilter -joelib2.filter.2.descriptionFile =docs/process/orFilter -joelib2.filter.3.name =ANDFilter -joelib2.filter.3.representation =joelib2.process.filter.ANDFilter -joelib2.filter.3.descriptionFile =docs/process/andFilter -joelib2.filter.4.name =HasDataFilter -joelib2.filter.4.representation =joelib2.process.filter.HasDataFilter -joelib2.filter.4.descriptionFile =docs/process/hasDataFilter -joelib2.filter.5.name =DescriptorFilter -joelib2.filter.5.representation =joelib2.process.filter.DescriptorFilter -joelib2.filter.5.descriptionFile =docs/process/descriptorFilter -joelib2.filter.6.name =NativeValueFilter -joelib2.filter.6.representation =joelib2.process.filter.NativeValueFilter -joelib2.filter.6.descriptionFile =docs/process/nativeValueFilter - -############################################################################## -# processes -############################################################################## -joelib2.process.1.name =ProcessPipe -joelib2.process.1.representation =joelib2.process.ProcessPipe -joelib2.process.1.descriptionFile =docs/process/processPipe -joelib2.process.2.name =FeatureSelectionWriter -joelib2.process.2.representation =joelib2.process.types.FeatureSelectionWriter -joelib2.process.2.descriptionFile =docs/process/featureSelectionWriter -joelib2.process.3.name =DescriptorStatistic -joelib2.process.3.representation =joelib2.process.types.DescStatistic -joelib2.process.3.descriptionFile =docs/process/descriptorStatistic -################ -joelib2.process.4.name =DescriptorBinning -joelib2.process.4.representation =joelib2.process.types.DescBinning -joelib2.process.4.descriptionFile =docs/process/descriptorBinning -joelib2.process.types.DescBinning.numberOfBins=20 -################ -joelib2.process.5.name =DistanceCalculation -joelib2.process.5.representation =joelib2.process.types.DistanceCalculation -joelib2.process.5.descriptionFile =docs/process/distanceCalculation - -############################################################################## -# miscellaneous -############################################################################## - -#SD Files -# if set to false aromatic bonds are stored, so this structure can be used -# as QUERY structure. That's only an export feature, internally you can have -# both types by using the kekule bonds or the 'normal/aromatic' bonds. -joelib2.io.types.MDLSD.writeAromaticityAsKekuleSystem=true - -#SMILES -joelib2.smiles.SMILESGenerator.assignCisTransInformations=true -joelib2.smiles.SMILESGenerator.assignChiralityInformations=true -joelib2.io.types.Smiles.canonical=false -joelib2.io.types.Smiles.lineStructure=SMILES|TITLE -joelib2.io.types.Smiles.lineStructure.delimiter=| -joelib2.io.types.Smiles.lineStructure.input.delimiter=\u0020\t\n\r -joelib2.io.types.Smiles.lineStructure.output.delimiter=\u0020 - -# MolconnZ -joelib2.io.types.MolconnZ.parserDefinition=joelib2/data/plain/molconnz350.txt - -# Flat -joelib2.io.types.Flat.lineStructure.input.delimiter=\u0020\t\n\r -joelib2.io.types.Flat.lineStructure.output.delimiter=\t -joelib2.io.types.Flat.lineStructure.delimiter=\u0020\t -joelib2.io.types.Flat.lineStructure=TITLE - -########### -# CML -# version: 1.0 and 2.0 -# ouput: attributearray, array, large, huge -# delimiter: if you comment this line, standard white space will be used -# force.formalCharge: formal charges will be always written, even when they are zero -# partialCharge: write partial atom charge -# hydrogen=joelib2.feature.types.count: write number of implicite+explicite hydrogens -########### -## use slower memory saving preparser for avoiding to load the complete data set into memory -## This flag will be automatically switched 'ON' for CML files in compressed ZIP files ! -## The basic convert does not need it, because it uses already another sequential -## SAX reader (forced by a callback) -joelib2.io.types.ChemicalMarkupLanguage.useSlowerMemorySavingPreparser=false -########### -joelib2.io.types.ChemicalMarkupLanguage.output.defaultVersion=2.0 -joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=\u0020 -#joelib2.io.types.ChemicalMarkupLanguage.defaultDelimiter=| -joelib2.io.types.ChemicalMarkupLanguage.output=huge -joelib2.io.types.ChemicalMarkupLanguage.output.force.formalCharge=false -joelib2.io.types.ChemicalMarkupLanguage.output.partialCharge=true -joelib2.io.types.ChemicalMarkupLanguage.output.hydrogenCount=true -joelib2.io.types.ChemicalMarkupLanguage.output.useNamespace=true -joelib2.io.types.ChemicalMarkupLanguage.output.namespace=cml -joelib2.io.types.ChemicalMarkupLanguage.output.xmlDeclaration=http://www.xml-cml.org/schema/cml2/core -joelib2.io.types.ChemicalMarkupLanguage.DTD.resourceDir=joelib2/io/types/cml/data/ -########### -## a first step to 'reproducable' descriptor calculation algorithms -joelib2.io.types.ChemicalMarkupLanguage.output.storeChemistryKernelInfo=true -## these informations are not really a CML standard -########### -joelib2.io.types.ChemicalMarkupLanguage.output.symmetryInformations=false -########### - -# PovRay -# ouput type can be: stick, sphere, ball_and_stick -joelib2.io.types.POVRay.output=ball_and_stick -joelib2.io.types.POVRay.atomPropertyColoring=false -joelib2.io.types.POVRay.atomProperty=Gasteiger_Marsili - -# Image writer -joelib2.gui.render2D.Mol2Image.defaultWidth=500 -joelib2.gui.render2D.Mol2Image.defaultHeight=400 - -# PDF writer -joelib2.io.types.PDF.fontSize=10 -joelib2.io.types.PDF.fontOffset=2 -joelib2.io.types.PDF.pageBorder=20 - -joelib2.temporary.directory.windows=C:\\temp -joelib2.temporary.directory.linux=/tmp - -joelib2.process.types.DescBinning.descriptors2ignore=joelib2/data/plain/desc2ignore.txt -joelib2.process.types.DescStatistic.descriptors2ignore=joelib2/data/plain/desc2ignore.txt -joelib2.process.types.DescVarianceNorm.descriptors2ignore=joelib2/data/plain/desc2ignore.txt -joelib2.feature.data.MolDesc=joelib2.feature.types.counter.descriptors2ignore=joelib2/data/plain/desc2ignore.txt -joelib2.feature.data.MoleculesDescriptorMatrix.descriptors2ignore=joelib2/data/plain/desc2ignore.txt - -joelib2.feature.data.MoleculesDescriptorMatrix.normalizeOnLoad=true -#joelib2.feature.data.MoleculesDescriptorMatrix.normalizeStatFile=../../datasets/test.sdf - -############################################################################## -# number output (!!!) format -# import not implemented for locale!=en and/or groupingUsed!=false -############################################################################## - -# initialize the number ouput format ! -# number of '0' means the minimum number of digits to use -# number of '#' means the maximum number of digits to use -# in the property file you must use \# to quote the #'s -# If not used all digits will be used. -# deviant to the Java standard the exponential terms with E0 are removed. - -#wsi.ra.text.DecimalFormatHelper.double.format=0.\#\#\#\#\#E0 - -# the both following parameters should be used carefully, because -# the import is not implemented correctly !!! -# e.g.: en, de - -#wsi.ra.text.DecimalFormatHelper.double.locale=en -#wsi.ra.text.DecimalFormatHelper.double.groupingUsed=false - -############################################################################## -# external processes -############################################################################## -joelib2.external.1.name =Title2Data -joelib2.external.1.representation =joelib2.ext.Title2Data -joelib2.external.1.descriptionFile =docs/ext/title2Data -joelib2.external.1.linux =../lib/linux/title2data -joelib2.external.1.windows =..\lib\windows\title2data.exe -joelib2.external.1.argument.1 =MOL_TITLE - -############################################################################## -# Features and feature properties -############################################################################## -joelib2.feature.addIfNotExist=true -############################################## -joelib2.feature.0.representation =joelib2.ring.RingFinderSSSR -joelib2.feature.1.representation =joelib2.algo.BFS -joelib2.feature.2.representation =joelib2.algo.DFS -joelib2.feature.3.representation =joelib2.algo.APropertyBFS -joelib2.feature.4.representation =joelib2.feature.types.atomlabel.AtomBondOrderSum -joelib2.feature.5.representation =joelib2.feature.types.atomlabel.AtomElectronAffinity -joelib2.feature.6.representation =joelib2.feature.types.atomlabel.AtomENAllredRochow -joelib2.feature.7.representation =joelib2.feature.types.atomlabel.AtomENPauling -joelib2.feature.8.representation =joelib2.feature.types.atomlabel.AtomENSanderson -joelib2.feature.9.representation =joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount -joelib2.feature.10.representation =joelib2.feature.types.atomlabel.AtomFreeElectronsCount -joelib2.feature.11.representation =joelib2.feature.types.atomlabel.AtomFreeOxygenCount -joelib2.feature.12.representation =joelib2.feature.types.atomlabel.AtomHeavyValence -joelib2.feature.13.representation =joelib2.feature.types.atomlabel.AtomHeteroValence -joelib2.feature.14.representation =joelib2.feature.types.atomlabel.AtomHybridisation -joelib2.feature.15.representation =joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount -joelib2.feature.16.representation =joelib2.feature.types.atomlabel.AtomImplicitValence -joelib2.feature.17.representation =joelib2.feature.types.atomlabel.AtomInAcceptor -joelib2.feature.18.representation =joelib2.feature.types.atomlabel.AtomInAromaticSystem -joelib2.feature.19.representation =joelib2.feature.types.atomlabel.AtomInConjEnvironment -joelib2.feature.20.representation =joelib2.feature.types.atomlabel.AtomInDonAcc -joelib2.feature.21.representation =joelib2.feature.types.atomlabel.AtomInDonor -joelib2.feature.22.representation =joelib2.feature.types.atomlabel.AtomInRing -joelib2.feature.23.representation =joelib2.feature.types.atomlabel.AtomInRingsCount -joelib2.feature.24.representation =joelib2.feature.types.atomlabel.AtomInTerminalCarbon -joelib2.feature.25.representation =joelib2.feature.types.atomlabel.AtomIsAlphaBetaUnsaturated -joelib2.feature.26.representation =joelib2.feature.types.atomlabel.AtomIsAmideNitrogen -joelib2.feature.27.representation =joelib2.feature.types.atomlabel.AtomIsAntiClockwise -joelib2.feature.28.representation =joelib2.feature.types.atomlabel.AtomIsAromaticNOxide -joelib2.feature.29.representation =joelib2.feature.types.atomlabel.AtomIsAxial -joelib2.feature.30.representation =joelib2.feature.types.atomlabel.AtomIsCarbon -joelib2.feature.31.representation =joelib2.feature.types.atomlabel.AtomIsCarboxylOxygen -joelib2.feature.32.representation =joelib2.feature.types.atomlabel.AtomIsChiral -joelib2.feature.33.representation =joelib2.feature.types.atomlabel.AtomIsClockwise -joelib2.feature.34.representation =joelib2.feature.types.atomlabel.AtomIsElectronegative -joelib2.feature.35.representation =joelib2.feature.types.atomlabel.AtomIsHalogen -joelib2.feature.36.representation =joelib2.feature.types.atomlabel.AtomIsHeteroatom -joelib2.feature.37.representation =joelib2.feature.types.atomlabel.AtomIsHydrogen 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-RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -# LopP Atomic Contributions -# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. Sci., 1999, 39, 868-873. -# Table below is adapted from above ref. uncommon p- and d-block elements have not been included. -######################################################################## -;hydrogen -[*] 0.1125 -[#6] 0.123 -[#1] 0.123 -[O][CX4] -0.2677 -[O]c -0.2677 -[O][#5] -0.2677 -[O][#14] -0.2677 -[O][#15] -0.2677 -[O][#33] -0.2677 -[O][#50] -0.2677 -[#5] -0.2677 -[#14] -0.2677 -[#15] -0.2677 -[#16] -0.2677 -[#50] -0.2677 -[#7] 0.2142 -[O][#7] 0.2142 -[O]C=[#6] 0.298 -[O]C=[#7] 0.298 -[O]C=O 0.298 -[O]C=S 0.298 -[O]O 0.298 -[O]S 0.298 -;heavy -[*] 0 -[#6] 0.0813 -[CH4] 0.1441 -[CH3]C 0.1441 -[CH2](C)C 0.1441 -[CH](C)(C)C 0 -[C](C)(C)(C)C 0 -[CH3][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2035 -[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2035 -[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2051 -[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2051 -[C]=[A!#6] -0.2783 -[CH2]=C 0.1551 -[CH1](=C)A 0.1551 -[CH0](=C)(A)A 0.1551 -[C](=C)=C 0.1551 -[CX2]#A 0.0017 -[CH3]c 0.0845 -[CH3][a!#6] -0.1444 -[CH2X4]a -0.0516 -[CHX4]a 0.1193 -[CH0X4]a -0.0967 -[c][#5,#14,#15,#33,#34,#50,#80] -0.5443 -[c][#9] 0 -[c][#17] 0.245 -[c][#35] 0.198 -[c][#53] 0 -[cH] 0.1581 -[c](:a)(:a):a 0.2955 -[c](:a)(:a)-a 0.2713 -[c](:a)(:a)-C 0.136 -[c](:a)(:a)-N 0.4619 -[c](:a)(:a)-O 0.5437 -[c](:a)(:a)-S 0.1893 -[c](:a)(:a)=C -0.8186 -[c](:a)(:a)=N -0.8186 -[c](:a)(:a)=O -0.8186 -[C](=C)(a)A 0.264 -[C](=C)(c)a 0.264 -[CH](=C)a 0.264 -[C]=c 0.264 -[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53] 0.2148 -[#7] -0.4806 -[NH2+0]A -1.019 -[NH+0](A)A -0.7096 -[NH2+0]a -1.027 -[NH+0](A)a -0.5188 -[NH+0](a)a -0.5188 -[NH+0]=A 0.0839 -[NH+0]=a 0.0839 -[N+0](=A)A 0.1836 -[N+0](=A)a 0.1836 -[N+0](=a)A 0.1836 -[N+0](=a)a 0.1836 -[N+0](A)(A)A -0.3187 -[N+0](a)(A)A -0.4458 -[N+0](a)(a)A -0.4458 -[N+0](a)(a)a -0.4458 -[N+0]#A 0.01508 -[NH3+*] -1.95 -[NH2+*] -1.95 -[NH+*] -1.95 -[n+0] -0.3239 -[n+*] -1.119 -[NH0+*](A)(A)(A)A -0.3396 -[NH0+*](=A)(A)A -0.3396 -[NH0+*](=A)(A)a -0.3396 -[NH0+*](=[#6])=[#7] -0.3396 -[N+*]#A 0.2887 -[N-*] 0.2887 -[N+*](=[N-*])=N 0.2887 -[#8] -0.1188 -[o] 0.1552 -[OH] -0.2893 -[OH2] -0.2893 -[O](C)C -0.0684 -[OH0](C)[A!#6] -0.0684 -[OH0]([A!#6])[A!#6] -0.0684 -[O](A)a -0.4195 -[O](a)a -0.4195 -[O]=[#8] 0.0335 -[O]=[#7] 0.0335 -[OX1-*][#7] 0.0335 -[OX1-*][#16] -0.3339 -[OX1-*][#15;#33;#43;#53] -1.189 -[O]=c 0.1788 -[O]=[CH]C -0.1526 -[O]=C(C)C -0.1526 -[O]=[CH0](C)[A;!6] -0.1526 -[O]=[CH]N -0.1526 -[O]=[CH]O -0.1526 -[O]=[CH2] -0.1526 -[O]=[CX2]=O -0.1526 -[O]=[CH]c 0.1129 -[O]=C(C)c 0.1129 -[O]=C(c)c 0.1129 -[O]=[CH0](c)[a!#6] 0.1129 -[O]=[CH0](c)[A!#6] 0.1129 -[O]=[CH0](C)[a!#6] 0.1129 -[O]=C([A!#6])[A!#6] 0.4833 -[O]=C([A!#6])[a!#6] 0.4833 -[O]=C([a!#6])[a!#6] 0.4833 -[O-1]C(=O) -1.326 -[#9-0] 0.4202 -[#17-0] 0.6895 -[#35-0] 0.8456 -[#53-0] 0.8857 -[#9-*] -2.996 -[#17-*] -2.996 -[#35-*] -2.996 -[#53-*] -2.996 -[#53+*] -2.996 -[#15] 0.8612 -[S-0] 0.6482 -[S-*] -0.0024 -[S+*] -0.0024 -[s] 0.6237 -[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] -0.3808 -[Fe,Cu,Zn,Tc,Cd,Pt,Au,Hg] -0.0025 \ No newline at end of file diff --git a/java/joelib2/data/plain/MR.contributions b/java/joelib2/data/plain/MR.contributions deleted file mode 100644 index 45a47ff..0000000 --- a/java/joelib2/data/plain/MR.contributions +++ /dev/null @@ -1,168 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -# MR Atomic Contributions -# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. Sci., 1999, 39, 868-873. -# Table below is adapted from above ref. uncommon p- and d-block elements have not been included. -######################################################################## -;hydrogen -[*] 1.112 -[#6] 1.057 -[#1] 1.057 -[O][CX4] 1.395 -[O]c 1.395 -[O][#5] 1.395 -[O][#14] 1.395 -[O][#15] 1.395 -[O][#33] 1.395 -[O][#50] 1.395 -[#5] 1.395 -[#14] 1.395 -[#15] 1.395 -[#16] 1.395 -[#50] 1.395 -[#7] 0.9627 -[O][#7] 0.9627 -[O]C=[#6] 1.805 -[O]C=[#7] 1.805 -[O]C=O 1.805 -[O]C=S 1.805 -[O]O 1.805 -[O]S 1.805 -;heavy -[*] 0 -[#6] 3.243 -[CH4] 2.503 -[CH3]C 2.503 -[CH2](C)C 2.503 -[CH](C)(C)C 2.433 -[C](C)(C)(C)C 2.433 -[CH3][O,N,F,Cl,Br,#15,#16,#53;!a] 2.753 -[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.753 -[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.731 -[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.731 -[C]=[A!#6] 5.007 -[CH2]=C 3.513 -[CH1](=C)A 3.513 -[CH0](=C)(A)A 3.513 -[C](=C)=C 3.513 -[CX2]#A 3.888 -[CH3]c 2.464 -[CH3][a!#6] 2.412 -[CH2X4]a 2.488 -[CHX4]a 2.582 -[CH0X4]a 2.576 -[c][#5,#14,#15,#33,#34,#50,#80] 4.041 -[c][#9] 3.257 -[c][#17] 3.564 -[c][#35] 3.18 -[c][#53] 3.104 -[cH] 3.35 -[c](:a)(:a):a 4.346 -[c](:a)(:a)-a 3.904 -[c](:a)(:a)-C 3.509 -[c](:a)(:a)-N 4.067 -[c](:a)(:a)-O 3.853 -[c](:a)(:a)-S 2.673 -[c](:a)(:a)=C 3.135 -[c](:a)(:a)=N 3.135 -[c](:a)(:a)=O 3.135 -[C](=C)(a)A 4.305 -[C](=C)(c)a 4.305 -[CH](=C)a 4.305 -[C]=c 4.305 -[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53] 2.693 -[#7] 2.134 -[NH2+0]A 2.262 -[NH+0](A)A 2.173 -[NH2+0]a 2.827 -[NH+0](A)a 3 -[NH+0](a)a 3 -[NH+0]=A 1.757 -[NH+0]=a 1.757 -[N+0](=A)A 2.428 -[N+0](=A)a 2.428 -[N+0](=a)A 2.428 -[N+0](=a)a 2.428 -[N+0](A)(A)A 1.839 -[N+0](a)(A)A 2.819 -[N+0](a)(a)A 2.819 -[N+0](a)(a)a 2.819 -[N+0]#A 1.725 -[NH3+*] 2.134 -[NH2+*] 2.134 -[NH+*] 2.134 -[n+0] 2.202 -[n+*] 2.134 -[NH0+*](A)(A)(A)A 0.2604 -[NH0+*](=A)(A)A 0.2604 -[NH0+*](=A)(A)a 0.2604 -[NH0+*](=[#6])=[#7] 0.2604 -[N+*]#A 3.359 -[N-*] 3.359 -[N+*](=[N-*])=N 3.359 -[#8] 0.6865 -[o] 1.08 -[OH] 0.8238 -[OH2] 0.8238 -[O](C)C 1.085 -[OH0](C)[A!#6] 1.085 -[OH0]([A!#6])[A!#6] 1.085 -[O](A)a 1.182 -[O](a)a 1.182 -[O]=[#8] 3.367 -[O]=[#7] 3.367 -[OX1-*][#7] 3.367 -[OX1-*][#16] 0.7774 -[OX1-*][#15;#33;#43;#53] 0 -[O]=c 3.135 -[O]=[CH]C 0 -[O]=C(C)C 0 -[O]=[CH0](C)[A;!6] 0 -[O]=[CH]N 0 -[O]=[CH]O 0 -[O]=[CH2] 0 -[O]=[CX2]=O 0 -[O]=[CH]c 0.2215 -[O]=C(C)c 0.2215 -[O]=C(c)c 0.2215 -[O]=[CH0](c)[a!#6] 0.2215 -[O]=[CH0](c)[A!#6] 0.2215 -[O]=[CH0](C)[a!#6] 0.2215 -[O]=C([A!#6])[A!#6] 0.389 -[O]=C([A!#6])[a!#6] 0.389 -[O]=C([a!#6])[a!#6] 0.389 -[O-1]C(=O) 0.6865 -[#9-0] 1.108 -[#17-0] 5.853 -[#35-0] 8.927 -[#53-0] 14.02 -[#9-*] 1.108 -[#17-*] 5.853 -[#35-*] 8.927 -[#53-*] 14.02 -[#53+*] 14.02 -[#15] 6.92 -[S-0] 7.591 -[S-*] 7.365 -[S+*] 7.365 -[s] 6.691 -[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] -0.3808 \ No newline at end of file diff --git a/java/joelib2/data/plain/PSA.contributions b/java/joelib2/data/plain/PSA.contributions deleted file mode 100644 index 56f1597..0000000 --- a/java/joelib2/data/plain/PSA.contributions +++ /dev/null @@ -1,68 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -# Atomic Contributions to Polar Surface Area PSA -# ref. Ertl P., Rohde R., Selzer P., J. Med. Chem. 2000, 43, 3714-3717 -######################################################################## -[*] 0.00 -[N](-*)(-*)-* 3.24 -[N](-*)=* 12.36 -[N]#* 23.79 -[N](-*)(=*)=* 11.68 -[N](=*)#* 13.60 -[N]1(-*)-*-*-1 3.01 -[NH](-*)-* 12.03 -[NH]1-*-*-1 21.94 -[NH]=* 23.85 -[NH2]-* 26.02 -[N+](-*)(-*)(-*)-* 0.00 -[N+](-*)(-*)=* 3.01 -[N+](-*)#* 4.36 -[NH+](-*)(-*)-* 4.44 -[NH+](-*)=* 13.97 -[NH2+](-*)-* 16.61 -[NH2+]=* 25.59 -[NH3+]-* 27.64 -[n](:*):* 12.89 -[n](:*)(:*):* 4.41 -[n](-*)(:*):* 4.93 -[n](=*)(:*):* 8.39 -[nH](:*):* 15.79 -[n+](:*)(:*):* 4.10 -[n+](-*)(:*):* 3.88 -[nH+](:*):* 14.14 -[O](-*)-* 9.23 -[O]1-*-*-1 12.53 -[O]=* 17.07 -[OH]-* 20.23 -[O-]-* 23.06 -[o](:*):* 13.14 -[S](-*)-* 25.30 -[S]=* 32.09 -[S](-*)(-*)=* 19.21 -[S](-*)(-*)(=*)=* 8.38 -[SH]-* 38.80 -[s](:*):* 28.24 -[s](=*)(:*):* 21.70 -[P](-*)(-*)-* 13.59 -[P](-*)=* 34.14 -[P](-*)(-*)(-*)=* 9.81 -[PH](-*)(-*)=* 23.47 diff --git a/java/joelib2/data/plain/aromatic.txt b/java/joelib2/data/plain/aromatic.txt deleted file mode 100644 index 0d7c9c5..0000000 --- a/java/joelib2/data/plain/aromatic.txt +++ /dev/null @@ -1,54 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.4 $ -RELEASE_DATE: $Date: 2005/02/08 20:25:34 $ - -######################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -#PATTERN MIN MAX -#carbon patterns -[#6Q2r+,#6Q3r+] 1 1 -[#6r]=@* 1 1 -[#6rQ3]=!@* 1 1 -# external double bonds to hetero atoms contribute no electrons to the -# aromatic system. This makes sense, because chinoid systems are non- -# aromatic, e.g. 1,4-Benzochinon -[#6rQ3]=!@[!#6] 0 0 -[#6rQ3-] 2 2 - -#nitrogen patterns -[#7r](-@*)-@* 2 2 -[#7rQ2]=@* 1 1 -[#7Q3+] 1 1 -[#7rQ3]=O 1 1 -[#7Q2-] 2 2 - -#oxygen patterns -[#8r] 2 2 -[#8r+] 1 1 - -#sulfur patterns -[#16rQ2] 2 2 -[#16rQ2+] 1 1 -[#16rQ3]=!@O 2 2 - -#other misc patterns -[#15rQ3] 2 2 -#[#34rQ2] 2 2 -#[#52rQ2] 2 2 - diff --git a/java/joelib2/data/plain/atomtype.txt b/java/joelib2/data/plain/atomtype.txt deleted file mode 100644 index 4fd7605..0000000 --- a/java/joelib2/data/plain/atomtype.txt +++ /dev/null @@ -1,88 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.3 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -################################################################################ -# # -# Used to assign the internal atom type to an atom. # -# It is allowed to use assigned hybridisation patterns here, e.g. [#6^3] # -# The LAST PATTERN MATCHED is used to assign values. Additions to this file # -# should be placed in the EXTRA DEFINITIONS section # -# # -################################################################################ -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -[#7^3] N3 -[#7X4+] N3+ -[#7^2] Npl -[#7^1] N1 -[$(N=*)] N2 -[$([Nr0]C(=[Nr0])[Nr0])] Ng+ -[$([Nr0]=C([Nr0])[Nr0])] Ng+ -[$([NQ1]=C[NQ1])] Ng+ -[$([NQ1]C=[NQ1])] Ng+ -[$(N(O)*)] Nox -[$(NC=[O,S])] Nam -[$(N(~[OQ1])~[OQ1])] Ntr -[n] Nar - -[#6^3] C3 -[#6^2] C2 -[$(C(=O)[OQ1])] Cac -[c] Car -[#6^1] C1 -[#6+] C+ -[#6-] C- - -[#8^3] O3 -[#8^2] O2 -[$(Oa)] O2 -#Uncomment the following 2 lines for correct sybyl atom typing -[$([OQ2]C=[O,S])] O3 #ester oxygen -[$(Oa)] O3 #aromatic ether -[#8-] O- -[$([#8Q1]~[#6]~[#8Q1])] Oco2 - -[#15] P -[#15X4+] P3+ -[#15;$([#15Q4](~[OQ1])(~[OQ1])~[OQ1])] Pac -[#15;$([#15Q3](~[OQ1])~[OQ1])] Pac - -[#16] S3 -[#16Q3+,#16X3+] S3+ -[#16;s,$([SQ1]=*)] S2 -[#16Q4;$(S(=O)(=O))] So2 -[#16Q3;$(S(=O))] Sox -[#16;$([#16Q4](~[OQ1])(~[OQ1])~[OQ1])] Sac -[#16;$([#16Q3](~[OQ1])~[OQ1])] Sac - -[#5] B2 -[#5Q4] B3 - -######################## Add Extra Definitions Here ############################## - - -############################# End Extra Definitions ############################## - - - - - - - - diff --git a/java/joelib2/data/plain/desc2ignore.txt b/java/joelib2/data/plain/desc2ignore.txt deleted file mode 100644 index 141f73e..0000000 --- a/java/joelib2/data/plain/desc2ignore.txt +++ /dev/null @@ -1,54 +0,0 @@ -######################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -########## -#HUSKOONEN -########## -Entry_Number -#logS_expected -#melting_point -#residue_huuskonen -########## -#WANG -########## -#predicted_logP -#parameter1 -#molecule_sum_formula -########## -# MISC -########## -ID -id -SID -Sid -#IC50 -########## -# Yoshida -########## -#activity_class -########## -# SOL -########## -#TRUE_CLASS -########## -# HIA -########## -#hia_measured -########## -# NIPS feature selection challenge -########## -true_value \ No newline at end of file diff --git a/java/joelib2/data/plain/element.txt b/java/joelib2/data/plain/element.txt deleted file mode 100644 index c48a656..0000000 --- a/java/joelib2/data/plain/element.txt +++ /dev/null @@ -1,151 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -# - atomic number (used as an index to the vector as well) -# - elemental symbol -# - covalent radii -# - "bond order radii" (usd in B.O. calc) -# - van der Waals radii -# - maximum bond valence -# - RGB values (used by 2D and Java3D rendering) -# - IUPAC recommended atomic masses (in amu) -# - number of electrons -# - period -# - group -# - electronegativity (Allred-Rochow) (missing values set to 0) -# - electronegativity (Pauling) (missing values set to 0) -# - electronegativity (Sanderson) (missing values set to 0) -# - electronaffinity (missing values set to 0) -# - chemical abstract service (CAS) atom identifier (incomplete) -######################################################################### -# Num Symb RCov RChains RBO RVdW Max_Bnd Red Green Blue Mass extEl period group EN_allred_rochow EN_pauling EN_sanderson electroaffinity CAS -0 Xx 0 0 0 0 0 0.07 0.5 0.7 0 s0 0 0 0 0 0 0 0 -1 H 0.23 0.32 0.33 1.2 1 1 1 1 1.008 s1 1 1 2.2 2.1 2.31 -0.756 1333-74-0 -2 He 0.93 1.6 0.7 1.4 0 0.85 1 1 4.003 s2 1 18 5.5 0 0 0.5 7440-59-7 -3 Li 0.68 0.68 1.23 1.82 1 0.8 0.5 1 6.941 s1 2 1 0.97 1 0.86 -0.618 7439-93-2 -4 Be 0.35 0.352 0.9 1.7 2 0.76 1 0 9.012 s2 2 2 1.47 1.5 1.61 0.5 7440-41-7 -5 B 0.83 0.832 0.82 2.08 3 1 0.71 0.71 10.812 s2p1 2 13 2.01 2 1.88 -0.277 7440-42-8 -6 C 0.68 0.72 0.77 1.95 4 0.5 0.5 0.5 12.011 s2p2 2 14 2.5 2.5 2.47 -1.263 7782-42-5 -#6 C 0.68 0.72 0.77 1.95 4 0 0.63 0.63 12.011 s2p2 2 14 2.5 2.5 2.47 -1.263 7782-42-5 -7 N 0.68 0.68 0.7 1.85 4 0.05 0.05 1 14.007 s2p3 2 15 3.07 2.5 2.93 0.07 7727-37-9 -8 O 0.68 0.68 0.66 1.7 2 1 0.05 0.05 15.999 s2p4 2 16 3.5 3.5 3.46 -1.461 -9 F 0.64 0.64 0.611 1.73 1 0.7 1 1 18.998 s2p5 2 17 4.1 4 3.92 -3.399 -10 Ne 0.7 1.12 0.7 1.54 0 0.7 0.89 0.96 20.18 s2p6 2 18 4.8 0 0 1.2 -11 Na 0.97 0.972 1.54 2.27 1 0.67 0.36 0.95 22.99 s1 3 1 1.01 0.9 0.85 -0.546 -12 Mg 1.1 1.1 1.36 1.73 2 0.54 1 0 24.305 s2 3 2 1.23 1.2 1.42 0.4 -13 Al 1.35 1.352 1.18 2.05 6 0.75 0.65 0.65 26.982 s2p1 3 13 1.47 1.5 1.54 -0.456 -14 Si 1.2 1.2 0.937 2.1 6 0.5 0.6 0.6 28.086 s2p2 3 14 1.74 1.8 1.74 -1.385 -15 P 0.75 1.048 0.89 2.08 5 1 0.5 0 30.974 s2p3 3 15 2.06 2.1 2.16 -0.747 -16 S 1.02 1.02 1.04 2 6 1 1 0.19 32.067 s2p4 3 16 2.44 2.5 2.66 -2.077 -17 Cl 0.99 1 0.997 1.97 1 0.12 0.94 0.12 35.453 s2p5 3 17 2.83 3 3.28 -3.617 -18 Ar 0.7 1.568 1.74 1.88 0 0.5 0.82 0.89 39.948 s2p6 3 18 3.2 0 0 1 -19 K 1.33 1.328 2.03 2.75 1 0.56 0.25 0.83 39.098 s1 4 1 0.91 0.8 0.74 -0.502 -20 Ca 0.99 0.992 1.74 1.973 2 0.24 1 0 40.078 s2 4 2 1.04 1 1.06 0.3 -21 Sc 1.44 1.44 1.44 1.7 6 0.9 0.9 0.9 44.956 s2d1 4 3 1.2 1.3 1.09 0 -22 Ti 1.47 1.472 1.32 1.7 6 0.75 0.76 0.78 47.867 s2d2 4 4 1.32 1.5 1.13 -0.21 -23 V 1.33 1.328 1.22 1.7 6 0.65 0.65 0.67 50.942 s2d3 4 5 1.45 1.6 1.24 -0.52 -24 Cr 1.35 1.352 1.18 1.7 6 0.54 0.6 0.78 51.996 s1d5 4 6 1.56 1.6 1.35 -0.66 -25 Mn 1.35 1.352 1.17 1.7 8 0.61 0.48 0.78 54.938 s2d5 4 7 1.6 1.5 1.47 0 -26 Fe 1.34 1.34 1.17 1.7 6 0.5 0.48 0.78 55.845 s2d6 4 8 1.64 1.8 1.47 -0.25 -27 Co 1.33 1.328 1.16 1.7 6 0.44 0.48 0.78 58.933 s2d7 4 9 1.7 1.9 1.47 -0.73 -28 Ni 1.5 1.5 1.15 1.63 6 0.36 0.48 0.76 58.693 s2d8 4 10 1.75 1.9 1.47 -1.15 -29 Cu 1.52 1.52 1.17 1.4 6 1 0.48 0.38 63.546 s1d10 4 11 1.75 1.9 1.74 -1.226 -30 Zn 1.45 1.448 1.25 1.39 6 0.49 0.5 0.69 65.39 s2d10 4 12 1.66 1.6 1.86 0 -31 Ga 1.22 1.22 1.26 1.87 3 0.76 0.56 0.56 69.723 s2p1 4 13 1.82 1.6 2.1 -0.3 -32 Ge 1.17 1.168 1.188 1.7 4 0.4 0.56 0.56 72.61 s2p2 4 14 2.02 1.8 2.31 -1.244 -33 As 1.21 1.208 1.2 1.85 3 0.74 0.5 0.89 74.922 s2p3 4 15 2.2 2 2.53 -0.8 -34 Se 1.22 1.22 1.17 1.9 2 1 0.63 0 78.96 s2p4 4 16 2.48 2.4 2.76 -2.021 -35 Br 1.21 1.208 1.167 2.1 1 0.65 0.16 0.16 79.904 s2p5 4 17 2.74 2.8 2.96 -3.365 -36 Kr 1.91 1.6 1.91 2.02 0 0.36 0.72 0.82 83.8 s2p6 4 18 2.9 0 2.91 1 -37 Rb 1.47 1.472 2.16 1.7 1 0.44 0.18 0.69 85.468 s1 5 1 0.89 0.8 0.7 -0.486 -38 Sr 1.12 1.12 1.91 1.7 2 0 1 0 87.62 s2 5 2 0.99 1 0.96 0.3 -39 Y 1.78 1.78 1.62 1.7 6 0.58 1 1 88.906 s2d1 5 3 1.11 1.2 0.98 0 -40 Zr 1.56 1.56 1.45 1.7 6 0.58 0.88 0.88 91.224 s2d2 5 4 1.22 1.4 1 -0.52 -41 Nb 1.48 1.48 1.34 1.7 6 0.45 0.76 0.79 92.906 s1d4 5 5 1.23 1.6 1.12 -1.04 -42 Mo 1.47 1.472 1.3 1.7 6 0.33 0.71 0.71 95.94 s1d5 5 6 1.3 1.8 1.24 -1.04 -43 Tc 1.35 1.352 1.27 1.7 6 0.23 0.62 0.62 98 s1d6 5 7 1.36 1.9 1.33 -0.72 -44 Ru 1.4 1.4 1.25 1.7 6 0.14 0.56 0.56 101.07 s1d7 5 8 1.42 2.2 1.4 -1.14 -45 Rh 1.45 1.448 1.25 1.7 6 0.04 0.49 0.55 102.906 s1d8 5 9 1.45 2.2 1.47 -1.24 -46 Pd 1.5 1.5 1.28 1.63 6 0 0.41 0.52 106.42 s0d10 5 10 1.3 2.2 1.57 -0.62 -47 Ag 1.59 1.592 1.34 1.72 6 0.88 0.88 1 107.868 s1d10 5 11 1.42 1.9 1.72 -1.303 -48 Cd 1.69 1.688 1.48 1.58 6 1 0.85 0.56 112.412 s2d10 5 12 1.46 1.7 1.73 0 -49 In 1.63 1.632 1.44 1.93 3 0.65 0.46 0.45 114.818 s2p1 5 13 1.49 1.7 1.88 -0.3 -50 Sn 1.46 1.46 1.385 2.17 4 0.4 0.5 0.5 118.711 s2p2 5 14 1.72 1.8 2.02 -1.254 -51 Sb 1.46 1.46 1.4 2.2 3 0.62 0.39 0.71 121.76 s2p3 5 15 1.82 1.9 2.19 -1.047 -52 Te 1.47 1.472 1.378 2.06 2 0.83 0.48 0 127.6 s2p4 5 16 2.01 2.1 2.34 -1.971 -53 I 1.4 1.4 1.387 2.15 1 0.58 0 0.58 126.904 s2p5 5 17 2.21 2.5 2.5 -3.059 -54 Xe 1.98 1.7 1.98 2.16 0 0.26 0.62 0.69 131.29 s2p6 5 18 2.4 0 2.34 0.8 -55 Cs 1.67 1.672 2.35 1.7 1 0.34 0.09 0.56 132.905 s1 6 1 0.86 0.7 0.69 -0.471 -56 Ba 1.34 1.34 1.98 1.7 2 0 0.79 0 137.328 s2 6 2 0.97 0.9 0.93 0.48 -57 La 1.87 1.872 1.69 1.7 12 0.44 0.83 1 138.906 s2f0d1 6 Lanthanoids 1.08 1.08 1.08 0 -58 Ce 1.83 1.832 1.83 1.7 6 1 1 0.78 140.116 s2f2 6 Lanthanoids 1.08 1.08 1.08 0 -59 Pr 1.82 1.82 1.82 1.7 6 0.85 1 0.78 140.908 s2f3 6 Lanthanoids 1.07 1.07 1.07 0 -60 Nd 1.81 1.808 1.81 1.7 6 0.78 1 0.78 144.24 s2f4 6 Lanthanoids 1.07 1.07 1.07 0 -61 Pm 1.8 1.8 1.8 1.7 6 0.64 1 0.78 145 s2f5 6 Lanthanoids 1.07 1.07 1.07 0 -62 Sm 1.8 1.8 1.8 1.7 6 0.56 1 0.78 150.36 s2f6 6 Lanthanoids 1.07 1.07 1.07 0 -63 Eu 1.99 1.992 1.99 1.7 6 0.38 1 0.78 151.964 s2f7 6 Lanthanoids 1.1 1.1 1.1 0 -64 Gd 1.79 1.792 1.79 1.7 6 0.27 1 0.78 157.25 s2f7d1 6 Lanthanoids 1.11 1.11 1.11 0 -65 Tb 1.76 1.76 1.76 1.7 6 0.19 1 0.78 158.925 s2f9 6 Lanthanoids 1.1 1.1 1.1 0 -66 Dy 1.75 1.752 1.75 1.7 6 0.12 1 0.78 162.5 s2f10 6 Lanthanoids 1.1 1.1 1.1 0 -67 Ho 1.74 1.74 1.74 1.7 6 0 1 0.61 164.93 s2f11 6 Lanthanoids 1.1 1.1 1.1 0 -68 Er 1.73 1.728 1.73 1.7 6 0 0.9 0.46 167.26 s2f12 6 Lanthanoids 1.11 1.11 1.11 0 -69 Tm 1.72 1.72 1.72 1.7 6 0 0.83 0.32 168.934 s2f13 6 Lanthanoids 1.11 1.11 1.11 0 -70 Yb 1.94 1.94 1.94 1.7 6 0 0.75 0.22 173.04 s2f14 6 Lanthanoids 1.06 1.06 1.06 0 -71 Lu 1.72 1.72 1.72 1.7 6 0 0.67 0.14 174.967 s2d1 6 3 1.14 1.14 1.14 0 -72 Hf 1.57 1.568 1.44 1.7 6 0.3 0.76 1 178.49 s2d2 6 4 1.23 1.3 0.98 0 -73 Ta 1.43 1.432 1.34 1.7 6 0.3 0.65 1 180.948 s2d3 6 5 1.33 1.5 1.04 -0.62 -74 W 1.37 1.368 1.3 1.7 6 0.13 0.58 0.84 183.84 s2d4 6 6 1.4 1.7 1.13 -0.62 -75 Re 1.35 1.352 1.28 1.7 6 0.15 0.49 0.67 186.207 s2d5 6 7 1.46 1.9 1.19 -0.16 -76 Os 1.37 1.368 1.26 1.7 6 0.15 0.4 0.59 190.23 s2d6 6 8 1.52 2.2 1.26 -1.14 -77 Ir 1.32 1.32 1.27 1.7 6 0.09 0.33 0.53 192.217 s2d7 6 9 1.55 2.2 1.33 -1.66 -78 Pt 1.5 1.5 1.3 1.72 6 0.96 0.93 0.82 195.078 s1d9 6 10 1.42 2.2 1.36 -2.128 -79 Au 1.5 1.5 1.34 1.66 6 0.8 0.82 0.12 196.967 s1d10 6 11 1.42 2.4 1.72 -2.308 -80 Hg 1.7 1.7 1.49 1.55 6 0.71 0.71 0.76 200.59 s2d10 6 12 1.44 1.9 1.92 0 -81 Tl 1.55 1.552 1.48 1.96 3 0.65 0.33 0.3 204.383 s2p1 6 13 1.44 1.8 1.96 -0.31 -82 Pb 1.54 1.54 1.48 2.02 4 0.34 0.35 0.38 207.2 s2p2 6 14 1.55 1.9 2.01 -1.14 -83 Bi 1.54 1.54 1.45 1.7 3 0.62 0.31 0.71 208.98 s2p3 6 15 1.67 1.9 2.06 -1.14 -84 Po 1.68 1.68 1.46 1.7 2 0.67 0.36 0 209 s2p4 6 16 1.76 2 0 -1.87 -85 At 0.7 1.208 1.45 1.7 1 0.46 0.31 0.27 210 s2p5 6 17 1.96 2.2 0 -2.8 -86 Rn 2.4 1.9 2.4 1.7 0 0.26 0.51 0.59 222 s2p6 6 18 2.1 0 0 0.4 -87 Fr 2 1.8 2 1.7 1 0.26 0 0.4 223 s1 7 1 0.86 0.7 0 -0.46 -88 Ra 1.9 1.432 1.9 1.7 2 0 0.49 0 226 s2 7 2 0.97 0.9 0 0 -89 Ac 1.88 1.18 1.88 1.7 6 0.44 0.67 0.98 227 s2f0d1 7 Actinoids 1 1 1 0 -90 Th 1.79 1.02 1.79 1.7 6 0 0.73 1 232.038 s2f0d2 7 Actinoids 1.11 1.11 1.11 0 -91 Pa 1.61 0.888 1.61 1.7 6 0 0.63 1 231.036 s2f2d1 7 Actinoids 1.14 1.14 1.14 0 -92 U 1.58 0.968 1.58 1.86 6 0 0.56 1 238.029 s2f3d1 7 Actinoids 1.22 1.22 1.22 0 -93 Np 1.55 0.952 1.55 1.7 6 0 0.5 1 237 s2f4d1 7 Actinoids 1.22 1.22 1.22 0 -94 Pu 1.53 0.928 1.53 1.7 6 0 0.42 1 244 s2f6 7 Actinoids 1.22 1.22 1.22 0 -95 Am 1.51 0.9 1.07 1.7 6 0.33 0.36 0.95 243 s2f7 7 Actinoids 1.2 1.2 1.2 0 -96 Cm 0 0.912 0 1.7 6 0.47 0.36 0.89 247 s2f7d1 7 Actinoids 1.2 1.2 1.2 0 -97 Bk 0 0.9 0 1.7 6 0.54 0.31 0.89 247 s2f9 7 Actinoids 1.2 1.2 1.2 0 -98 Cf 0 0.888 0 1.7 6 0.63 0.21 0.83 251 s2f10 7 Actinoids 1.2 1.2 1.2 0 -99 Es 0 0.88 0 1.7 6 0.7 0.12 0.83 252 s2f11 7 Actinoids 1.2 1.2 1.2 0 -100 Fm 0 0.872 0 1.7 6 0.7 0.12 0.73 257 s2f12 7 Actinoids 1.2 1.2 1.2 0 -101 Md 0 0.86 0 1.7 6 0.7 0.05 0.65 258 s2f13 7 Actinoids 1.2 1.2 1.2 0 -102 No 0 0.848 0 1.7 6 0.74 0.05 0.53 259 s2f14 7 Actinoids 1.2 1.2 1.2 0 -103 Lr 0 0.84 0 1.7 6 0.78 0 0.4 262 s2d1 7 3 1.2 1.2 1.2 0 -104 Rf 0 0 0 1.7 6 0.8 0 0.35 261 s2d2 7 4 0 0 0 0 -105 Db 0 0 0 1.7 6 0.82 0 0.31 262 s2d3 7 5 0 0 0 0 -106 Sg 0 0 0 1.7 6 0.85 0 0.27 263 s2d4 7 6 0 0 0 0 -107 Bh 0 0 0 1.7 6 0.88 0 0.22 264 s2d5 7 7 0 0 0 0 -108 Hs 0 0 0 1.7 6 0.9 0 0.18 265 s2d6 7 8 0 0 0 0 -109 Mt 0 0 0 1.7 6 0.92 0 0.15 268 s2d7 7 9 0 0 0 0 -110 Uun 0 0 0 1.7 6 0.95 0 0.11 269 s2d8 7 10 0 0 0 0 diff --git a/java/joelib2/data/plain/hybridisation.txt b/java/joelib2/data/plain/hybridisation.txt deleted file mode 100644 index bef5a04..0000000 --- a/java/joelib2/data/plain/hybridisation.txt +++ /dev/null @@ -1,61 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.3 $ -RELEASE_DATE: $Date: 2005/01/08 22:23:25 $ - -################################################################################ -# # -# Used to assign the hybridisation values valence of an atom. # -# It is NOT allowed to use assigned hybridisation patterns here, e.g. [#6^3] # -# The LAST PATTERN MATCHED is used to assign values. Additions to this file # -# should be placed in the EXTRA DEFINITIONS section # -# # -################################################################################ -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -[C] 3 #sp3 carbon -[c,$(C=*)] 2 #sp2 carbon -[$([#6]([#8Q1])[#8Q1])] 2 #sp2 carbon -[$(C#*),$(C(=*)=*)] 1 #sp carbon -[N] 3 #sp3 nitrogen -[n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen -[$(N#*),$([NQ2](=*)=*)] 1 #sp nitrogen -[O] 3 #sp3 oxygen -[o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen -[$([#8Q1][#6][#8Q1])] 2 #sp2 oxygen -[$(O#*)] 1 #sp oxygen -[Q4] 3 #any 4 valent atom - -[P] 3 #sp3 phosphorus -[#15;$([PQ1]=*)] 2 #sp2 phosphorus -[S] 3 #sp3 sulfur -[#16;s,$([SQ1]=*)] 2 #sp2 sulfur -[B] 2 #sp2 boron -[BQ4] 3 #sp3 boron - -######################## Add Extra Definitions Here ############################## - - -############################# End Extra Definitions ############################## - - - - - - - - diff --git a/java/joelib2/data/plain/implicitValence.txt b/java/joelib2/data/plain/implicitValence.txt deleted file mode 100644 index d82bd72..0000000 --- a/java/joelib2/data/plain/implicitValence.txt +++ /dev/null @@ -1,94 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.3 $ -RELEASE_DATE: $Date: 2005/01/08 22:23:25 $ - -######################################################################## -# -# Used to assign the implicit valence of an atom. -# It is allowed to use assigned hybridisation patterns here, e.g. [#6^3] -# The LAST PATTERN MATCHED is used to assign values. Additions to this file -# should be placed in the EXTRA DEFINITIONS section -# -######################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -[#6^3] 4 -[#6^2] 3 -[#6^1] 2 -[#6^3-] 3 -[#6^2-] 2 -[c+] 2 - -[#8^3] 2 -[#8^2] 2 -[$([#8]=*)] 1 -[#8-] 1 -[$([#8Q1]~[#7Q3]~[#8Q1])] 1 -#[$([#8Q1]~[#6]~[#8Q1])] 1 -[$([#8Q1]-[#6]=[#8Q1])] 2 -[$([#8-Q1]-[#6]=[#8Q1])] 1 - -[N^3] 3 -[N^3+] 4 -[N^2] 3 -[N^2-,N^3-] 2 -[NQ1^1] 1 -[NQ2^1] 2 -[$(N([OQ1])*)] 3 -[$(NC=O)] 3 -[$(N(~[OQ1])~[OQ1])] 3 -[$([Nr0]C=[Nr0])] 3 -[$(N=*)] 2 -#uncomment this line for cansmi testing -#[$([Nr0]=C[Nr0])] 2 -[$([#7Q1-]=*)] 1 -[n] 2 -[n-] 2 -[n+] 3 - -[#15Q4] 4 -[#15Q3] 3 -[#15Q2] 3 -[#15Q1^3] 3 -[#15Q1^2] 3 -[$([#15]=[#6])] 2 -[pQ2] 2 - -[#16Q4] 4 -[#16Q3] 3 -[#16Q2] 2 -[$([#16Q1]-*)] 2 -[#16Q1^2] 1 -[s] 2 -[#16Q1-] 1 - -[#5] 3 -[as] 3 - -######################## Add Extra Definitions Here ############################## - - -############################# End Extra Definitions ############################## - - - - - - - - diff --git a/java/joelib2/data/plain/isotope-small.txt b/java/joelib2/data/plain/isotope-small.txt deleted file mode 100644 index ceffe1f..0000000 --- a/java/joelib2/data/plain/isotope-small.txt +++ /dev/null @@ -1,137 +0,0 @@ -############################################################################## -# # -# Open Babel file: isotope-small.txt # -# # -# Copyright (c) 2002-2003 by Geoffrey R. Hutchison # -# Part of the Open Babel package, under the GNU General Public License (GPL)# -# # -# Small isotope table with most frequently-used isotopes (as default data) # -# (GRH currently trimmed up to atomic # 40 and #100+) # -# # -# This file has a series of lines, one for each element # -# (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.) # -# Each line: Atomic #, 0 then exact mass of most abundant isotope # -# then a list of isotopes as int, float pairs corresponding to masses # -# # -# CAUTION: Masses have been zero-padded to 6 decimal places # -# (we don't currently have a math package that can deal with sig. fig.) # -# so trailing zeros may not be significant and/or useful # -# # -# Values are compiled from "The 1995 update to the atomic mass evaluation" # -# by G.Audi and A.H.Wapstra # -# Nuclear Physics A595 vol. 4 p.409-480, December 25, 1995. # -# as made available in the mass_rmd.mas95 file # -# # -# Currently: 110 lines (neutron, H to Mt) # -# # -############################################################################## -0 0 0.000000 1 1.008664 -1 0 1.007825 1 1.007825 2 2.014101 3 3.016049 -2 0 4.002603 3 3.016029 4 4.002603 5 5.012220 6 6.018888 7 7.028030 8 8.033922 9 9.043820 10 10.052400 -3 0 7.016004 5 5.012540 6 6.015122 7 7.016004 8 8.022486 9 9.026789 10 10.035481 11 11.043796 -4 0 9.012182 6 6.019726 7 7.016929 8 8.005305 9 9.012182 10 10.013533 11 11.021658 12 12.026921 14 14.042820 -5 0 11.009305 7 7.029920 8 8.024606 9 9.013328 10 10.012937 11 11.009305 12 12.014352 13 13.017780 14 14.025404 15 15.031097 17 17.046930 19 19.063730 -6 0 12.000000 8 8.037675 9 9.031040 10 10.016853 11 11.011433 12 12.000000 13 13.003354 14 14.003241 15 15.010599 16 16.014701 17 17.022584 18 18.026760 19 19.035250 20 20.040320 -7 0 14.003074 12 12.018613 13 13.005738 14 14.003074 15 15.000108 16 16.006101 17 17.008450 18 18.014082 19 19.017027 20 20.023370 21 21.027090 22 22.034440 23 23.040510 -8 0 15.994914 12 12.034405 13 13.024810 14 14.008595 15 15.003065 16 15.994914 17 16.999131 18 17.999160 19 19.003579 20 20.004076 21 21.008655 22 22.009970 23 23.015690 24 24.020370 -9 0 18.998403 15 15.018010 16 16.011466 17 17.002095 18 18.000937 19 18.998403 20 19.999981 21 20.999948 22 22.002999 23 23.003570 24 24.008100 25 25.012090 26 26.019630 27 27.026890 -10 0 19.992440 16 16.025757 17 17.017700 18 18.005697 19 19.001879 20 19.992440 21 20.993846 22 21.991385 23 22.994467 24 23.993615 25 24.997790 26 26.000460 27 27.007620 28 28.012110 29 29.019350 -11 0 22.989769 19 19.013879 20 20.007348 21 20.997655 22 21.994436 23 22.989769 24 23.990963 25 24.989954 26 25.992590 27 26.994010 28 27.998890 29 29.002810 30 30.009230 31 31.013600 32 32.019650 33 33.027390 34 34.034900 35 35.044180 -12 0 23.985041 20 20.018863 21 21.011714 22 21.999574 23 22.994124 24 23.985041 25 24.985837 26 25.982593 27 26.984340 28 27.983876 29 28.988550 30 29.990460 31 30.996550 32 31.999150 33 33.005590 -13 0 26.981538 22 22.019520 23 23.007265 24 23.999941 25 24.990428 26 25.986891 27 26.981538 28 27.981910 29 28.980444 30 29.982960 31 30.983946 32 31.988120 33 32.990870 34 33.996930 35 34.999940 36 36.006350 -14 0 27.976926 22 22.034530 24 24.011546 25 25.004107 26 25.992330 27 26.986704 28 27.976926 29 28.976494 30 29.973770 31 30.975363 32 31.974148 33 32.978001 34 33.978576 35 34.984580 36 35.986690 37 36.993000 38 37.995980 39 39.002300 -15 0 30.973761 26 26.011780 27 26.999190 28 27.992312 29 28.981801 30 29.978313 31 30.973761 32 31.973907 33 32.971725 34 33.973636 35 34.973314 36 35.978260 37 36.979610 38 37.984470 39 38.986420 40 39.991050 41 40.994800 42 42.000090 -16 0 31.972070 27 27.018800 28 28.004370 29 28.996610 30 29.984903 31 30.979554 32 31.972070 33 32.971458 34 33.967866 35 34.969032 36 35.967080 37 36.971125 38 37.971163 39 38.975140 40 39.975470 41 40.980030 42 41.981490 43 42.986600 44 43.988320 -17 0 34.968852 31 30.992420 32 31.985689 33 32.977451 34 33.973761 35 34.968852 36 35.968306 37 36.965902 38 37.968010 39 38.968007 40 39.970420 41 40.970650 42 41.973170 43 42.974200 44 43.978540 45 44.979700 46 45.984120 47 46.987950 -18 0 39.962383 31 31.012130 32 31.997660 33 32.989930 34 33.980270 35 34.975256 36 35.967546 37 36.966775 38 37.962732 39 38.964313 40 39.962383 41 40.964500 42 41.963050 43 42.965670 44 43.965365 45 44.968090 46 45.968090 47 46.972190 -19 0 38.963706 35 34.988012 36 35.981293 37 36.973376 38 37.969080 39 38.963706 40 39.963998 41 40.961825 42 41.962403 43 42.960716 44 43.961560 45 44.960700 46 45.961976 47 46.961678 48 47.965513 49 48.967450 50 49.972780 51 50.976380 52 51.982610 53 52.987120 54 53.993990 -20 0 39.962591 35 35.004770 36 35.993090 37 36.985872 38 37.976319 39 38.970717 40 39.962591 41 40.962278 42 41.958618 43 42.958766 44 43.955481 45 44.956185 46 45.953692 47 46.954546 48 47.952534 49 48.955673 50 49.957518 51 50.961470 52 51.965100 53 52.970050 -21 0 44.955910 40 39.977964 41 40.969251 42 41.965516 43 42.961151 44 43.959403 45 44.955910 46 45.955170 47 46.952408 48 47.952235 49 48.950024 50 49.952187 51 50.953603 52 51.956650 53 52.959240 54 53.963000 55 54.967430 -22 0 47.947947 39 39.001320 40 39.990500 41 40.983130 42 41.973032 43 42.968523 44 43.959690 45 44.958124 46 45.952629 47 46.951763 48 47.947947 49 48.947870 50 49.944792 51 50.946616 52 51.946898 53 52.949730 54 53.950870 55 54.955120 56 55.957990 57 56.962900 58 57.966110 -23 0 50.943963 43 42.980650 44 43.974400 45 44.965782 46 45.960199 47 46.954906 48 47.952254 49 48.948516 50 49.947162 51 50.943963 52 51.944779 53 52.944343 54 53.946444 55 54.947240 56 55.950360 57 56.952360 58 57.956650 59 58.959300 60 59.964500 61 60.967410 -24 0 51.940511 43 42.997710 44 43.985470 45 44.979160 46 45.968362 47 46.962907 48 47.954036 49 48.951341 50 49.946049 51 50.944771 52 51.940511 53 52.940653 54 53.938884 55 54.940844 56 55.940645 57 56.943750 58 57.944250 59 58.948630 60 59.949730 61 60.954090 62 61.955800 63 62.961860 -25 0 54.938049 46 45.986720 47 46.976100 48 47.968870 49 48.959623 50 49.954244 51 50.948215 52 51.945570 53 52.941294 54 53.940363 55 54.938049 56 55.938909 57 56.938287 58 57.939990 59 58.940450 60 59.943190 61 60.944460 62 61.947970 63 62.949810 64 63.953730 65 64.956100 66 65.960820 -26 0 55.934942 46 46.000810 47 46.992890 48 47.980560 49 48.973610 50 49.962990 51 50.956825 52 51.948117 53 52.945312 54 53.939614 55 54.938298 56 55.934942 57 56.935398 58 57.933280 59 58.934880 60 59.934077 61 60.936749 62 61.936770 63 62.940120 64 63.940870 65 64.944940 66 65.945980 67 66.950000 68 67.952510 69 68.957700 -27 0 58.933200 50 49.981540 51 50.970720 52 51.963590 53 52.954225 54 53.948464 55 54.942003 56 55.939843 57 56.936296 58 57.935757 59 58.933200 60 59.933822 61 60.932479 62 61.934054 63 62.933615 64 63.935814 65 64.936485 66 65.939830 67 66.940610 68 67.944360 69 68.945200 70 69.949810 71 70.951730 -28 0 57.935347 51 50.987720 52 51.975680 53 52.968460 54 53.957910 55 54.951336 56 55.942136 57 56.939800 58 57.935347 59 58.934351 60 59.930790 61 60.931060 62 61.928348 63 62.929672 64 63.927969 65 64.930088 66 65.929115 67 66.931570 68 67.931845 69 68.935180 70 69.936140 71 70.940000 72 71.941300 73 72.946080 74 73.947910 -29 0 62.929601 55 54.966050 56 55.958560 57 56.949216 58 57.944540 59 58.939504 60 59.937368 61 60.933462 62 61.932587 63 62.929601 64 63.929767 65 64.927793 66 65.928873 67 66.927750 68 67.929640 69 68.929425 70 69.932409 71 70.932620 72 71.935520 73 72.936490 74 73.940200 75 74.941700 76 75.945990 77 76.947950 78 77.952810 79 78.955280 -30 0 63.929146 57 56.964910 58 57.954600 59 58.949270 60 59.941832 61 60.939514 62 61.934334 63 62.933215 64 63.929146 65 64.929245 66 65.926036 67 66.927130 68 67.924847 69 68.926553 70 69.925325 71 70.927727 72 71.926861 73 72.929780 74 73.929460 75 74.932940 76 75.933390 77 76.937090 78 77.938570 79 78.942680 80 79.944410 81 80.950480 -31 0 68.925581 61 60.949170 62 61.944180 63 62.939140 64 63.936838 65 64.932739 66 65.931592 67 66.928204 68 67.927983 69 68.925581 70 69.926028 71 70.924705 72 71.926369 73 72.925170 74 73.926940 75 74.926501 76 75.928930 77 76.929280 78 77.931660 79 78.932920 80 79.936590 81 80.937750 82 81.943160 83 82.946870 84 83.952340 -32 0 73.921178 61 60.963790 62 61.954650 63 62.949640 64 63.941570 65 64.939440 66 65.933850 67 66.932738 68 67.928097 69 68.927972 70 69.924250 71 70.924954 72 71.922076 73 72.923459 74 73.921178 75 74.922859 76 75.921402 77 76.923548 78 77.922853 79 78.925400 80 79.925445 81 80.928820 82 81.929550 83 82.934510 84 83.937310 85 84.942690 -33 0 74.921596 65 64.949480 66 65.944370 67 66.939190 68 67.936790 69 68.932280 70 69.930930 71 70.927115 72 71.926753 73 72.923825 74 73.923929 75 74.921596 76 75.922393 77 76.920647 78 77.921829 79 78.920948 80 79.922578 81 80.922133 82 81.924500 83 82.924980 84 83.929060 85 84.931810 86 85.936230 87 86.939580 -34 0 79.916521 65 64.964660 67 66.950090 68 67.941870 69 68.939560 70 69.933500 71 70.932270 72 71.927112 73 72.926767 74 73.922476 75 74.922523 76 75.919214 77 76.919914 78 77.917309 79 78.918499 80 79.916521 81 80.917992 82 81.916700 83 82.919119 84 83.918465 85 84.922240 86 85.924271 87 86.928520 88 87.931420 89 88.936020 90 89.939420 91 90.945370 -35 0 78.918337 69 68.950180 70 69.944620 71 70.939250 72 71.936500 73 72.931790 74 73.929891 75 74.925776 76 75.924542 77 76.921380 78 77.921146 79 78.918337 80 79.918530 81 80.916291 82 81.916805 83 82.915180 84 83.916504 85 84.915608 86 85.918797 87 86.920711 88 87.924070 89 88.926390 90 89.930630 91 90.933970 92 91.939260 93 92.943100 94 93.948680 -36 0 83.911507 71 70.950510 72 71.941910 73 72.938930 74 73.933260 75 74.931034 76 75.925948 77 76.924668 78 77.920386 79 78.920083 80 79.916378 81 80.916592 82 81.913484 83 82.914136 84 83.911507 85 84.912527 86 85.910610 87 86.913354 88 87.914447 89 88.917630 90 89.919524 91 90.923440 92 91.926153 93 92.931270 94 93.934360 95 94.939840 97 96.948560 -37 0 84.911789 74 73.944470 75 74.938569 76 75.935071 77 76.930407 78 77.928141 79 78.923997 80 79.922519 81 80.918994 82 81.918208 83 82.915112 84 83.914385 85 84.911789 86 85.911167 87 86.909183 88 87.911319 89 88.912280 90 89.914809 91 90.916534 92 91.919725 93 92.922033 94 93.926407 95 94.929319 96 95.934284 97 96.937340 98 97.941700 99 98.945420 100 99.949870 101 100.953200 102 101.959210 -38 0 87.905614 76 75.941610 77 76.937760 78 77.932179 79 78.929707 80 79.924525 81 80.923213 82 81.918401 83 82.917555 84 83.913425 85 84.912933 86 85.909262 87 86.908879 88 87.905614 89 88.907452 90 89.907737 91 90.910210 92 91.911030 93 92.914022 94 93.915360 95 94.919358 96 95.921680 97 96.926149 98 97.928471 99 98.933320 100 99.935350 101 100.940520 102 101.943020 -39 0 88.905847 78 77.943500 79 78.937350 80 79.934340 81 80.929130 82 81.926790 83 82.922350 84 83.920390 85 84.916427 86 85.914888 87 86.910877 88 87.909503 89 88.905847 90 89.907151 91 90.907303 92 91.908947 93 92.909582 94 93.911594 95 94.912824 96 95.915898 97 96.918131 98 97.922220 99 98.924635 100 99.927760 101 100.930310 102 101.933560 -40 0 89.904703 80 79.940550 81 80.936820 82 81.931090 83 82.928650 84 83.923250 85 84.921470 86 85.916470 87 86.914817 88 87.910226 89 88.908889 90 89.904703 91 90.905645 92 91.905040 93 92.906475 94 93.906315 95 94.908042 96 95.908276 97 96.910951 98 97.912746 99 98.916511 100 99.917760 101 100.921140 102 101.922980 103 102.926600 104 103.928780 105 104.933050 -41 0 92.906377 82 81.943130 83 82.936700 84 83.933570 85 84.927910 86 85.925040 87 86.920360 88 87.917960 89 88.913500 90 89.911264 91 90.906991 92 91.907193 93 92.906377 94 93.907283 95 94.906835 96 95.908100 97 96.908097 98 97.910331 99 98.911618 100 99.914181 101 100.915252 102 101.918040 103 102.919140 104 103.922460 105 104.923930 106 105.928190 107 106.930310 -42 0 97.905407 84 83.940090 85 84.936590 86 85.930700 87 86.927330 88 87.921953 89 88.919481 90 89.913936 91 90.911751 92 91.906810 93 92.906812 94 93.905087 95 94.905841 96 95.904678 97 96.906021 98 97.905407 99 98.907711 100 99.907477 101 100.910347 102 101.910297 103 102.913200 104 103.913760 105 104.916970 106 105.918134 107 106.921690 108 107.923580 109 108.927810 110 109.929730 -43 0 97.907216 86 85.942880 87 86.936530 88 87.932830 89 88.927540 90 89.923560 91 90.918430 92 91.915260 93 92.910248 94 93.909656 95 94.907656 96 95.907871 97 96.906365 98 97.907216 99 98.906254 100 99.907657 101 100.907314 102 101.909213 103 102.909179 104 103.911440 105 104.911660 106 105.914355 107 106.915080 108 107.918480 109 108.919630 110 109.923390 111 110.925050 112 111.929240 113 112.931330 -44 0 101.904349 88 87.940420 89 88.936110 90 89.929780 91 90.926380 92 91.920120 93 92.917050 94 93.911360 95 94.910413 96 95.907598 97 96.907555 98 97.905287 99 98.905939 100 99.904219 101 100.905582 102 101.904349 103 102.906323 104 103.905430 105 104.907750 106 105.907327 107 106.909910 108 107.910190 109 108.913200 110 109.913970 111 110.917560 112 111.918550 113 112.922540 114 113.924000 115 114.928310 -45 0 102.905504 90 89.942870 91 90.936550 92 91.931980 93 92.925740 94 93.921700 95 94.915900 96 95.914518 97 96.911340 98 97.910716 99 98.908132 100 99.908117 101 100.906164 102 101.906843 103 102.905504 104 103.906655 105 104.905692 106 105.907285 107 106.906751 108 107.908730 109 108.908736 110 109.910950 111 110.911660 112 111.914610 113 112.915420 114 113.918850 115 114.920120 116 115.923710 117 116.925350 -46 0 105.903483 92 91.940420 93 92.935910 94 93.928770 95 94.924690 96 95.918220 97 96.916480 98 97.912721 99 98.911768 100 99.908505 101 100.908289 102 101.905608 103 102.906087 104 103.904035 105 104.905084 106 105.903483 107 106.905128 108 107.903894 109 108.905954 110 109.905152 111 110.907640 112 111.907313 113 112.910150 114 113.910365 115 114.913680 116 115.914160 117 116.917840 118 117.918980 119 118.922680 120 119.924030 -47 0 106.905093 94 93.942780 95 94.935480 96 95.930680 97 96.924000 98 97.921760 99 98.917600 100 99.916070 101 100.912800 102 101.912000 103 102.908972 104 103.908628 105 104.906528 106 105.906666 107 106.905093 108 107.905954 109 108.904756 110 109.906110 111 110.905295 112 111.907004 113 112.906566 114 113.908808 115 114.908760 116 115.911360 117 116.911680 118 117.914580 119 118.915670 120 119.918790 121 120.919850 122 121.923320 123 122.924900 124 123.928530 -48 0 113.903358 97 96.934940 98 97.927580 99 98.925010 100 99.920230 101 100.918680 102 101.914780 103 102.913419 104 103.909848 105 104.909468 106 105.906458 107 106.906614 108 107.904183 109 108.904986 110 109.903006 111 110.904182 112 111.902757 113 112.904400 114 113.903358 115 114.905431 116 115.904755 117 116.907218 118 117.906914 119 118.909920 120 119.909851 121 120.912980 122 121.913500 123 122.917000 124 123.917650 125 124.921250 126 125.922350 127 126.926430 128 127.927760 129 128.932260 130 129.933980 -49 0 114.903878 99 98.934610 100 99.931150 101 100.926560 102 101.924710 103 102.919914 104 103.918340 105 104.914673 106 105.913461 107 106.910292 108 107.909720 109 108.907154 110 109.907169 111 110.905111 112 111.905533 113 112.904061 114 113.904917 115 114.903878 116 115.905260 117 116.904516 118 117.906355 119 118.905846 120 119.907960 121 120.907849 122 121.910280 123 122.910439 124 123.913180 125 124.913600 126 125.916460 127 126.917340 128 127.920170 129 128.921660 130 129.924850 131 130.926770 132 131.932920 133 132.938340 134 133.944660 -50 0 119.902196 100 99.938950 101 100.936060 102 101.930490 103 102.928130 104 103.923190 105 104.921390 106 105.916880 107 106.915670 108 107.911970 109 108.911287 110 109.907853 111 110.907735 112 111.904821 113 112.905173 114 113.902782 115 114.903346 116 115.901744 117 116.902954 118 117.901606 119 118.903309 120 119.902196 121 120.904236 122 121.903440 123 122.905721 124 123.905274 125 124.907784 126 125.907654 127 126.910351 128 127.910535 129 128.913440 130 129.913850 131 130.916920 132 131.917744 133 132.923810 134 133.928460 -51 0 120.903818 106 105.928760 107 106.924150 108 107.922160 109 108.918136 110 109.916760 111 110.913210 112 111.912395 113 112.909378 114 113.909100 115 114.906599 116 115.906797 117 116.904840 118 117.905532 119 118.903946 120 119.905074 121 120.903818 122 121.905175 123 122.904215 124 123.905937 125 124.905248 126 125.907250 127 126.906915 128 127.909167 129 128.909150 130 129.911546 131 130.911950 132 131.914413 133 132.915240 134 133.920550 135 134.925170 136 135.930660 -52 0 129.906222 106 105.937700 107 106.935040 108 107.929490 109 108.927460 110 109.922410 111 110.921120 112 111.917060 113 112.915930 114 113.912060 115 114.911580 116 115.908420 117 116.908634 118 117.905825 119 118.906408 120 119.904020 121 120.904930 122 121.903047 123 122.904273 124 123.902819 125 124.904424 126 125.903305 127 126.905217 128 127.904461 129 128.906596 130 129.906222 131 130.908521 132 131.908524 133 132.910940 134 133.911540 135 134.916450 136 135.920100 137 136.925320 138 137.929220 -53 0 126.904468 108 107.943290 109 108.938190 110 109.935210 111 110.930280 112 111.927970 113 112.923640 114 113.921850 115 114.917920 116 115.916740 117 116.913650 118 117.913380 119 118.910180 120 119.910048 121 120.907366 122 121.907592 123 122.905598 124 123.906211 125 124.904624 126 125.905619 127 126.904468 128 127.905805 129 128.904987 130 129.906674 131 130.906124 132 131.907995 133 132.907806 134 133.909877 135 134.910050 136 135.914660 137 136.917873 138 137.922380 139 138.926090 140 139.931210 141 140.934830 142 141.940180 -54 0 131.904154 110 109.944480 111 110.941630 112 111.935670 113 112.933380 114 113.928150 115 114.926540 116 115.921740 117 116.920560 118 117.916570 119 118.915550 120 119.912150 121 120.911386 122 121.908550 123 122.908471 124 123.905895 125 124.906398 126 125.904269 127 126.905180 128 127.903530 129 128.904779 130 129.903507 131 130.905081 132 131.904154 133 132.905906 134 133.905394 135 134.907207 136 135.907220 137 136.911563 138 137.913990 139 138.918787 140 139.921640 141 140.926650 142 141.929700 143 142.934890 144 143.938230 145 144.943670 -55 0 132.905447 112 111.950330 113 112.944540 114 113.941420 115 114.935940 116 115.932910 117 116.928640 118 117.926555 119 118.922371 120 119.920678 121 120.917184 122 121.916122 123 122.912990 124 123.912246 125 124.909725 126 125.909448 127 126.907418 128 127.907748 129 128.906063 130 129.906706 131 130.905460 132 131.906430 133 132.905447 134 133.906713 135 134.905972 136 135.907306 137 136.907084 138 137.911011 139 138.913358 140 139.917277 141 140.920044 142 141.924292 143 142.927330 144 143.932030 145 144.935390 146 145.940160 147 146.943860 148 147.948900 -56 0 137.905241 117 116.938860 119 118.931050 120 119.926050 121 120.924490 122 121.920260 123 122.918850 124 123.915088 125 124.914620 126 125.911244 127 126.911120 128 127.908309 129 128.908674 130 129.906310 131 130.906931 132 131.905056 133 132.906002 134 133.904503 135 134.905683 136 135.904570 137 136.905821 138 137.905241 139 138.908835 140 139.910599 141 140.914406 142 141.916448 143 142.920617 144 143.922940 145 144.926920 146 145.930110 147 146.933990 148 147.937680 149 148.942460 -57 0 138.906348 120 119.938070 122 121.930710 123 122.926240 124 123.924530 125 124.920670 126 125.919370 127 126.916160 128 127.915450 129 128.912670 130 129.912320 131 130.910110 132 131.910110 133 132.908400 134 133.908490 135 134.906971 136 135.907650 137 136.906470 138 137.907107 139 138.906348 140 139.909473 141 140.910957 142 141.914074 143 142.916059 144 143.919590 145 144.921640 146 145.925700 147 146.927820 148 147.932190 149 148.934370 -58 0 139.905434 123 122.935510 124 123.930520 125 124.928540 126 125.924100 127 126.922750 128 127.918870 129 128.918090 130 129.914690 131 130.914420 132 131.911490 133 132.911550 134 133.909030 135 134.909146 136 135.907140 137 136.907780 138 137.905986 139 138.906647 140 139.905434 141 140.908271 142 141.909240 143 142.912381 144 143.913643 145 144.917230 146 145.918690 147 146.922510 148 147.924390 149 148.928290 150 149.930230 151 150.934040 152 151.936380 -59 0 140.907648 124 123.942960 126 125.935310 127 126.930830 128 127.928800 129 128.924860 130 129.923380 131 130.920060 132 131.919120 133 132.916200 134 133.915670 135 134.913140 136 135.912650 137 136.910680 138 137.910749 139 138.908932 140 139.909071 141 140.907648 142 141.910040 143 142.910812 144 143.913301 145 144.914507 146 145.917590 147 146.918980 148 147.922180 149 148.923791 150 149.927000 151 150.928230 152 151.931600 153 152.933650 154 153.937390 -60 0 141.907719 127 126.940500 128 127.935390 129 128.933250 130 129.928780 131 130.927100 132 131.923120 133 132.922210 134 133.918650 135 134.918240 136 135.915020 137 136.914640 138 137.911930 139 138.911920 140 139.909310 141 140.909605 142 141.907719 143 142.909810 144 143.910083 145 144.912569 146 145.913112 147 146.916096 148 147.916889 149 148.920144 150 149.920887 151 150.923825 152 151.924680 153 152.927695 154 153.929480 155 154.932630 156 155.935200 -61 0 144.912744 130 129.940450 132 131.933750 133 132.929720 134 133.928490 135 134.924620 136 135.923450 137 136.920710 138 137.919450 139 138.916760 140 139.915800 141 140.913607 142 141.912950 143 142.910928 144 143.912586 145 144.912744 146 145.914692 147 146.915134 148 147.917468 149 148.918329 150 149.920979 151 150.921203 152 151.923490 153 152.924113 154 153.926550 155 154.928100 156 155.931060 157 156.933200 158 157.936690 -62 0 151.919728 131 130.945890 133 132.938730 134 133.934020 135 134.932350 136 135.928300 137 136.927050 138 137.923540 139 138.922302 140 139.918991 141 140.918469 142 141.915193 143 142.914624 144 143.911995 145 144.913406 146 145.913037 147 146.914893 148 147.914818 149 148.917180 150 149.917271 151 150.919928 152 151.919728 153 152.922094 154 153.922205 155 154.924636 156 155.925526 157 156.928350 158 157.929990 159 158.933200 160 159.935140 -63 0 152.921226 134 133.946320 135 134.941720 136 135.939500 137 136.935210 138 137.933450 139 138.929840 140 139.928080 141 140.924890 142 141.923400 143 142.920287 144 143.918774 145 144.916261 146 145.917200 147 146.916741 148 147.918154 149 148.917926 150 149.919698 151 150.919846 152 151.921740 153 152.921226 154 153.922975 155 154.922889 156 155.924751 157 156.925419 158 157.927840 159 158.929084 160 159.931970 161 160.933680 162 161.937040 -64 0 157.924101 137 136.944650 138 137.939970 139 138.938080 140 139.933950 141 140.932210 142 141.928230 143 142.926740 144 143.922790 145 144.921690 146 145.918305 147 146.919089 148 147.918110 149 148.919336 150 149.918655 151 150.920344 152 151.919788 153 152.921746 154 153.920862 155 154.922619 156 155.922120 157 156.923957 158 157.924101 159 158.926385 160 159.927051 161 160.929666 162 161.930981 163 162.933990 164 163.935860 -65 0 158.925343 140 139.945540 141 140.941160 142 141.938860 143 142.934750 144 143.932530 145 144.928880 146 145.927180 147 146.924037 148 147.924300 149 148.923242 150 149.923654 151 150.923098 152 151.924070 153 152.923431 154 153.924690 155 154.923500 156 155.924744 157 156.924021 158 157.925410 159 158.925343 160 159.927164 161 160.927566 162 161.929480 163 162.930644 164 163.933350 165 164.934880 -66 0 163.929171 141 140.951190 142 141.946270 143 142.943830 144 143.939070 145 144.936950 146 145.932720 147 146.930880 148 147.927180 149 148.927334 150 149.925580 151 150.926180 152 151.924714 153 152.925761 154 153.924422 155 154.925749 156 155.924278 157 156.925461 158 157.924405 159 158.925736 160 159.925194 161 160.926930 162 161.926795 163 162.928728 164 163.929171 165 164.931700 166 165.932803 167 166.935650 168 167.937230 169 168.940300 -67 0 164.930319 144 143.951640 146 145.944100 147 146.939840 148 147.937270 149 148.933790 150 149.933350 151 150.931681 152 151.931740 153 152.930195 154 153.930596 155 154.929079 156 155.929710 157 156.928190 158 157.928950 159 158.927709 160 159.928726 161 160.927852 162 161.929092 163 162.928730 164 163.930231 165 164.930319 166 165.932281 167 166.933126 168 167.935500 169 168.936868 170 169.939610 171 170.941460 172 171.944820 -68 0 165.930290 147 146.949310 148 147.944440 149 148.942170 150 149.937760 151 150.937460 152 151.935080 153 152.935093 154 153.932777 155 154.933200 156 155.931020 157 156.931950 158 157.929910 159 158.930681 160 159.929080 161 160.930001 162 161.928775 163 162.930029 164 163.929197 165 164.930723 166 165.930290 167 166.932045 168 167.932368 169 168.934588 170 169.935460 171 170.938026 172 171.939352 173 172.942400 174 173.944340 -69 0 168.934211 146 145.966500 147 146.961080 148 147.957550 149 148.952650 150 149.949670 151 150.945430 152 151.944300 153 152.942028 154 153.941420 155 154.939192 156 155.939010 157 156.936760 158 157.937000 159 158.934810 160 159.935090 161 160.933400 162 161.933970 163 162.932648 164 163.933451 165 164.932432 166 165.933553 167 166.932849 168 167.934170 169 168.934211 170 169.935798 171 170.936426 172 171.938396 173 172.939600 174 173.942160 175 174.943830 176 175.946990 -70 0 173.938858 151 150.955250 152 151.950170 153 152.949210 154 153.946240 155 154.945790 156 155.942850 157 156.942660 158 157.939858 159 158.940150 160 159.937560 161 160.937850 162 161.935750 163 162.936270 164 163.934520 165 164.935398 166 165.933880 167 166.934947 168 167.933894 169 168.935187 170 169.934759 171 170.936322 172 171.936377 173 172.938206 174 173.938858 175 174.941272 176 175.942568 177 176.945257 178 177.946643 179 178.950170 180 179.952330 -71 0 174.940767 150 149.972670 151 150.967150 152 151.963610 153 152.958690 154 153.957100 155 154.954230 156 155.952910 157 156.950102 158 157.949170 159 158.946620 160 159.946020 161 160.943540 162 161.943220 163 162.941200 164 163.941220 165 164.939610 166 165.939760 167 166.938310 168 167.938700 169 168.937649 170 169.938472 171 170.937910 172 171.939082 173 172.938927 174 173.940333 175 174.940767 176 175.942682 177 176.943755 178 177.945951 179 178.947324 180 179.949880 181 180.951970 182 181.955210 183 182.957570 -72 0 179.946548 154 153.964250 155 154.962760 156 155.959250 157 156.958130 158 157.954650 159 158.954000 160 159.950710 161 160.950330 162 161.947203 163 162.947060 164 163.944420 165 164.944540 166 165.942250 167 166.942600 168 167.940630 169 168.941160 170 169.939650 171 170.940490 172 171.939460 173 172.940650 174 173.940040 175 174.941503 176 175.941401 177 176.943220 178 177.943697 179 178.945815 180 179.946548 181 180.949099 182 181.950553 183 182.953530 184 183.955450 185 184.958780 -73 0 180.947996 156 155.971690 157 156.968150 158 157.966370 159 158.962910 160 159.961360 161 160.958370 162 161.957150 163 162.954320 164 163.953570 165 164.950820 166 165.950470 167 166.947970 168 167.947790 169 168.945920 170 169.946090 171 170.944460 172 171.944740 173 172.943540 174 173.944170 175 174.943650 176 175.944740 177 176.944472 178 177.945750 179 178.945934 180 179.947466 181 180.947996 182 181.950152 183 182.951373 184 183.954009 185 184.955559 186 185.958550 -74 0 183.950932 158 157.973940 159 158.972280 160 159.968370 161 160.967090 162 161.963340 163 162.962530 164 163.958980 165 164.958340 166 165.955020 167 166.954670 168 167.951860 169 168.951760 170 169.949290 171 170.949460 172 171.947420 173 172.947830 174 173.946160 175 174.946770 176 175.945590 177 176.946620 178 177.945850 179 178.947072 180 179.946706 181 180.948198 182 181.948206 183 182.950224 184 183.950932 185 184.953420 186 185.954362 187 186.957158 188 187.958487 189 188.961910 190 189.963180 -75 0 186.955750 160 159.981490 161 160.977660 162 161.975710 163 162.971970 164 163.970320 165 164.967050 166 165.965800 167 166.962560 168 167.961610 169 168.958830 170 169.958160 171 170.955550 172 171.955290 173 172.953060 174 173.953110 175 174.951390 176 175.951570 177 176.950270 178 177.950850 179 178.949980 180 179.950790 181 180.950065 182 181.951210 183 182.950821 184 183.952524 185 184.952955 186 185.954987 187 186.955750 188 187.958112 189 188.959228 190 189.961820 191 190.963124 192 191.965960 -76 0 191.961479 162 161.983820 163 162.982050 164 163.977930 165 164.976480 166 165.972530 167 166.971550 168 167.967830 169 168.967080 170 169.963570 171 170.963040 172 171.960080 173 172.959790 174 173.957120 175 174.957080 176 175.954950 177 176.955050 178 177.953350 179 178.953950 180 179.952350 181 180.953270 182 181.952186 183 182.953110 184 183.952491 185 184.954043 186 185.953838 187 186.955747 188 187.955836 189 188.958144 190 189.958445 191 190.960928 192 191.961479 193 192.964148 194 193.965179 195 194.968120 196 195.969620 -77 0 192.962924 166 165.985510 167 166.981540 168 167.979970 169 168.976390 170 169.975030 171 170.971780 172 171.970640 173 172.967710 174 173.966800 175 174.964280 176 175.963510 177 176.961170 178 177.961080 179 178.959150 180 179.959250 181 180.957640 182 181.958130 183 182.956810 184 183.957390 185 184.956590 186 185.957951 187 186.957361 188 187.958852 189 188.958716 190 189.960590 191 190.960591 192 191.962602 193 192.962924 194 193.965076 195 194.965977 196 195.968380 197 196.969636 198 197.972280 -78 0 194.964774 168 167.988040 169 168.986420 170 169.982330 171 170.981250 172 171.977380 173 172.976500 174 173.972811 175 174.972280 176 175.969000 177 176.968450 178 177.965710 179 178.965480 180 179.963220 181 180.963180 182 181.961270 183 182.961730 184 183.959900 185 184.960750 186 185.959430 187 186.960560 188 187.959396 189 188.960832 190 189.959930 191 190.961685 192 191.961035 193 192.962985 194 193.962664 195 194.964774 196 195.964935 197 196.967323 198 197.967876 199 198.970576 200 199.971424 201 200.974500 202 201.975740 -79 0 196.966552 172 171.990110 173 172.986400 174 173.984920 175 174.981550 176 175.980270 177 176.977220 178 177.975980 179 178.973410 180 179.972400 181 180.969950 182 181.969620 183 182.967620 184 183.967470 185 184.965810 186 185.966000 187 186.964560 188 187.965090 189 188.963890 190 189.964699 191 190.963650 192 191.964810 193 192.964132 194 193.965339 195 194.965018 196 195.966551 197 196.966552 198 197.968225 199 198.968748 200 199.970720 201 200.971641 202 201.973790 203 202.975137 204 203.977710 205 204.979610 -80 0 201.970626 175 174.991410 176 175.987410 177 176.986340 178 177.982476 179 178.981780 180 179.978320 181 180.977810 182 181.974750 183 182.974560 184 183.971900 185 184.971980 186 185.969460 187 186.969790 188 187.967560 189 188.968130 190 189.966280 191 190.967060 192 191.965570 193 192.966644 194 193.965382 195 194.966640 196 195.965815 197 196.967195 198 197.966752 199 198.968262 200 199.968309 201 200.970285 202 201.970626 203 202.972857 204 203.973476 205 204.976056 206 205.977499 207 206.982580 208 207.985940 -81 0 204.974412 179 178.991470 182 181.985610 183 182.982700 184 183.981760 185 184.979100 186 185.978550 187 186.976170 188 187.975920 189 188.973690 190 189.973790 191 190.971890 192 191.972140 193 192.970550 194 193.971050 195 194.969650 196 195.970520 197 196.969540 198 197.970470 199 198.969810 200 199.970945 201 200.970804 202 201.972091 203 202.972329 204 203.973849 205 204.974412 206 205.976095 207 206.977408 208 207.982005 209 208.985349 210 209.990066 -82 0 207.976636 182 181.992676 183 182.991930 184 183.988200 185 184.987580 186 185.984300 187 186.984030 188 187.981060 189 188.980880 190 189.978180 191 190.978200 192 191.975760 193 192.976080 194 193.973970 195 194.974470 196 195.972710 197 196.973380 198 197.971980 199 198.972910 200 199.971816 201 200.972850 202 201.972144 203 202.973375 204 203.973029 205 204.974467 206 205.974449 207 206.975881 208 207.976636 209 208.981075 210 209.984173 211 210.988731 212 211.991887 213 212.996500 214 213.999798 -83 0 208.980383 187 186.993460 188 187.992170 189 188.989510 190 189.988520 191 190.986050 192 191.985370 193 192.983060 194 193.982750 195 194.980750 196 195.980610 197 196.978930 198 197.979020 199 198.977580 200 199.978140 201 200.976970 202 201.977670 203 202.976868 204 203.977805 205 204.977375 206 205.978483 207 206.978455 208 207.979727 209 208.980383 210 209.984105 211 210.987258 212 211.991272 213 212.994375 214 213.998699 215 215.001830 216 216.006200 -84 0 208.982416 192 191.991520 193 192.991100 194 193.988280 195 194.988050 196 195.985510 197 196.985570 198 197.983340 199 198.983600 200 199.981740 201 200.982210 202 201.980700 203 202.981410 204 203.980307 205 204.981170 206 205.980465 207 206.981578 208 207.981231 209 208.982416 210 209.982857 211 210.986637 212 211.988852 213 212.992843 214 213.995186 215 214.999415 216 216.001905 217 217.006250 218 218.008965 -85 0 209.987131 196 195.995700 197 196.993290 198 197.992750 199 198.990630 200 199.990290 201 200.988490 202 201.988450 203 202.986850 204 203.987260 205 204.986040 206 205.986600 207 206.985776 208 207.986583 209 208.986159 210 209.987131 211 210.987481 212 211.990735 213 212.992921 214 213.996356 215 214.998641 216 216.002409 217 217.004710 218 218.008681 219 219.011300 220 220.015300 221 221.018140 222 222.022330 223 223.025340 -86 0 222.017570 198 197.998780 199 198.998310 200 199.995680 201 200.995540 202 201.993220 203 202.993320 204 203.991370 205 204.991670 206 205.990160 207 206.990730 208 207.989631 209 208.990380 210 209.989680 211 210.990585 212 211.990689 213 212.993868 214 213.995346 215 214.998729 216 216.000258 217 217.003915 218 218.005586 219 219.009475 220 220.011384 221 221.015460 222 222.017570 223 223.021790 224 224.024090 225 225.028440 226 226.030890 227 227.035410 228 228.038080 -87 0 223.019730 201 201.003990 202 202.003290 203 203.001050 204 204.000590 205 204.998660 206 205.998490 207 206.996860 208 207.997130 209 208.995920 210 209.996398 211 210.995529 212 211.996195 213 212.996175 214 213.998955 215 215.000326 216 216.003188 217 217.004616 218 218.007563 219 219.009241 220 220.012313 221 221.014246 222 222.017544 223 223.019730 224 224.023240 225 225.025607 226 226.029340 227 227.031830 228 228.035720 229 229.038430 230 230.042510 231 231.045410 232 232.049650 -88 0 226.025402 206 206.003780 207 207.003730 208 208.001780 209 209.001940 210 210.000450 211 211.000890 212 211.999783 213 213.000350 214 214.000091 215 215.002704 216 216.003518 217 217.006306 218 218.007124 219 219.010069 220 220.011015 221 221.013908 222 222.015362 223 223.018497 224 224.020202 225 225.023604 226 226.025402 227 227.029170 228 228.031064 229 229.034820 230 230.037080 231 231.041220 232 232.043690 233 233.048000 234 234.050550 -89 0 227.027747 207 207.012090 208 208.011490 209 209.009570 210 210.009260 211 211.007650 212 212.007810 213 213.006570 214 214.006890 215 215.006450 216 216.008721 217 217.009333 218 218.011630 219 219.012400 220 220.014750 221 221.015580 222 222.017829 223 223.019126 224 224.021708 225 225.023221 226 226.026090 227 227.027747 228 228.031014 229 229.032930 230 230.036030 231 231.038550 232 232.042020 233 233.044550 234 234.048420 -90 0 232.038050 212 212.012920 213 213.012960 214 214.011450 215 215.011730 216 216.011051 217 217.013070 218 218.013268 219 219.015520 220 220.015733 221 221.018171 222 222.018454 223 223.020795 224 224.021459 225 225.023941 226 226.024891 227 227.027699 228 228.028731 229 229.031755 230 230.033126 231 231.036297 232 232.038050 233 233.041576 234 234.043595 235 235.047500 236 236.049710 237 237.053890 -91 0 231.035878 215 215.019100 216 216.019110 217 217.018290 218 218.020010 219 219.019880 220 220.021880 221 221.021860 222 222.023730 223 223.023960 224 224.025610 225 225.026120 226 226.027933 227 227.028793 228 228.031037 229 229.032089 230 230.034533 231 231.035878 232 232.038582 233 233.040240 234 234.043302 235 235.045440 236 236.048680 237 237.051140 238 238.054500 -92 0 238.050782 218 218.023490 219 219.024920 220 220.024710 221 221.026350 222 222.026070 223 223.027720 224 224.027590 225 225.029380 226 226.029340 227 227.031140 228 228.031366 229 229.033496 230 230.033927 231 231.036289 232 232.037146 233 233.039628 234 234.040945 235 235.043923 236 236.045561 237 237.048724 238 238.050782 239 239.054287 240 240.056586 241 241.060330 242 242.062930 -93 0 237.048167 226 226.035130 227 227.034960 228 228.036180 229 229.036250 230 230.037810 231 231.038230 232 232.040100 233 233.040730 234 234.042889 235 235.044055 236 236.046560 237 237.048167 238 238.050940 239 239.052931 240 240.056169 241 241.058250 242 242.061640 -94 0 244.064198 228 228.038730 229 229.040140 230 230.039646 231 231.041260 232 232.041179 233 233.042990 234 234.043305 235 235.045282 236 236.046048 237 237.048403 238 238.049553 239 239.052156 240 240.053807 241 241.056845 242 242.058736 243 243.061997 244 244.064198 245 245.067739 246 246.070198 -95 0 243.061372 232 232.046590 234 234.047790 237 237.049970 238 238.051980 239 239.053018 240 240.055288 241 241.056822 242 242.059543 243 243.061372 244 244.064279 245 245.066445 246 246.069768 247 247.072090 -96 0 247.070347 236 236.051410 237 237.052890 238 238.053020 239 239.054950 240 240.055519 241 241.057646 242 242.058829 243 243.061382 244 244.062746 245 245.065485 246 246.067217 247 247.070347 248 248.072342 249 249.075947 250 250.078351 251 251.082278 -97 0 247.070299 238 238.058270 242 242.062050 243 243.063002 244 244.065168 245 245.066355 246 246.068670 247 247.070299 248 248.073080 249 249.074980 250 250.078311 251 251.080753 -98 0 251.079580 239 239.062580 240 240.062300 241 241.063720 242 242.063690 243 243.065420 244 244.065990 245 245.068040 246 246.068798 247 247.070992 248 248.072178 249 249.074847 250 250.076400 251 251.079580 252 252.081620 253 253.085127 254 254.087316 255 255.091040 -99 0 252.082970 243 243.069630 244 244.070970 245 245.071320 246 246.072970 247 247.073650 248 248.075460 249 249.076410 250 250.078650 251 251.079984 252 252.082970 253 253.084818 254 254.088016 255 255.090266 256 256.093590 -100 0 257.095099 242 242.073430 243 243.074510 244 244.074080 245 245.075380 246 246.075280 247 247.076820 248 248.077184 249 249.079020 250 250.079515 251 251.081566 252 252.082460 253 253.085176 254 254.086848 255 255.089955 256 256.091767 257 257.095099 258 258.097070 259 259.100590 -101 0 258.098425 247 247.081800 248 248.082910 249 249.083000 250 250.084490 251 251.084920 252 252.086630 253 253.087280 254 254.089730 255 255.091075 256 256.094050 257 257.095535 258 258.098425 259 259.100500 260 260.103650 -102 0 259.101020 250 250.087490 251 251.088960 252 252.088966 253 253.090650 254 254.090949 255 255.093232 256 256.094276 257 257.096850 258 258.098200 259 259.101020 262 262.107520 -103 0 262.109690 253 253.095260 254 254.096590 255 255.096770 256 256.098760 257 257.099610 258 258.101880 259 259.102990 260 260.105570 261 261.106940 262 262.109690 -104 0 261.108750 253 253.100680 254 254.100170 255 255.101490 256 256.101180 257 257.103070 258 258.103570 259 259.105630 260 260.106430 261 261.108750 262 262.109920 263 263.112540 -105 0 262.114150 255 255.107400 257 257.107860 258 258.109440 259 259.109720 260 260.111430 261 261.112110 262 262.114150 263 263.115080 -106 0 263.118310 259 259.114650 260 260.114440 261 261.116200 263 263.118310 265 265.121070 266 266.121930 -107 0 264.124730 261 261.121800 262 262.123010 264 264.124730 -108 0 265.130000 263 263.128710 264 264.128410 265 265.130000 -109 0 268.138820 266 266.137940 268 268.138820 diff --git a/java/joelib2/data/plain/isotope.txt b/java/joelib2/data/plain/isotope.txt deleted file mode 100644 index 8310b4d..0000000 --- a/java/joelib2/data/plain/isotope.txt +++ /dev/null @@ -1,151 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright OpenBabel: Geoffrey R. Hutchison -# 2002,2003 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -# -# This file has a series of lines, one for each element -# (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.) -# Each line: Atomic #, 0 then exact mass of most abundant isotope -# then a list of isotopes as int, float pairs corresponding to masses -# -# CAUTION: Masses have been zero-padded to 9 decimal places -# (we don't currently have a math package that can deal with sig. fig.) -# so trailing zeros may not be significant and/or useful -# -# Values are compiled from "The 1995 update to the atomic mass evaluation" -# by G.Audi and A.H.Wapstra -# Nuclear Physics A595 vol. 4 p.409-480, December 25, 1995. -# as made available in the mass_rmd.mas95 file -# -# Currently: 110 lines (neutron, H to Mt) -# -######################################################################## -0 0 0.000000000 1 1.008664915 -1 0 1.007825032 1 1.007825032 2 2.014101778 3 3.016049268 4 4.027830000 5 5.039540000 6 6.044940000 -2 0 4.002603250 3 3.016029310 4 4.002603250 5 5.012220000 6 6.018888100 7 7.028030000 8 8.033922000 9 9.043820000 10 10.052400000 -3 0 7.016004000 4 4.027180000 5 5.012540000 6 6.015122300 7 7.016004000 8 8.022486700 9 9.026789100 10 10.035481000 11 11.043796000 12 12.053780000 -4 0 9.012182100 5 5.040790000 6 6.019726000 7 7.016929200 8 8.005305090 9 9.012182100 10 10.013533700 11 11.021658000 12 12.026921000 13 13.036130000 14 14.042820000 -5 0 11.009305500 7 7.029920000 8 8.024606700 9 9.013328800 10 10.012937000 11 11.009305500 12 12.014352100 13 13.017780300 14 14.025404000 15 15.031097000 16 16.039810000 17 17.046930000 18 18.056170000 19 19.063730000 -6 0 12.000000000 8 8.037675000 9 9.031040100 10 10.016853100 11 11.011433800 12 12.000000000 13 13.003354838 14 14.003241988 15 15.010599300 16 16.014701000 17 17.022584000 18 18.026760000 19 19.035250000 20 20.040320000 21 21.049340000 22 22.056450000 -7 0 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212.996175000 214 213.998955000 215 215.000326000 216 216.003188000 217 217.004616000 218 218.007563000 219 219.009241000 220 220.012313000 221 221.014246000 222 222.017544000 223 223.019730700 224 224.023240000 225 225.025607000 226 226.029340000 227 227.031830000 228 228.035720000 229 229.038430000 230 230.042510000 231 231.045410000 232 232.049650000 -88 0 226.025402600 203 203.009210000 204 204.006480000 205 205.006190000 206 206.003780000 207 207.003730000 208 208.001780000 209 209.001940000 210 210.000450000 211 211.000890000 212 211.999783000 213 213.000350000 214 214.000091000 215 215.002704000 216 216.003518000 217 217.006306000 218 218.007124000 219 219.010069000 220 220.011015000 221 221.013908000 222 222.015362000 223 223.018497000 224 224.020202000 225 225.023604000 226 226.025402600 227 227.029170700 228 228.031064100 229 229.034820000 230 230.037080000 231 231.041220000 232 232.043690000 233 233.048000000 234 234.050550000 -89 0 227.027747000 207 207.012090000 208 208.011490000 209 209.009570000 210 210.009260000 211 211.007650000 212 212.007810000 213 213.006570000 214 214.006890000 215 215.006450000 216 216.008721000 217 217.009333000 218 218.011630000 219 219.012400000 220 220.014750000 221 221.015580000 222 222.017829000 223 223.019126000 224 224.021708000 225 225.023221000 226 226.026090000 227 227.027747000 228 228.031014800 229 229.032930000 230 230.036030000 231 231.038550000 232 232.042020000 233 233.044550000 234 234.048420000 235 235.051100000 236 236.055180000 -90 0 232.038050400 210 210.015030000 211 211.014860000 212 212.012920000 213 213.012960000 214 214.011450000 215 215.011730000 216 216.011051000 217 217.013070000 218 218.013268000 219 219.015520000 220 220.015733000 221 221.018171000 222 222.018454000 223 223.020795000 224 224.021459000 225 225.023941000 226 226.024891000 227 227.027699000 228 228.028731300 229 229.031755000 230 230.033126600 231 231.036297100 232 232.038050400 233 233.041576900 234 234.043595000 235 235.047500000 236 236.049710000 237 237.053890000 238 238.056240000 -91 0 231.035878900 213 213.021180000 214 214.020740000 215 215.019100000 216 216.019110000 217 217.018290000 218 218.020010000 219 219.019880000 220 220.021880000 221 221.021860000 222 222.023730000 223 223.023960000 224 224.025610000 225 225.026120000 226 226.027933000 227 227.028793000 228 228.031037000 229 229.032089000 230 230.034533000 231 231.035878900 232 232.038582000 233 233.040240200 234 234.043302000 235 235.045440000 236 236.048680000 237 237.051140000 238 238.054500000 239 239.057130000 240 240.060980000 -92 0 238.050782600 218 218.023490000 219 219.024920000 220 220.024710000 221 221.026350000 222 222.026070000 223 223.027720000 224 224.027590000 225 225.029380000 226 226.029340000 227 227.031140000 228 228.031366000 229 229.033496000 230 230.033927000 231 231.036289000 232 232.037146300 233 233.039628000 234 234.040945600 235 235.043923100 236 236.045561900 237 237.048724000 238 238.050782600 239 239.054287800 240 240.056586000 241 241.060330000 242 242.062930000 -93 0 237.048167300 225 225.033900000 226 226.035130000 227 227.034960000 228 228.036180000 229 229.036250000 230 230.037810000 231 231.038230000 232 232.040100000 233 233.040730000 234 234.042889000 235 235.044055900 236 236.046560000 237 237.048167300 238 238.050940500 239 239.052931400 240 240.056169000 241 241.058250000 242 242.061640000 243 243.064270000 244 244.067850000 -94 0 244.064198000 228 228.038730000 229 229.040140000 230 230.039646000 231 231.041260000 232 232.041179000 233 233.042990000 234 234.043305000 235 235.045282000 236 236.046048100 237 237.048403800 238 238.049553400 239 239.052156500 240 240.053807500 241 241.056845300 242 242.058736800 243 243.061997000 244 244.064198000 245 245.067739000 246 246.070198000 247 247.074070000 -95 0 243.061372700 231 231.045560000 232 232.046590000 233 233.046470000 234 234.047790000 235 235.048030000 236 236.049570000 237 237.049970000 238 238.051980000 239 239.053018000 240 240.055288000 241 241.056822900 242 242.059543000 243 243.061372700 244 244.064279400 245 245.066445000 246 246.069768000 247 247.072090000 248 248.075750000 249 249.078480000 -96 0 247.070347000 233 233.050800000 234 234.050240000 235 235.051590000 236 236.051410000 237 237.052890000 238 238.053020000 239 239.054950000 240 240.055519000 241 241.057646700 242 242.058829300 243 243.061382200 244 244.062746300 245 245.065485600 246 246.067217600 247 247.070347000 248 248.072342000 249 249.075947000 250 250.078351000 251 251.082278000 252 252.084870000 -97 0 247.070299000 235 235.056580000 236 236.057330000 237 237.057130000 238 238.058270000 239 239.058360000 240 240.059750000 241 241.060220000 242 242.062050000 243 243.063002000 244 244.065168000 245 245.066355400 246 246.068670000 247 247.070299000 248 248.073080000 249 249.074980000 250 250.078311000 251 251.080753000 252 252.084300000 253 253.086880000 254 254.090600000 -98 0 251.079580000 237 237.062070000 238 238.061410000 239 239.062580000 240 240.062300000 241 241.063720000 242 242.063690000 243 243.065420000 244 244.065990000 245 245.068040000 246 246.068798800 247 247.070992000 248 248.072178000 249 249.074847000 250 250.076400000 251 251.079580000 252 252.081620000 253 253.085127000 254 254.087316000 255 255.091040000 256 256.093440000 -99 0 252.082970000 240 240.068920000 241 241.068660000 242 242.069700000 243 243.069630000 244 244.070970000 245 245.071320000 246 246.072970000 247 247.073650000 248 248.075460000 249 249.076410000 250 250.078650000 251 251.079984000 252 252.082970000 253 253.084818000 254 254.088016000 255 255.090266000 256 256.093590000 257 257.095980000 -100 0 257.095099000 242 242.073430000 243 243.074510000 244 244.074080000 245 245.075380000 246 246.075280000 247 247.076820000 248 248.077184000 249 249.079020000 250 250.079515000 251 251.081566000 252 252.082460000 253 253.085176000 254 254.086848000 255 255.089955000 256 256.091767000 257 257.095099000 258 258.097070000 259 259.100590000 -101 0 258.098425000 245 245.081020000 246 246.081930000 247 247.081800000 248 248.082910000 249 249.083000000 250 250.084490000 251 251.084920000 252 252.086630000 253 253.087280000 254 254.089730000 255 255.091075000 256 256.094050000 257 257.095535000 258 258.098425000 259 259.100500000 260 260.103650000 -102 0 259.101020000 249 249.087820000 250 250.087490000 251 251.088960000 252 252.088966000 253 253.090650000 254 254.090949000 255 255.093232000 256 256.094276000 257 257.096850000 258 258.098200000 259 259.101020000 260 260.102640000 261 261.105740000 262 262.107520000 -103 0 262.109690000 251 251.094360000 252 252.095330000 253 253.095260000 254 254.096590000 255 255.096770000 256 256.098760000 257 257.099610000 258 258.101880000 259 259.102990000 260 260.105570000 261 261.106940000 262 262.109690000 263 263.111390000 -104 0 261.108750000 253 253.100680000 254 254.100170000 255 255.101490000 256 256.101180000 257 257.103070000 258 258.103570000 259 259.105630000 260 260.106430000 261 261.108750000 262 262.109920000 263 263.112540000 264 264.113980000 -105 0 262.114150000 255 255.107400000 256 256.108110000 257 257.107860000 258 258.109440000 259 259.109720000 260 260.111430000 261 261.112110000 262 262.114150000 263 263.115080000 264 264.117470000 265 265.118660000 -106 0 263.118310000 258 258.113150000 259 259.114650000 260 260.114440000 261 261.116200000 262 262.116480000 263 263.118310000 264 264.118920000 265 265.121070000 266 266.121930000 -107 0 264.124730000 260 260.121800000 261 261.121800000 262 262.123010000 263 263.123150000 264 264.124730000 265 265.125200000 266 266.127010000 267 267.127740000 -108 0 265.130000000 263 263.128710000 264 264.128410000 265 265.130000000 266 266.130040000 267 267.131770000 268 268.132160000 269 269.134110000 -109 0 268.138820000 265 265.136570000 266 266.137940000 267 267.137530000 268 268.138820000 269 269.139110000 270 270.140720000 271 271.141230000 diff --git a/java/joelib2/data/plain/knownResults.txt b/java/joelib2/data/plain/knownResults.txt deleted file mode 100644 index 33805fc..0000000 --- a/java/joelib2/data/plain/knownResults.txt +++ /dev/null @@ -1,775 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.5 $ -RELEASE_DATE: $Date: 2006/02/22 02:18:22 $ - -######################################################################### -# Here are the results stored which are known in JOELib. -# -# With the joelib2.feature.ResultFactory you can have a look at known -# results and the class which can parse this result type. -# -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -################################################################################# -$JOELIB_RESULT$ joelib2.feature.result.AtomDynamicResult -A_AROMATIC -A_CHARGECENTER -A_ENLP -A_ENPI -A_ENSIG -A_FORMCHARGE -A_FREEEL -A_HASH -A_HGROUP -A_ISMETAL -A_IUPAC_GROUP -A_LPSTAB -A_NEIGHBOR -A_NEL -A_NONHNEIGHBOR -A_PERIPH -A_PICENTER -A_PISYS -A_POLARIZABILITY -A_QPI -A_QSIG -A_QTOT -A_RADICCENTER -A_RINGSIZE -################################################################################# -#$JOELIB_RESULT$ joelib2.feature.result.BondDynamicResult -# -# now me must use the ASYM_BOND_PROPERTY_INDEX property -# to access this descriptor data correctly -# It's necessary to define a -# joelib2.feature.result.AsymBondDynamicResult class !!! -# the BondDynamicResult is DEPRECATED !!! -# -#B_BDE -#B_BOORD -#B_DENPI -#B_DENSIG -#B_DQPI -#B_DQSIG -#B_DQTOT -#B_NDELOC -#B_NSTAB -#B_PDELOC -#B_POLARIZABILITY -#B_PSTAB -#B_RINGSIZE -#B_SDELOC -#B_SQIT -#B_STABRS -#B_TBDE -################################################################################# -## When normalizing the data, the integers will be stored as double values AND -## can be also loaded as double values !!! -## -$JOELIB_RESULT$ joelib2.feature.result.IntResult -## -$REGEXP$ SMARTS_c_.* -Entry_Number -TRUE_CLASS -#activity_class -# -# PETRA descriptors -# -E_CHARGE -E_DELTAHF -E_HASH -E_POLARIZABILITY -E_RADICAL -E_STABIL -E_STRAIN -M_CHARGE -M_DELTAHF -M_HASH -M_HGROUP -M_NAME -M_POLARIZABILITY -M_RADICAL -M_STABIL -M_STRAIN -# -# Molconn Z 350 -# -id -nvx -nrings -ncirc -nelem -#aname -$REGEXP$ nas\p{Upper}\p{Lower}* -$REGEXP$ nd\d -$REGEXP$ ne\d+ -tg -tg3 -tm -tm3 -$REGEXP$ n\dpe\d+ -$REGEXP$ ec\d+ -$REGEXP$ NHBint\d+ -$REGEXP$ count\d -# -# MOE descriptors -# -a_acc -a_acid -a_base -a_don -a_hyd -a_aro -a_count -a_nH -a_heavy -a_nB -a_nBr -a_nC -a_nCl -a_nF -a_nI -a_nN -a_nO -a_nP -a_nS -b_heavy -b_1rotN -b_ar -b_count -b_double -b_rotN -b_single -b_triple -################################################################################# -$JOELIB_RESULT$ joelib2.feature.result.APropDoubleArrResult -Auto_correlation -$REGEXP$ .*Burden_modified_eigenvalues:[^:]+ -$REGEXP$ .*Auto_correlation:[^:]+ -$REGEXP$ .*RDF:[^:]+ -$REGEXP$ .*BurdenModifiedEigenvalues:[^:]+ -$REGEXP$ .*Autocorrelation:[^:]+ -$REGEXP$ .*RadialDistributionFunction:[^:]+ -################################################################################# -$JOELIB_RESULT$ joelib2.feature.result.APropDoubleResult -$REGEXP$ NONE:s\d+:.*:F\d+:\d+ -$REGEXP$ APkPCA:s\d+:.*:F\d+:\d+ -$REGEXP$ APskPCA:s\d+:.*:F\d+:\d+ -$REGEXP$ APPCA:s\d+:.*:F\d+:\d+ -$REGEXP$ :*Global_topological_charge_index:.+ -#$REGEXP$ .*Burden_modified_eigenvalues:.+:\d+ -################################################################################# -$JOELIB_RESULT$ joelib2.feature.result.DoubleResult -## -TRUE -### -LOGBB -IC50 -activity_class -hia_measured -logS_expected -residue_huuskonen -XlogP -Number_of_HBA_2 -predicted_logP -pIC50 -Moriguchi_logP -Rekker_logP -Hansch_Leo_logP -Suzuki_Kudo_logP -####Achim's sensors -$REGEXP$ S1_W\d+.* -$REGEXP$ S2_W\d+.* -$REGEXP$ S3_W\d+.* -$REGEXP$ S1_STD\d+.* -$REGEXP$ S2_STD\d+.* -$REGEXP$ S3_STD\d+.* -#melting_point:::contains also 'liq' entries ! -#melting_point -# pca, kpca extracted eigenvalue projection and inner product features -$REGEXP$ feature\d+ -# -# Molconn Z 350 -# -$REGEXP$ SHBint\d+ -Qv -SHCsats -SHCsatu -SHvin -SHtvin -SHavin -SHarom -SHHBD -SHWHBD -SHHBA -petitjeanSC -fw -x0 -x1 -x2 -xp3 -xp4 -xp5 -xp6 -xp7 -xp8 -xp9 -xp10 -xv0 -xv1 -xv2 -xvp3 -xvp4 -xvp5 -xvp6 -xvp7 -xvp8 -xvp9 -xvp10 -xc3 -xc4 -xpc4 -xch3 -xch4 -xch5 -xch6 -xch7 -xch8 -xch9 -xch10 -xvc3 -xvc4 -xvpc4 -xvch3 -xvch4 -xvch5 -xvch6 -xvch7 -xvch8 -xvch9 -xvch10 -dx0 -dx1 -dx2 -dxp3 -dxp4 -dxp5 -dxp6 -dxp7 -dxp8 -dxp9 -dxp10 -dxv0 -dxv1 -dxv2 -dxvp3 -dxvp4 -dxvp5 -dxvp6 -dxvp7 -dxvp8 -dxvp9 -dxvp10 -k0 -k1 -k2 -k3 -ka1 -ka2 -ka3 -si -totop -sumI -sumDELI -tets2 -phia -$REGEXP$ s\d+ -SHsOH -SHdNH -SHsSH -SHsNH2 -SHssNH -SHtCH -SHother -SHCHnX -Hmax -Gmax -Hmin -Gmin -Hmaxpos -Hminneg -SsLi -SssBe -SssssBem -SssBH -SsssB -SssssBm -SsCH3 -SdCH2 -SssCH2 -StCH -SdsCH -SaaCH -SsssCH -SddC -StsC -SdssC -SaasC -SaaaC -SssssC -SsNH3p -SsNH2 -SssNH2p -SdNH -SssNH -SaaNH -StN -SsssNHp -SdsN -SaaN -SsssN -SddsN -SaasN -SssssNp -SsOH -SdO -SssO -SaaO -SsF -SsSiH3 -SssSiH2 -SsssSiH -SssssSi -SsPH2 -SssPH -SsssP -SdsssP -SsssssP -SsSH -SdS -SssS -SaaS -SdssS -SddssS -SssssssS -SsCl -SsGeH3 -SssGeH2 -SsssGeH -SssssGe -SsAsH2 -SssAsH -SsssAs -SdsssAs -SsssssAs -SsSeH -SdSe -SssSe -SaaSe -SdssSe -SddssSe -SsBr -SsSnH3 -SssSnH2 -SsssSnH -SssssSn -SsI -SsPbH3 -SssPbH2 -SsssPbH -SssssPb -CHsOH -CHdNH -CHsSH -CHsNH2 -CHssNH -CHtCH -CHother -CHCHnX -CHmax -CGmax -CHmin -CGmin -CHmaxpos -CHminneg -CsLi -CssBe -CssssBe -CssBH -CsssB -CssssB -CsCH3 -CdCH2 -CssCH2 -CtCH -CdsCH -CaaCH -CsssCH -CddC -CtsC -CdssC -CaasC -CaaaC -CssssC -CsNH3 -CsNH2 -CssNH2 -CdNH -CssNH -CaaNH -CtN -CsssNH -CdsN -CaaN -CsssN -CddsN -CaasN -CssssNp -CsOH -CdO -CssO -CaaO -CsF -CsSiH3 -CssSiH2 -CsssSiH -CssssSi -CsPH2 -CssPH -CsssP -CdsssP -CsssssP -CsSH -CdS -CssS -CaaS -CdssS -CddssS -CssssssS -CsCl -CsGeH3 -CssGeH2 -CsssGeH -CssssGe -CsAsH2 -CssAsH -CsssAs -CdsssAs -CsssssAs -CsSeH -CdSe -CssSe -CaaSe -CdssSe -CddssSe -CsBr -CsSnH3 -CssSnH2 -CsssSnH -CssssSn -CsI -CsPbH3 -CssPbH2 -CsssPbH -CssssPb -$REGEXP$ Hs\d+ -idw -idwbar -idc -idcbar -W -Wp -pf -Wt -knotp -knotpv -nclass -numHBd -numwHBd -numHBa -$REGEXP$ nxp\d+ -nxc3 -nxc4 -nxpc4 -$REGEXP$ nxch\d+ -ntpath -diam -muldiam -rad -mulrad -ishape -# -# MOE descriptors -# -a_IC -a_ICM -b_rotR -b_1rotR -diameter -petitjean -radius -VDistEq -VDistMa -weinerPath -weinerPol -chi0v -chi0v_C -chi1v -chi1v_C -reactive -Weight -chi0 -chi0_C -chi1 -chi1_C -FCharge -VAdjEq -VAdjMa -zagreb -balabanJ -PEOE_PC+ -PEOE_PC- -PEOE_RPC+ -PEOE_RPC- -$REGEXP$ PEOE_VSA[-+]\d -PEOE_VSA_FHYD -PEOE_VSA_FNEG -PEOE_VSA_FPNEG -PEOE_VSA_FPOL -PEOE_VSA_FPOS -PEOE_VSA_FPPOS -PEOE_VSA_HYD -PEOE_VSA_NEG -PEOE_VSA_PNEG -PEOE_VSA_POL -PEOE_VSA_POS -PEOE_VSA_PPOS -PC+ -PC- -Q_PC+ -Q_PC- -Q_RPC+ -Q_RPC- -Q_VSA_FHYD -Q_VSA_FNEG -Q_VSA_FPNEG -Q_VSA_FPOL -Q_VSA_FPOS -Q_VSA_FPPOS -Q_VSA_HYD -Q_VSA_NEG -Q_VSA_PNEG -Q_VSA_POL -Q_VSA_POS -Q_VSA_PPOS -RPC+ -RPC- -E -E_ang -E_ele -E_nb -E_oop -E_sol -E_stb -E_str -E_strain -E_tor -E_vdw -E_rele -E_rnb -E_rsol -E_rvdw -Kier1 -Kier2 -Kier3 -KierA1 -KierA2 -KierA3 -KierFlex -apol -bpol -mr -dipole -dipoleX -dipoleY -dipoleZ -pmi -pmiX -pmiY -pmiZ -rgyr -vsa_acc -vsa_acid -vsa_base -vsa_don -vsa_hyd -vsa_other -vsa_pol -SlogP -$REGEXP$ SlogP_VSA\d+ -SMR -$REGEXP$ SMR_VSA\d+ -ASA -ASA+ -ASA- -ASA_H -ASA_P -CASA+ -CASA- -DASA -DCASA -FASA+ -FASA- -FASA_H -FASA_P -FCASA+ -FCASA- -VSA -TPSA -density -vdw_area -vdw_vol -dens -glob -std_dim1 -std_dim2 -std_dim3 -vol -logP(o/w) -# -# Human Intestinal Absorption (HIA) -# -connolly_surface_polar -connolly_surf_hydrophob -rotatable_bonds -hydrogen_donors -eccentricity -std_dim1 -hia_measured -molecular_weight -connolly_surf_pol_percent -logP -hydrogen_acceptors -dipol -# -# JOELib resolved atom property transformation descriptors -# -$REGEXP$ Global_topological_charge_index_\d+ -$REGEXP$ .*Auto_correlation:.+:\d+ -$REGEXP$ .*Atom_mass:\d+ -$REGEXP$ [^:]+Atom_valence:\d+ -$REGEXP$ .*Atom_valence:\d+ -$REGEXP$ .*Atom_van_der_waals_volume:\d+ -$REGEXP$ .*Atom_in_conjugated_environment:\d+ -$REGEXP$ .*Burden_modified_eigenvalues:.+:\d+ -$REGEXP$ .*Conjugated_electrotopological_state_index:\d+ -$REGEXP$ .*Conjugated_topological_distance:\d+ -$REGEXP$ .*Electronegativity_pauling:\d+ -$REGEXP$ .*Electrotopological_state_index:\d+ -$REGEXP$ .*Electrogeometrical_state_index:\d+ -$REGEXP$ .*Electron_affinity:\d+ -$REGEXP$ .*Gasteiger_Marsili:\d+ -$REGEXP$ .*Graph_potentials:\d+ -$REGEXP$ .*Intrinsic_state:\d+ -$REGEXP$ .*Atom_is_negative:\d+ -$REGEXP$ .*Atom_in_acceptor:\d+ -$REGEXP$ .*Atom_in_donor_or_acceptor:\d+ -$REGEXP$ .*Atom_in_donor:\d+ -$REGEXP$ .*Atom_in_ring:\d+ -$REGEXP$ .*Atom_is_positive:\d+ -$REGEXP$ .*Atom_in_terminal_carbon:\d+ -$REGEXP$ .*AtomENAllredRochow:\d+ -$REGEXP$ .*AtomENPauling:\d+ -$REGEXP$ .*AtomElectronAffinity:\d+ -$REGEXP$ .*AtomExplicitHydrogenCount:\d+ -$REGEXP$ .*AtomFreeElectronsCount:\d+ -$REGEXP$ .*AtomFreeOxygenCount:\d+ -$REGEXP$ .*AtomHeavyValence:\d+ -$REGEXP$ .*AtomHeteroValence:\d+ -$REGEXP$ .*AtomImplicitHydrogenCount:\d+ -$REGEXP$ .*AtomImplicitValence:\d+ -$REGEXP$ .*AtomInAcceptor:\d+ -$REGEXP$ .*AtomInAromaticSystem:\d+ -$REGEXP$ .*AtomInConjEnvironment:\d+ -$REGEXP$ .*AtomInDonor:\d+ -$REGEXP$ .*AtomInTerminalCarbon:\d+ -$REGEXP$ .*AtomIsAmideNitrogen:\d+ -$REGEXP$ .*AtomIsAmideNitrogen:\d+ -$REGEXP$ .*AtomIsAromaticNOxide:\d+ -$REGEXP$ .*AtomIsAxial:\d+ -$REGEXP$ .*AtomIsCarbon:\d+ -$REGEXP$ .*AtomIsCarboxylOxygen:\d+ -$REGEXP$ .*AtomIsChiral:\d+ -$REGEXP$ .*AtomIsClockwise:\d+ -$REGEXP$ .*AtomIsClockwise:\d+ -$REGEXP$ .*AtomIsElectronegative:\d+ -$REGEXP$ .*AtomIsHalogen:\d+ -$REGEXP$ .*AtomIsHeteroatom:\d+ -$REGEXP$ .*AtomIsNegative:\d+ -$REGEXP$ .*AtomIsNitrogen:\d+ -$REGEXP$ .*AtomIsNonPolarHydrogen:\d+ -$REGEXP$ .*AtomIsOxygen:\d+ -$REGEXP$ .*AtomIsPhosphateOxygen:\d+ -$REGEXP$ .*AtomIsPhosphorus:\d+ -$REGEXP$ .*AtomIsPolarHydrogen:\d+ -$REGEXP$ .*AtomIsPositive:\d+ -$REGEXP$ .*AtomIsUnsaturated:\d+ -$REGEXP$ .*AtomIsUnsaturated:\d+ -$REGEXP$ .*AtomKekuleBondOrderSum:\d+ -$REGEXP$ .*AtomMass:\d+ -$REGEXP$ .*AtomVanDerWaalsVolume:\d+ -$REGEXP$ .*CharacteristicPolynomialCoefficients:\d+ -$REGEXP$ .*ConjElectroTopolState:\d+ -$REGEXP$ .*ElectrotopologicalState:\d+ -$REGEXP$ .*GraphPotentials:\d+ -$REGEXP$ .*IntrinsicState:\d+ -$REGEXP$ .*AtomIsAlphaBetaUnsaturated:\d+ -$REGEXP$ .*AtomIsSulfateOxygen:\d+ -$REGEXP$ .*AtomInDonAcc:\d+ -$REGEXP$ .*ConjugatedTopologicalDistance:\d+ -$REGEXP$ .*AtomBondOrderSum:\d+ -$REGEXP$ .*ElectrogeometricalState:\d+ -$REGEXP$ .*AtomIsSulfur:\d+ -$REGEXP$ .*AtomPartialCharge:\d+ -$REGEXP$ .*AtomIsHydrogen:\d+ -$REGEXP$ .*AtomValence:\d+ -$REGEXP$ .*AtomHybridisation:\d+ -$REGEXP$ .*AtomIsNitroOxygen:\d+ -$REGEXP$ .*AtomIsAntiClockwise:\d+ -$REGEXP$ .*AtomInRingsCount:\d+ -$REGEXP$ .*AtomENSanderson:\d+ -$REGEXP$ .*AtomInRing:\d+ -$REGEXP$ .*CharacteristicPolynomial:\d+ -$REGEXP$ .*AtomValenceSum:\d+ -################################################################################# -$JOELIB_RESULT$ joelib2.feature.result.BooleanResult -$REGEXP$ SMARTS_b_.* -$REGEXP$ SMARTS_MACCS_.* -$REGEXP$ SMARTS_SSKey_.* -################################################################################# -# -# MOE special descriptors -# -$JOELIB_RESULT$ joelib2.feature.result.IntBitArrayResult -FP:MACCS -################################################################################# -$JOELIB_RESULT$ joelib2.feature.result.BitArrayResult -dy_fp -################################################################################# -################################################################################# diff --git a/java/joelib2/data/plain/molconnz350.txt b/java/joelib2/data/plain/molconnz350.txt deleted file mode 100644 index 1118ef7..0000000 --- a/java/joelib2/data/plain/molconnz350.txt +++ /dev/null @@ -1,67 +0,0 @@ -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## -id nvx nrings ncirc nelem fw aname -x0 x1 x2 xp3 xp4 xp5 xp6 xp7 xp8 xp9 xp10 -xv0 xv1 xv2 xvp3 xvp4 xvp5 xvp6 xvp7 xvp8 xvp9 xvp10 -xc3 xc4 xpc4 xch3 xch4 xch5 xch6 xch7 xch8 xch9 xch10 -xvc3 xvc4 xvpc4 xvch3 xvch4 xvch5 xvch6 xvch7 xvch8 xvch9 xvch10 -dx0 dx1 dx2 dxp3 dxp4 dxp5 dxp6 dxp7 dxp8 dxp9 dxp10 -dxv0 dxv1 dxv2 dxvp3 dxvp4 dxvp5 dxvp6 dxvp7 dxvp8 dxvp9 dxvp10 -k0 k1 k2 k3 ka1 ka2 ka3 si totop sumI sumDELI tets2 phia -s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 -s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30 -s31 s32 s33 s34 s35 s36 s37 s38 s39 s40 s41 s42 s43 s44 s45 -s46 s47 s48 s49 s50 s51 s52 s53 s54 s55 s56 s57 s58 s59 s60 -s61 s62 s63 s64 s65 s66 s67 s68 s69 s70 s71 s72 s73 s74 s75 -s76 s77 s78 s79 s80 s81 s82 s83 s84 s85 s86 s87 s88 s89 s90 -SHsOH SHdNH SHsSH SHsNH2 SHssNH SHtCH SHother SHCHnX Hmax Gmax Hmin Gmin Hmaxpos Hminneg -SsLi SssBe SssssBem SssBH SsssB SssssBm SsCH3 SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC -StsC SdssC SaasC SaaaC SssssC SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN -SaaN SsssN SddsN SaasN SssssNp SsOH SdO SssO SaaO SsF SsSiH3 SssSiH2 SsssSiH SssssSi -SsPH2 SssPH SsssP SdsssP SsssssP SsSH SdS SssS SaaS SdssS SddssS SssssssS SsCl SsGeH3 -SssGeH2 SsssGeH SssssGe SsAsH2 SssAsH SsssAs SdsssAs SsssssAs SsSeH SdSe SssSe SaaSe SdssSe SddssSe -SsBr SsSnH3 SssSnH2 SsssSnH SssssSn SsI SsPbH3 SssPbH2 SsssPbH SssssPb -CHsOH CHdNH CHsSH CHsNH2 CHssNH CHtCH CHother CHCHnX CHmax CGmax CHmin CGmin CHmaxpos CHminneg -CsLi CssBe CssssBe CssBH CsssB CssssB CsCH3 CdCH2 CssCH2 CtCH CdsCH CaaCH CsssCH CddC -CtsC CdssC CaasC CaaaC CssssC CsNH3 CsNH2 CssNH2 CdNH CssNH CaaNH CtN CsssNH CdsN -CaaN CsssN CddsN CaasN CssssNp CsOH CdO CssO CaaO CsF CsSiH3 CssSiH2 CsssSiH CssssSi -CsPH2 CssPH CsssP CdsssP CsssssP CsSH CdS CssS CaaS CdssS CddssS CssssssS CsCl CsGeH3 -CssGeH2 CsssGeH CssssGe CsAsH2 CssAsH CsssAs CdsssAs CsssssAs CsSeH CdSe CssSe CaaSe CdssSe CddssSe -CsBr CsSnH3 CssSnH2 CsssSnH CssssSn CsI CsPbH3 CssPbH2 CsssPbH CssssPb -Hs1 Hs2 Hs3 Hs4 Hs5 Hs6 Hs7 Hs8 Hs9 Hs10 Hs11 Hs12 Hs13 Hs14 Hs15 -Hs16 Hs17 Hs18 Hs19 Hs20 Hs21 Hs22 Hs23 Hs24 Hs25 Hs26 Hs27 Hs28 Hs29 Hs30 -Hs31 Hs32 Hs33 Hs34 Hs35 Hs36 Hs37 Hs38 Hs39 Hs40 Hs41 Hs42 Hs43 Hs44 Hs45 -Hs46 Hs47 Hs48 Hs49 Hs50 Hs51 Hs52 Hs53 Hs54 Hs55 Hs56 Hs57 Hs58 Hs59 Hs60 -Hs61 Hs62 Hs63 Hs64 Hs65 Hs66 Hs67 Hs68 Hs69 Hs70 Hs71 Hs72 Hs73 Hs74 Hs75 -Hs76 Hs77 Hs78 Hs79 Hs80 Hs81 Hs82 Hs83 Hs84 Hs85 Hs86 Hs87 Hs88 Hs89 Hs90 -idw idwbar idc idcbar W Wp pf Wt knotp knotpv nclass numHBd numwHBd numHBa -nxp1 nxp2 nxp3 nxp4 nxp5 nxp6 nxp7 nxp8 nxp9 nxp10 nxc3 nxc4 nxpc4 nxch3 nxch4 nxch5 nxch6 nxch7 nxch8 nxch9 nxch10 ntpath diam muldiam rad mulrad ishape -nasH nasHe nasLi nasBe nasB nasC nasN nasO nasF nasNe nasNa nasMg nasAl nasSi nasP nasS nasCl nasAr nasK nasCa nasSc nasTi nasV nasCr nasMn nasFe nasCo nasNi nasCu nasZn -nasGa nasGe nasAs nasSe nasBr nasKr nasRb nasSr nasY nasZr nasNb nasMo nasTc nasRu nasRh nasPd nasAg nasCd nasIn nasSn nasSb nasTe nasI nasXe nasCs nasBa nasLa nasHf nasTa nasW -nasRe nasOs nasIr nasPt nasAu nasHg nasTl nasPb nasBi nasPo nasAt nasRn -nd1 nd2 nd3 nd4 nd5 nd6 ne11 ne12 ne13 ne14 ne15 ne16 ne22 ne23 ne24 ne25 ne26 ne33 ne34 ne35 ne36 ne44 ne45 ne46 ne55 ne56 ne66 tg tg3 tm tm3 -n2pe11 n2pe12 n2pe13 n2pe14 n2pe15 n2pe16 n2pe22 n2pe23 n2pe24 n2pe25 n2pe26 n2pe33 n2pe34 n2pe35 n2pe36 n2pe44 n2pe45 n2pe46 n2pe55 n2pe56 n2pe66 -n3pe11 n3pe12 n3pe13 n3pe14 n3pe15 n3pe16 n3pe22 n3pe23 n3pe24 n3pe25 n3pe26 n3pe33 n3pe34 n3pe35 n3pe36 n3pe44 n3pe45 n3pe46 n3pe55 n3pe56 n3pe66 -n4pe11 n4pe12 n4pe13 n4pe14 n4pe15 n4pe16 n4pe22 n4pe23 n4pe24 n4pe25 n4pe26 n4pe33 n4pe34 n4pe35 n4pe36 n4pe44 n4pe45 n4pe46 n4pe55 n4pe56 n4pe66 -ec1 ec2 ec3 ec4 ec5 ec6 ec7 ec8 ec9 ec10 ec11 ec12 ec13 ec14 ec15 ec16 ec17 ec18 ec19 ec20 ec21 ec22 ec23 ec24 ec25 ec26 ec27 ec28 ec29 ec30 -ec31 ec32 ec33 ec34 ec35 ec36 ec37 ec38 ec39 ec40 ec41 ec42 ec43 ec44 ec45 ec46 ec47 ec48 ec49 ec50 ec51 ec52 ec53 ec54 ec55 ec56 ec57 ec58 ec59 ec60 -ec61 ec62 ec63 ec64 ec65 ec66 ec67 ec68 ec69 ec70 ec71 ec72 ec73 ec74 ec75 ec76 ec77 ec78 ec79 ec80 ec81 ec82 ec83 ec84 ec85 ec86 ec87 ec88 ec89 ec90 -SHCsats SHCsatu SHvin SHtvin SHavin SHarom SHHBD SHWHBD SHHBA Qv -NHBint2 NHBint3 NHBint4 NHBint5 NHBint6 NHBint7 NHBint8 NHBint9 NHBint10 SHBint2 SHBint3 SHBint4 SHBint5 SHBint6 SHBint7 SHBint8 SHBint9 SHBint10 -elem1 elem2 elem3 elem4 elem5 elem6 elem7 elem8 -count1 count2 count3 count4 count5 count6 count7 count8 diff --git a/java/joelib2/data/plain/phmodel.txt b/java/joelib2/data/plain/phmodel.txt deleted file mode 100644 index 5ae19fa..0000000 --- a/java/joelib2/data/plain/phmodel.txt +++ /dev/null @@ -1,127 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.3 $ -RELEASE_DATE: $Date: 2005/01/28 13:49:11 $ - -########################################################################## -# -# TRANSFORM: chemical transforms can be used to modify formal charges, bond -# orders, and to delete atoms (i.e hydrogens). Changes are applied -# to vector bound atoms (use the [:#] SMARTS notation) and bonds -# between vector bound atoms. -# SEEDCHARGE: used to seed partial charges. Seed partial charges -# are used as initial values in Gasteiger-Marsili charge calculation -# -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -#carboxylic acid -TRANSFORM O=CO[#1:1] >> O=CO -TRANSFORM O=C[OQ1-0:1] >> O=C[O-:1] - -#charged amine -TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] - -#imidazole: note pKa=7.0, histidine pKa=6.0 -#if you uncomment this, also uncomment the seedcharge statement below -#TRANSFORM [nQ2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 - -#imine -TRANSFORM [NQ3+0:1]=[#6] >> [NQ3+:1]=[#6] - -#tetrazole -TRANSFORM [nQ2:1]([#1:2])1[nQ2-0][nQ2-0][nQ2-0]c1 >> [n-:1]1nnnc1 -TRANSFORM [nQ2-0]1[nQ2:1]([#1:2])[nQ2-0][nQ2-0]c1 >> n1[n-:1]nnc1 -TRANSFORM [nQ2-0:1]1[nQ2-0][nQ2-0][nQ2-0]c1 >> [n-:1]1nnnc1 - -#azide -TRANSFORM [NQ2:1]=[NQ2:2]=A >> [N:1]=[N+:2]=A -TRANSFORM [NQ1:1]=[NQ2:2]=A >> [N-:1]=[N+:2]=A - -#hydroxamic acid -TRANSFORM O=CN[OQ1-0:1][#1:2] >> O=CN[O-:1] -TRANSFORM O=CN[OQ1-0:1] >> O=CN[O-:1] - -#sulfinic acid -TRANSFORM [SQ3](=O)[OQ1:1] >> [SQ3](=O)[O-:1] -TRANSFORM [SQ3](=O)[O:1][#1:2] >> [SQ3](=O)[O-:1] - -#sulfonic acid -TRANSFORM [SQ4]([!Q1])(=O)(=O)[OQ1:1] >> [SQ4]([!Q1])(=O)(=O)[O-:1] -TRANSFORM [SQ4]([!Q1])(=O)(=O)[O:1][#1:2] >> [SQ4]([!Q1])(=O)(=O)[O-:1] - -#sulfuric acid -TRANSFORM [SQ4]([!Q1])(=O)(=O)[OQ1:1] >> [SQ4]([!Q1])(=O)(=O)[O-:1] -TRANSFORM [SQ4]([!Q1])(=O)(=O)[O:1][#1:2] >> [SQ4]([!Q1])(=O)(=O)[O-:1] - -#guanidine or amidine -# causes problem in SMARTS parser -#TRANSFORM [#6^2+0:1](=[N^2+0:2])(-[N^2]) >> [#6+:1](=N-:2)(-N) - -#phosphoate ester -TRANSFORM [PQ4](=O)([OQ2])([OQ2])[OQ1:1] >> [PQ4](=O)([OQ2])([OQ2])[O-:1] -TRANSFORM [PQ4](=O)([OQ2])([OQ2])[OQ1:1][#1:2] >> [PQ4](=O)([OQ2])([OQ2])[O-:1] - -#phosphoric acid -TRANSFORM O=P([!Q1])([O:1][#1:2])[O:3][#1:4] >> O=P([*Q2,*Q3])([O:1])[O:3] -TRANSFORM O=P([!Q1])([O:1][#1:2])[OQ1] >> O=P([!Q1])([O:1])O -TRANSFORM O=P([*Q2,*Q3])([OQ1:1])[OQ1:2] >> O=P([*Q2,*Q3])([O-:1])[O-:2] - -#phosphate - -# -# Seeding partial charges for gasteiger-marsili calculation -# -#carboxylic acid -SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5 - -#amines -SEEDCHARGE [N+] 1.0 -#tetrazole -SEEDCHARGE [nQ2]1[nQ2][nQ2][nQ2]c1 -0.2 -0.2 -0.2 -0.2 -0.2 - -#sulfinic -SEEDCHARGE [SQ3](=O)[O-] 0.0 -0.5 -0.5 -#sulfuric acid -SEEDCHARGE [SQ4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0 -#sulfonic acid -SEEDCHARGE [SQ4]([Q2])(~[OQ1])(~[OQ1])~[OQ1] 0.0 0.0 -0.33 -0.33 -0.33 - -#guanidine -SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33 - -#amidine -SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5 - -#phosphoate ester -SEEDCHARGE [PQ4](=O)([OQ2])([OQ2])[OQ1] 0.0 -0.5 0.0 0.0 -0.5 -#phosphoric acid -SEEDCHARGE O=P([!Q1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66 - - -#phosphuric acid -SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5 -#phosphonic acid -SEEDCHARGE [#6]P(~[OQ1])(~[OQ1])~[OQ1] 0.0 0.0 -0.33 -0.33 -0.33 - -#hydroxamic acid -SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OQ1] -0.5 0.0 0.0 -0.5 -SEEDCHARGE O=CN([OQ1])NC=O -0.33 0.0 0.0 -0.33 0.0 -0.33 - -#imidazole: note pKa=7.0, histidine pKa=6.0 -#if you uncomment this, also uncomment the seedcharge statement below -#SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0 diff --git a/java/joelib2/data/plain/resdata.txt b/java/joelib2/data/plain/resdata.txt deleted file mode 100644 index d96496b..0000000 --- a/java/joelib2/data/plain/resdata.txt +++ /dev/null @@ -1,1145 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -RES ALA -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 3HB CB 1 -END - -RES ARG -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM NE Ng+ 2 -ATOM CZ C+ 2 -ATOM NH2 Ng+ 2 -ATOM NH1 Ng+ 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD NE 1 -BOND NE CZ 2 -BOND CZ NH2 1 -BOND CZ NH1 1 -BOND N H 1 -BOND HN N 1 -BOND NH1 1HH1 1 -BOND NH1 2HH1 1 -BOND NE HE 1 -BOND NH2 1HH2 1 -BOND NH2 2HH2 1 -BOND NH1 HH1 1 -BOND NH2 HH2 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD 1 -BOND 2HD CD 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -END - -RES ARZ -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM NE Ng+ 2 -ATOM CZ C+ 2 -ATOM NH2 Ng+ 2 -ATOM NH1 Ng+ 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD NE 1 -BOND NE CZ 1 -BOND CZ NH2 1 -BOND CZ NH1 2 -BOND N H 1 -BOND N HN 1 -BOND NH1 HH1 1 -BOND NE HE 1 -BOND NH2 1HH2 1 -BOND NH2 2HH2 1 -END - -RES ASN -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM ND2 Nam 2 -ATOM OD1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND2 1 -BOND CG OD1 2 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND ND2 1HD2 1 -BOND ND2 2HD2 1 -BOND ND2 HD2 1 -END - -RES ASP -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM OD2 O2 2 -ATOM OD1 O3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG OD2 2 -BOND CG OD1 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -END - -RES ASH -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM OD2 O3 3 -ATOM OD1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG OD2 1 -BOND CG OD1 2 -BOND N H 1 -BOND N HN 1 -BOND OD2 HD2 1 -END - -RES CYS -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM SG S3 3 -BOND SG CB 1 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB SG 1 -BOND N H 1 -BOND N HN 1 -BOND CA HA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND SG HG 1 -END - -RES CYX -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM SG S3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB SG 1 -BOND N H 1 -END - -RES GLN -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C2 2 -ATOM NE2 Nam 2 -ATOM OE1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD NE2 1 -BOND CD OE1 2 -BOND N H 1 -BOND N HN 1 -BOND CA HA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND NE2 1HE2 1 -BOND NE2 2HE2 1 -BOND NE2 HE2 1 -END - -RES GLU -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C2 2 -ATOM OE2 O3 3 -ATOM OE1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD OE2 1 -BOND CD OE1 2 -BOND N H 1 -BOND N 1H 1 -BOND N 2H 1 -BOND N 3H 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -END - -RES GLY -ATOM CA C3 3 -ATOM N Nam 2 -ATOM C Cac 2 -ATOM O O2 2 -BOND CA N 1 -BOND CA C 1 -BOND C O 2 -BOND N H 1 -BOND N HN 1 -BOND 1HA CA 1 -BOND 2HA CA 1 -END - -RES GLZ -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C2 2 -ATOM OE2 O3 3 -ATOM OE1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD OE2 1 -BOND CD OE1 2 -BOND N H 1 -BOND OE2 HE2 1 -END - -RES HID -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C C3 3 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 N2 2 -ATOM CE1 C2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 2 -BOND CE1 ND1 1 -BOND N H 1 -BOND ND1 HD1 1 -END - -RES HIE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 Npl 2 -ATOM CE1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 1 -BOND CE1 ND1 1 -BOND N H 1 -BOND NE2 HE2 1 -END - -RES HIP -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 Npl 2 -ATOM CE1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 1 -BOND CE1 ND1 1 -BOND N H 1 -BOND ND1 HD1 1 -BOND NE2 HE2 1 -END - -RES HIS -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 Npl 2 -ATOM CE1 C2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 2 -BOND CE1 ND1 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD ND1 1 -BOND 2HD CD2 1 -BOND 1HE CE1 1 -BOND ND1 HD1 1 -BOND NE2 HE2 1 -END - -RES ILE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG2 C3 3 -ATOM CG1 C3 3 -ATOM CD1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG2 1 -BOND CB CG1 1 -BOND CG1 CD1 1 -BOND N H 1 -BOND N HN 1 -BOND CA HA 1 -BOND HB CB 1 -BOND 1HG1 CG1 1 -BOND 2HG1 CG1 1 -BOND 1HG2 CG2 1 -BOND 2HG2 CG2 1 -BOND 3HG2 CG2 1 -BOND 1HD1 CD1 1 -BOND 2HD1 CD1 1 -BOND 3HD1 CD1 1 -END - -RES LEU -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD1 C3 3 -ATOM CD2 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 1 -BOND CG CD2 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD1 CD1 1 -BOND 2HD1 CD1 1 -BOND 3HD1 CD1 1 -BOND 1HD2 CD2 1 -BOND 2HD2 CD2 1 -BOND 3HD2 CD2 1 -BOND HG CG 1 -END - -RES LYS -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM CE C3 3 -ATOM NZ N3+ 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD CE 1 -BOND CE NZ 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD 1 -BOND 2HD CD 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND 1HE CE 1 -BOND 2HE CE 1 -BOND NZ 3HZ 1 -BOND NZ HZ3 1 -BOND NZ 2HZ 1 -BOND NZ HZ2 1 -BOND NZ 1HZ 1 -BOND NZ HZ1 1 -END - -RES LYZ -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM CE C3 3 -ATOM NZ N3+ 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD CE 1 -BOND CE NZ 1 -BOND N H 1 -BOND NZ HZ2 1 -BOND NZ HZ1 1 -END - -RES MET -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM SD S3 3 -ATOM CE C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG SD 1 -BOND SD CE 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND 1HE CE 1 -BOND 2HE CE 1 -BOND 3HE CE 1 -END - -RES PHE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM CE1 Car 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 1 -BOND CG CD2 2 -BOND CD2 CE2 1 -BOND CE2 CZ 2 -BOND CZ CE1 1 -BOND CE1 CD1 2 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD1 1 -BOND 2HD CD2 1 -BOND 1HE CE1 1 -BOND 2HE CE2 1 -BOND HZ CZ 1 -END - -RES PRO -ATOM CA C3 3 -ATOM C Cac 2 -ATOM CB C3 3 -ATOM N Nam 2 -ATOM CD C3 3 -ATOM CG C3 3 -ATOM O O2 2 -BOND CA C 1 -BOND CA CB 1 -BOND CA N 1 -BOND N CD 1 -BOND CD CG 1 -BOND CG CB 1 -BOND C O 2 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND 1HD CD 1 -BOND 2HD CD 1 -BOND HA CA 1 -BOND HN N 1 -END - -RES PSE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM OG O3 3 -ATOM PD P3 3 -ATOM OE2 O- 3 -ATOM OE3 O- 3 -ATOM OE1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB OG 1 -BOND OG PD 1 -BOND PD OE2 1 -BOND PD OE3 1 -BOND PD OE1 1 -BOND N H 1 -END - -RES PSM -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM OG O3 3 -ATOM PD P3 3 -ATOM OE2 O- 3 -ATOM OE3 O- 3 -ATOM OE1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB OG 1 -BOND OG PD 1 -BOND PD OE2 1 -BOND PD OE3 1 -BOND PD OE1 1 -BOND N H 1 -BOND OE3 HE3 1 -END - -RES PTM -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM OH O3 3 -ATOM CE1 Car 2 -ATOM PQ P3 3 -ATOM OI3 O- 3 -ATOM OI2 O- 3 -ATOM OI1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE2 2 -BOND CE2 CZ 1 -BOND CZ OH 1 -BOND CZ CE1 2 -BOND CE1 CD1 1 -BOND OH PQ 1 -BOND PQ OI3 1 -BOND PQ OI2 1 -BOND PQ OI1 1 -BOND N H 1 -BOND OI2 HI2 1 -END - -RES PTY -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM OH O3 3 -ATOM CE1 Car 2 -ATOM PQ P3 3 -ATOM OI3 O- 3 -ATOM OI2 O- 3 -ATOM OI1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE2 2 -BOND CE2 CZ 1 -BOND CZ OH 1 -BOND CZ CE1 2 -BOND CE1 CD1 1 -BOND OH PQ 1 -BOND PQ OI3 1 -BOND PQ OI2 1 -BOND PQ OI1 1 -BOND N H 1 -END - -RES SER -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM OG O3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB OG 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND OG HG 1 -END - -RES THR -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG2 C3 3 -ATOM OG1 O3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG2 1 -BOND CB OG1 1 -BOND N H 1 -BOND HN N 1 -BOND N 1H 1 -BOND N 2H 1 -BOND N 3H 1 -BOND OG1 HG1 1 -BOND OG1 1HG 1 -BOND HB CB 1 -BOND HA CA 1 -BOND 1HG2 CG2 1 -BOND 2HG2 CG2 1 -BOND 3HG2 CG2 1 -END - -RES TRP -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE3 Car 2 -ATOM CE2 Car 2 -ATOM CZ2 Car 2 -ATOM NE1 Nar 2 -ATOM CH2 Car 2 -ATOM CZ3 Car 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE3 2 -BOND CD2 CE2 1 -BOND CE2 CZ2 2 -BOND CE2 NE1 1 -BOND NE1 CD1 1 -BOND CZ2 CH2 1 -BOND CH2 CZ3 2 -BOND CZ3 CE3 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD1 1 -BOND 1HE CE1 1 -BOND 2HZ CZ2 1 -BOND 3HZ CZ3 1 -BOND 3HE CE3 1 -BOND 2HH CH2 1 -BOND NE1 HE1 1 -BOND NE1 1HE 1 -END - -RES TYR -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM OH O3 3 -ATOM CE1 Car 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE2 2 -BOND CE2 CZ 1 -BOND CZ OH 1 -BOND CZ CE1 2 -BOND CE1 CD1 1 -BOND N H 1 -BOND OH HH 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD1 1 -BOND 2HD CD2 1 -BOND 1HE CE1 1 -BOND 2HE CE2 1 -BOND HZ CZ 1 -END - -RES VAL -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG2 C3 3 -ATOM CG1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG2 1 -BOND CB CG1 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND HB CB 1 -BOND 1HG1 CG1 1 -BOND 2HG1 CG1 1 -BOND 3HG1 CG1 1 -BOND 1HG2 CG2 1 -BOND 2HG2 CG2 1 -BOND 3HG2 CG2 1 -END - -RES TIP -ATOM OH2 O3 3 -BOND OH2 H1 1 -BOND OH2 H2 1 -END - -RES HOH -ATOM O O3 3 -ATOM 1H -ATOM 2H -BOND O 1H 1 -BOND O 2H 1 -END - -RES WAT -ATOM O O3 3 -ATOM H1 -ATOM H2 -BOND O H1 1 -BOND O H2 1 -END - -RES INH -ATOM P -ATOM O1P -ATOM O2P -ATOM O3P -ATOM O5 -ATOM C5 -ATOM C4 -ATOM O4 -ATOM C3 -ATOM C1 -ATOM O3 -ATOM C2 -ATOM O2 -ATOM N9 -ATOM C8 -ATOM N7 -ATOM C6 -ATOM O6 -ATOM N1 -ATOM N3 -BOND P O1P 2 -BOND P O2P 1 -BOND P O3P 1 -BOND P O5 1 -BOND O5 C5 1 -BOND C5 C4 1 -BOND C4 O4 1 -BOND C4 C3 1 -BOND O4 C1 1 -BOND C3 O3 1 -BOND C3 C2 1 -BOND O3 H1 1 -BOND C2 O2 1 -BOND C2 C1 1 -BOND O2 H2 1 -BOND C1 N9 1 -BOND N9 C8 1 -BOND N9 C4 1 -BOND C8 N7 2 -BOND N7 C5 1 -BOND C5 C6 1 -BOND C6 O6 2 -BOND C6 N1 1 -BOND N1 C2 1 -BOND N1 H3 1 -BOND C2 N3 2 -BOND N3 C4 1 -END - -RES UMP -ATOM N1 -ATOM C2 -ATOM C6 -ATOM C1 -ATOM N3 -ATOM O2 -ATOM C4 -ATOM C5 -ATOM O4 -ATOM C3 -ATOM O3 -ATOM O5 -ATOM P -ATOM O1P -ATOM O2P -ATOM O3P -BOND N1 C2 1 -BOND N1 C6 1 -BOND N1 C1 1 -BOND C2 N3 1 -BOND C2 O2 1 -BOND C2 H5 1 -BOND N3 C4 1 -BOND N3 H1 1 -BOND C4 C5 1 -BOND C4 O4 1 -BOND C4 H6 1 -BOND C5 C6 1 -BOND C5 H7 1 -BOND C5 H8 1 -BOND C6 H9 1 -BOND C6 H10 1 -BOND O2 H2 1 -BOND O4 H3 1 -BOND C1 C2 1 -BOND C1 O4 1 -BOND C1 H11 1 -BOND C2 C3 1 -BOND C2 H12 1 -BOND C2 H13 1 -BOND C3 C4 1 -BOND C3 O3 1 -BOND C3 H14 1 -BOND C4 H15 1 -BOND O3 H4 1 -BOND C5 O5 1 -BOND C5 H16 1 -BOND C5 H17 1 -BOND O5 P 1 -BOND P O1P 2 -BOND P O2P 2 -BOND P O3P 2 -END - -RES HED -ATOM C1 -ATOM O1 -ATOM C2 -ATOM S3 -ATOM S4 -ATOM C5 -ATOM C6 -ATOM O6 -BOND C1 O1 2 -BOND C1 C2 1 -BOND C2 S3 1 -BOND S3 S4 1 -BOND S4 C5 1 -BOND C5 C6 1 -BOND C6 O6 2 -END - -RES HEM -ATOM FE -ATOM NA -ATOM NB -ATOM NC -ATOM ND -ATOM CHA -ATOM C1A -ATOM C4D -ATOM CHB -ATOM C4A -ATOM C1B -ATOM CHC -ATOM C4B -ATOM C1C -ATOM CHD -ATOM C4C -ATOM C1D -ATOM C2A -ATOM C3A -ATOM CAA -ATOM CMA -ATOM CBA -ATOM CGA -ATOM O1A -ATOM O2A -ATOM C2B -ATOM C3B -ATOM CMB -ATOM CAB -ATOM CBB -ATOM C2C -ATOM C3C -ATOM CMC -ATOM CAC C3 3 -ATOM CBC -ATOM C2D -ATOM C3D -ATOM CMD -ATOM CAD -ATOM CBD -ATOM CGD -ATOM O1D -ATOM O2D -BOND FE NA 1 -BOND FE NB 1 -BOND FE NC 1 -BOND FE ND 1 -BOND CHA C1A 1 -BOND CHA C4D 1 -BOND CHB C4A 1 -BOND CHB C1B 1 -BOND CHC C4B 1 -BOND CHC C1C 1 -BOND CHD C4C 1 -BOND CHD C1D 1 -BOND NA C1A 1 -BOND NA C4A 1 -BOND C1A C2A 1 -BOND C2A C3A 1 -BOND C2A CAA 1 -BOND C3A C4A 1 -BOND C3A CMA 1 -BOND CAA CBA 1 -BOND CBA CGA 1 -BOND CGA O1A 2 -BOND CGA O2A 1 -BOND NB C1B 1 -BOND NB C4B 1 -BOND C1B C2B 1 -BOND C2B C3B 1 -BOND C2B CMB 1 -BOND C3B C4B 1 -BOND C3B CAB 1 -BOND CAB CBB 1 -BOND NC C1C 1 -BOND NC C4C 1 -BOND C1C C2C 1 -BOND C2C C3C 1 -BOND C2C CMC 1 -BOND C3C C4C 1 -BOND C3C CAC 1 -BOND CAC CBC 1 -BOND ND C1D 1 -BOND ND C4D 1 -BOND C1D C2D 1 -BOND C2D C3D 1 -BOND C2D CMD 1 -BOND C3D C4D 1 -BOND C3D CAD 1 -BOND CAD CBD 1 -BOND CBD CGD 1 -BOND CGD O1D 2 -BOND CGD O2D 1 -END diff --git a/java/joelib2/data/plain/residue.txt b/java/joelib2/data/plain/residue.txt deleted file mode 100644 index d96496b..0000000 --- a/java/joelib2/data/plain/residue.txt +++ /dev/null @@ -1,1145 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -RES ALA -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 3HB CB 1 -END - -RES ARG -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM NE Ng+ 2 -ATOM CZ C+ 2 -ATOM NH2 Ng+ 2 -ATOM NH1 Ng+ 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD NE 1 -BOND NE CZ 2 -BOND CZ NH2 1 -BOND CZ NH1 1 -BOND N H 1 -BOND HN N 1 -BOND NH1 1HH1 1 -BOND NH1 2HH1 1 -BOND NE HE 1 -BOND NH2 1HH2 1 -BOND NH2 2HH2 1 -BOND NH1 HH1 1 -BOND NH2 HH2 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD 1 -BOND 2HD CD 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -END - -RES ARZ -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM NE Ng+ 2 -ATOM CZ C+ 2 -ATOM NH2 Ng+ 2 -ATOM NH1 Ng+ 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD NE 1 -BOND NE CZ 1 -BOND CZ NH2 1 -BOND CZ NH1 2 -BOND N H 1 -BOND N HN 1 -BOND NH1 HH1 1 -BOND NE HE 1 -BOND NH2 1HH2 1 -BOND NH2 2HH2 1 -END - -RES ASN -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM ND2 Nam 2 -ATOM OD1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND2 1 -BOND CG OD1 2 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND ND2 1HD2 1 -BOND ND2 2HD2 1 -BOND ND2 HD2 1 -END - -RES ASP -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM OD2 O2 2 -ATOM OD1 O3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG OD2 2 -BOND CG OD1 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -END - -RES ASH -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM OD2 O3 3 -ATOM OD1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG OD2 1 -BOND CG OD1 2 -BOND N H 1 -BOND N HN 1 -BOND OD2 HD2 1 -END - -RES CYS -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM SG S3 3 -BOND SG CB 1 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB SG 1 -BOND N H 1 -BOND N HN 1 -BOND CA HA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND SG HG 1 -END - -RES CYX -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM SG S3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB SG 1 -BOND N H 1 -END - -RES GLN -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C2 2 -ATOM NE2 Nam 2 -ATOM OE1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD NE2 1 -BOND CD OE1 2 -BOND N H 1 -BOND N HN 1 -BOND CA HA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND NE2 1HE2 1 -BOND NE2 2HE2 1 -BOND NE2 HE2 1 -END - -RES GLU -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C2 2 -ATOM OE2 O3 3 -ATOM OE1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD OE2 1 -BOND CD OE1 2 -BOND N H 1 -BOND N 1H 1 -BOND N 2H 1 -BOND N 3H 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -END - -RES GLY -ATOM CA C3 3 -ATOM N Nam 2 -ATOM C Cac 2 -ATOM O O2 2 -BOND CA N 1 -BOND CA C 1 -BOND C O 2 -BOND N H 1 -BOND N HN 1 -BOND 1HA CA 1 -BOND 2HA CA 1 -END - -RES GLZ -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C2 2 -ATOM OE2 O3 3 -ATOM OE1 O2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD OE2 1 -BOND CD OE1 2 -BOND N H 1 -BOND OE2 HE2 1 -END - -RES HID -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C C3 3 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 N2 2 -ATOM CE1 C2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 2 -BOND CE1 ND1 1 -BOND N H 1 -BOND ND1 HD1 1 -END - -RES HIE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 Npl 2 -ATOM CE1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 1 -BOND CE1 ND1 1 -BOND N H 1 -BOND NE2 HE2 1 -END - -RES HIP -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 Npl 2 -ATOM CE1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 1 -BOND CE1 ND1 1 -BOND N H 1 -BOND ND1 HD1 1 -BOND NE2 HE2 1 -END - -RES HIS -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C2 2 -ATOM ND1 Npl 2 -ATOM CD2 C2 2 -ATOM NE2 Npl 2 -ATOM CE1 C2 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG ND1 1 -BOND CG CD2 2 -BOND CD2 NE2 1 -BOND NE2 CE1 2 -BOND CE1 ND1 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD ND1 1 -BOND 2HD CD2 1 -BOND 1HE CE1 1 -BOND ND1 HD1 1 -BOND NE2 HE2 1 -END - -RES ILE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG2 C3 3 -ATOM CG1 C3 3 -ATOM CD1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG2 1 -BOND CB CG1 1 -BOND CG1 CD1 1 -BOND N H 1 -BOND N HN 1 -BOND CA HA 1 -BOND HB CB 1 -BOND 1HG1 CG1 1 -BOND 2HG1 CG1 1 -BOND 1HG2 CG2 1 -BOND 2HG2 CG2 1 -BOND 3HG2 CG2 1 -BOND 1HD1 CD1 1 -BOND 2HD1 CD1 1 -BOND 3HD1 CD1 1 -END - -RES LEU -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD1 C3 3 -ATOM CD2 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 1 -BOND CG CD2 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD1 CD1 1 -BOND 2HD1 CD1 1 -BOND 3HD1 CD1 1 -BOND 1HD2 CD2 1 -BOND 2HD2 CD2 1 -BOND 3HD2 CD2 1 -BOND HG CG 1 -END - -RES LYS -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM CE C3 3 -ATOM NZ N3+ 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD CE 1 -BOND CE NZ 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD 1 -BOND 2HD CD 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND 1HE CE 1 -BOND 2HE CE 1 -BOND NZ 3HZ 1 -BOND NZ HZ3 1 -BOND NZ 2HZ 1 -BOND NZ HZ2 1 -BOND NZ 1HZ 1 -BOND NZ HZ1 1 -END - -RES LYZ -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM CD C3 3 -ATOM CE C3 3 -ATOM NZ N3+ 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD 1 -BOND CD CE 1 -BOND CE NZ 1 -BOND N H 1 -BOND NZ HZ2 1 -BOND NZ HZ1 1 -END - -RES MET -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG C3 3 -ATOM SD S3 3 -ATOM CE C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG SD 1 -BOND SD CE 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND 1HE CE 1 -BOND 2HE CE 1 -BOND 3HE CE 1 -END - -RES PHE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM CE1 Car 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 1 -BOND CG CD2 2 -BOND CD2 CE2 1 -BOND CE2 CZ 2 -BOND CZ CE1 1 -BOND CE1 CD1 2 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD1 1 -BOND 2HD CD2 1 -BOND 1HE CE1 1 -BOND 2HE CE2 1 -BOND HZ CZ 1 -END - -RES PRO -ATOM CA C3 3 -ATOM C Cac 2 -ATOM CB C3 3 -ATOM N Nam 2 -ATOM CD C3 3 -ATOM CG C3 3 -ATOM O O2 2 -BOND CA C 1 -BOND CA CB 1 -BOND CA N 1 -BOND N CD 1 -BOND CD CG 1 -BOND CG CB 1 -BOND C O 2 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HG CG 1 -BOND 2HG CG 1 -BOND 1HD CD 1 -BOND 2HD CD 1 -BOND HA CA 1 -BOND HN N 1 -END - -RES PSE -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM OG O3 3 -ATOM PD P3 3 -ATOM OE2 O- 3 -ATOM OE3 O- 3 -ATOM OE1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB OG 1 -BOND OG PD 1 -BOND PD OE2 1 -BOND PD OE3 1 -BOND PD OE1 1 -BOND N H 1 -END - -RES PSM -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM OG O3 3 -ATOM PD P3 3 -ATOM OE2 O- 3 -ATOM OE3 O- 3 -ATOM OE1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB OG 1 -BOND OG PD 1 -BOND PD OE2 1 -BOND PD OE3 1 -BOND PD OE1 1 -BOND N H 1 -BOND OE3 HE3 1 -END - -RES PTM -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM OH O3 3 -ATOM CE1 Car 2 -ATOM PQ P3 3 -ATOM OI3 O- 3 -ATOM OI2 O- 3 -ATOM OI1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE2 2 -BOND CE2 CZ 1 -BOND CZ OH 1 -BOND CZ CE1 2 -BOND CE1 CD1 1 -BOND OH PQ 1 -BOND PQ OI3 1 -BOND PQ OI2 1 -BOND PQ OI1 1 -BOND N H 1 -BOND OI2 HI2 1 -END - -RES PTY -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM OH O3 3 -ATOM CE1 Car 2 -ATOM PQ P3 3 -ATOM OI3 O- 3 -ATOM OI2 O- 3 -ATOM OI1 O- 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE2 2 -BOND CE2 CZ 1 -BOND CZ OH 1 -BOND CZ CE1 2 -BOND CE1 CD1 1 -BOND OH PQ 1 -BOND PQ OI3 1 -BOND PQ OI2 1 -BOND PQ OI1 1 -BOND N H 1 -END - -RES SER -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM OG O3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB OG 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND OG HG 1 -END - -RES THR -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG2 C3 3 -ATOM OG1 O3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG2 1 -BOND CB OG1 1 -BOND N H 1 -BOND HN N 1 -BOND N 1H 1 -BOND N 2H 1 -BOND N 3H 1 -BOND OG1 HG1 1 -BOND OG1 1HG 1 -BOND HB CB 1 -BOND HA CA 1 -BOND 1HG2 CG2 1 -BOND 2HG2 CG2 1 -BOND 3HG2 CG2 1 -END - -RES TRP -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE3 Car 2 -ATOM CE2 Car 2 -ATOM CZ2 Car 2 -ATOM NE1 Nar 2 -ATOM CH2 Car 2 -ATOM CZ3 Car 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE3 2 -BOND CD2 CE2 1 -BOND CE2 CZ2 2 -BOND CE2 NE1 1 -BOND NE1 CD1 1 -BOND CZ2 CH2 1 -BOND CH2 CZ3 2 -BOND CZ3 CE3 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD1 1 -BOND 1HE CE1 1 -BOND 2HZ CZ2 1 -BOND 3HZ CZ3 1 -BOND 3HE CE3 1 -BOND 2HH CH2 1 -BOND NE1 HE1 1 -BOND NE1 1HE 1 -END - -RES TYR -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG Car 2 -ATOM CD1 Car 2 -ATOM CD2 Car 2 -ATOM CE2 Car 2 -ATOM CZ Car 2 -ATOM OH O3 3 -ATOM CE1 Car 2 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG 1 -BOND CG CD1 2 -BOND CG CD2 1 -BOND CD2 CE2 2 -BOND CE2 CZ 1 -BOND CZ OH 1 -BOND CZ CE1 2 -BOND CE1 CD1 1 -BOND N H 1 -BOND OH HH 1 -BOND N HN 1 -BOND HA CA 1 -BOND 1HB CB 1 -BOND 2HB CB 1 -BOND 1HD CD1 1 -BOND 2HD CD2 1 -BOND 1HE CE1 1 -BOND 2HE CE2 1 -BOND HZ CZ 1 -END - -RES VAL -ATOM CA C3 3 -ATOM N Nam 2 -ATOM CB C3 3 -ATOM C Cac 2 -ATOM O O2 2 -ATOM CG2 C3 3 -ATOM CG1 C3 3 -BOND CA N 1 -BOND CA CB 1 -BOND CA C 1 -BOND C O 2 -BOND CB CG2 1 -BOND CB CG1 1 -BOND N H 1 -BOND N HN 1 -BOND HA CA 1 -BOND HB CB 1 -BOND 1HG1 CG1 1 -BOND 2HG1 CG1 1 -BOND 3HG1 CG1 1 -BOND 1HG2 CG2 1 -BOND 2HG2 CG2 1 -BOND 3HG2 CG2 1 -END - -RES TIP -ATOM OH2 O3 3 -BOND OH2 H1 1 -BOND OH2 H2 1 -END - -RES HOH -ATOM O O3 3 -ATOM 1H -ATOM 2H -BOND O 1H 1 -BOND O 2H 1 -END - -RES WAT -ATOM O O3 3 -ATOM H1 -ATOM H2 -BOND O H1 1 -BOND O H2 1 -END - -RES INH -ATOM P -ATOM O1P -ATOM O2P -ATOM O3P -ATOM O5 -ATOM C5 -ATOM C4 -ATOM O4 -ATOM C3 -ATOM C1 -ATOM O3 -ATOM C2 -ATOM O2 -ATOM N9 -ATOM C8 -ATOM N7 -ATOM C6 -ATOM O6 -ATOM N1 -ATOM N3 -BOND P O1P 2 -BOND P O2P 1 -BOND P O3P 1 -BOND P O5 1 -BOND O5 C5 1 -BOND C5 C4 1 -BOND C4 O4 1 -BOND C4 C3 1 -BOND O4 C1 1 -BOND C3 O3 1 -BOND C3 C2 1 -BOND O3 H1 1 -BOND C2 O2 1 -BOND C2 C1 1 -BOND O2 H2 1 -BOND C1 N9 1 -BOND N9 C8 1 -BOND N9 C4 1 -BOND C8 N7 2 -BOND N7 C5 1 -BOND C5 C6 1 -BOND C6 O6 2 -BOND C6 N1 1 -BOND N1 C2 1 -BOND N1 H3 1 -BOND C2 N3 2 -BOND N3 C4 1 -END - -RES UMP -ATOM N1 -ATOM C2 -ATOM C6 -ATOM C1 -ATOM N3 -ATOM O2 -ATOM C4 -ATOM C5 -ATOM O4 -ATOM C3 -ATOM O3 -ATOM O5 -ATOM P -ATOM O1P -ATOM O2P -ATOM O3P -BOND N1 C2 1 -BOND N1 C6 1 -BOND N1 C1 1 -BOND C2 N3 1 -BOND C2 O2 1 -BOND C2 H5 1 -BOND N3 C4 1 -BOND N3 H1 1 -BOND C4 C5 1 -BOND C4 O4 1 -BOND C4 H6 1 -BOND C5 C6 1 -BOND C5 H7 1 -BOND C5 H8 1 -BOND C6 H9 1 -BOND C6 H10 1 -BOND O2 H2 1 -BOND O4 H3 1 -BOND C1 C2 1 -BOND C1 O4 1 -BOND C1 H11 1 -BOND C2 C3 1 -BOND C2 H12 1 -BOND C2 H13 1 -BOND C3 C4 1 -BOND C3 O3 1 -BOND C3 H14 1 -BOND C4 H15 1 -BOND O3 H4 1 -BOND C5 O5 1 -BOND C5 H16 1 -BOND C5 H17 1 -BOND O5 P 1 -BOND P O1P 2 -BOND P O2P 2 -BOND P O3P 2 -END - -RES HED -ATOM C1 -ATOM O1 -ATOM C2 -ATOM S3 -ATOM S4 -ATOM C5 -ATOM C6 -ATOM O6 -BOND C1 O1 2 -BOND C1 C2 1 -BOND C2 S3 1 -BOND S3 S4 1 -BOND S4 C5 1 -BOND C5 C6 1 -BOND C6 O6 2 -END - -RES HEM -ATOM FE -ATOM NA -ATOM NB -ATOM NC -ATOM ND -ATOM CHA -ATOM C1A -ATOM C4D -ATOM CHB -ATOM C4A -ATOM C1B -ATOM CHC -ATOM C4B -ATOM C1C -ATOM CHD -ATOM C4C -ATOM C1D -ATOM C2A -ATOM C3A -ATOM CAA -ATOM CMA -ATOM CBA -ATOM CGA -ATOM O1A -ATOM O2A -ATOM C2B -ATOM C3B -ATOM CMB -ATOM CAB -ATOM CBB -ATOM C2C -ATOM C3C -ATOM CMC -ATOM CAC C3 3 -ATOM CBC -ATOM C2D -ATOM C3D -ATOM CMD -ATOM CAD -ATOM CBD -ATOM CGD -ATOM O1D -ATOM O2D -BOND FE NA 1 -BOND FE NB 1 -BOND FE NC 1 -BOND FE ND 1 -BOND CHA C1A 1 -BOND CHA C4D 1 -BOND CHB C4A 1 -BOND CHB C1B 1 -BOND CHC C4B 1 -BOND CHC C1C 1 -BOND CHD C4C 1 -BOND CHD C1D 1 -BOND NA C1A 1 -BOND NA C4A 1 -BOND C1A C2A 1 -BOND C2A C3A 1 -BOND C2A CAA 1 -BOND C3A C4A 1 -BOND C3A CMA 1 -BOND CAA CBA 1 -BOND CBA CGA 1 -BOND CGA O1A 2 -BOND CGA O2A 1 -BOND NB C1B 1 -BOND NB C4B 1 -BOND C1B C2B 1 -BOND C2B C3B 1 -BOND C2B CMB 1 -BOND C3B C4B 1 -BOND C3B CAB 1 -BOND CAB CBB 1 -BOND NC C1C 1 -BOND NC C4C 1 -BOND C1C C2C 1 -BOND C2C C3C 1 -BOND C2C CMC 1 -BOND C3C C4C 1 -BOND C3C CAC 1 -BOND CAC CBC 1 -BOND ND C1D 1 -BOND ND C4D 1 -BOND C1D C2D 1 -BOND C2D C3D 1 -BOND C2D CMD 1 -BOND C3D C4D 1 -BOND C3D CAD 1 -BOND CAD CBD 1 -BOND CBD CGD 1 -BOND CGD O1D 2 -BOND CGD O2D 1 -END diff --git a/java/joelib2/data/plain/ringlib.txt b/java/joelib2/data/plain/ringlib.txt deleted file mode 100644 index 3fc3d75..0000000 --- a/java/joelib2/data/plain/ringlib.txt +++ /dev/null @@ -1,563 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -#cyclopropane -1 [O,N,C]1~C~C1 - -1.087 0.515 1.689 - -0.366 0.112 0.388 - -1.903 0.058 0.465 -#5 membered aromatic -1 a1aaaa1 - -1.681 0.543 1.863 - -0.587 0.320 1.034 - -1.064 -0.122 -0.194 - -2.451 -0.171 -0.125 - -2.832 0.240 1.147 -#furan and pyrole -2 [O,N]1CCCC1 - -0.701 2.030 0.002 - 0.474 1.128 -0.196 - -0.012 -0.235 0.303 - -1.396 -0.233 -0.303 - -1.879 1.130 0.197 - 1.298 4.030 1.000 - 2.474 3.128 1.197 - 1.988 1.765 0.698 - 0.604 1.767 1.304 - 0.121 3.130 0.804 -#planar 5 membered ring -1 [N,O]1[CX3][CX3][a,A]=,:[a,A]1 - -1.340 -0.837 0.812 - 0.040 -0.970 0.586 - 0.581 0.160 -0.228 - -0.711 0.948 -0.423 - -1.756 0.359 0.171 -#planar 5 membered ring -1 [A]1=[A][A]=[A][A]1 - -1.340 -0.837 0.812 - 0.040 -0.970 0.586 - 0.581 0.160 -0.228 - -0.711 0.948 -0.423 - -1.756 0.359 0.171 -#planar 5 membered ring -1 a1aaaa1 - -1.340 -0.837 0.812 - 0.040 -0.970 0.586 - 0.581 0.160 -0.228 - -0.711 0.948 -0.423 - -1.756 0.359 0.171 -#diazeneone (planar 5 ring) -1 [C^2]1(NN=CC1) - -3.013 2.955 0.673 - -1.925 2.096 0.474 - -2.425 0.859 0.176 - -3.707 0.862 0.168 - -4.294 2.234 0.492 -#6 membered aromatic -1 a1aaaaa1 - -1.204 1.354 0.000 - 0.000 0.659 0.000 - 0.000 -0.732 0.000 - -1.204 -1.427 0.000 - -2.408 -0.732 0.000 - -2.408 0.658 0.000 -#cyclohexene -2 [CX4]1[CX4]C=C[CX4][CX4]1 - 1.621 1.921 -1.506 - 2.264 1.957 -0.108 - 1.371 1.303 0.926 - 0.353 0.500 0.595 - 0.016 0.157 -0.841 - 1.187 0.488 -1.785 - 1.032 -2.938 2.417 - 1.445 -2.273 3.743 - 0.836 -2.988 4.931 - -0.191 -3.837 4.812 - -0.851 -4.140 3.483 - -0.483 -3.087 2.422 -#piperidine (4 amino allowed) -2 [N,C]1[C^3][C^3][C,N,O][C^3][C^3]1 - -0.704 6.877 -0.788 - 0.228 5.686 -1.099 - -0.578 4.370 -1.041 - -1.719 4.418 -2.081 - -2.651 5.609 -1.770 - -1.845 6.925 -1.827 - -5.668 2.918 -0.256 - -4.407 2.189 0.256 - -4.407 0.733 -0.257 - -5.668 0.004 0.257 - -6.930 0.733 -0.256 - -6.929 2.189 0.257 -#cyclohexyl lactam -1 N1[$(C=O)](CCC[$(C=O)]1) - 2.559 3.485 -0.731 - 1.285 2.897 -0.417 - 1.063 1.423 -0.599 - 2.398 0.674 -0.466 - 3.454 1.205 -1.448 - 3.634 2.683 -1.252 -#lactone -2 C1([C^3][C^3][C^3]O1)=O - 4.666 4.849 3.925 - 4.984 5.534 5.232 - 6.475 5.815 5.080 - 6.914 4.540 4.338 - 5.773 4.209 3.477 - 3.630 4.839 3.319 - -4.666 4.849 3.925 - -4.984 5.534 5.232 - -6.475 5.815 5.080 - -6.914 4.540 4.338 - -5.773 4.209 3.477 - -3.630 4.839 3.319 -#quinone -1 C=1[$(C=*)](C=C[$(C=*)](C1)) - 0.466 -0.243 0.043 - 1.799 -0.836 -0.070 - 2.574 -0.666 -1.299 - 2.066 0.027 -2.316 - 0.733 0.621 -2.203 - -0.041 0.451 -0.974 -#aromatic bicyclo[4.3.0] (indole) -1 a1aa2a(aa1)aaa2 - -2.906 -1.171 1.365 - -1.550 -1.476 1.251 - -0.767 -0.588 0.531 - -1.280 0.537 -0.045 - -2.624 0.859 0.057 - -3.436 -0.018 0.776 - -0.314 1.200 -0.666 - 0.825 0.517 -0.501 - 0.587 -0.632 0.258 -1 a1aa2a(aa1)[$(C=O)]N[$(C=O)]2 - -2.906 -1.171 1.365 - -1.550 -1.476 1.251 - -0.767 -0.588 0.531 - -1.280 0.537 -0.045 - -2.624 0.859 0.057 - -3.436 -0.018 0.776 - -0.314 1.200 -0.666 - 0.825 0.517 -0.501 - 0.587 -0.632 0.258 -#indane -2 a1a2a(aaa1)[A][C^3][C^3]2 - -2.403 2.049 -0.078 - -1.184 1.390 -0.011 - -1.115 0.017 0.044 - -2.262 -0.764 0.035 - -3.493 -0.115 -0.025 - -3.563 1.278 -0.081 - 0.282 -0.480 0.090 - 1.022 0.834 0.542 - 0.157 2.026 -0.011 - -0.403 4.049 1.190 - 0.816 3.390 1.123 - 0.885 2.017 1.068 - -0.262 1.236 1.077 - -1.493 1.885 1.137 - -1.563 3.278 1.193 - 2.283 1.520 1.023 - 3.022 2.833 0.570 - 2.157 4.026 1.124 -#indole type cyclic ketal -1 a1a2a(aaa1)OCO2 - -1.881 1.937 0.461 - -0.694 1.252 0.240 - -0.688 -0.083 -0.070 - -1.868 -0.804 -0.178 - -3.069 -0.132 0.041 - -3.075 1.227 0.357 - 0.569 -0.576 -0.250 - 1.429 0.616 -0.011 - 0.558 1.785 0.299 -#thiq -2 a1a2a(aaa1)[C,N,O][CX4][CX4][C,N,O]2 - -3.280 2.234 0.041 - -2.069 1.573 -0.133 - -2.039 0.179 -0.193 - -3.224 -0.536 -0.057 - -4.432 0.125 0.121 - -4.462 1.514 0.164 - -0.805 -0.567 -0.397 - 0.377 0.277 -0.694 - 0.389 1.520 0.170 - -0.812 2.383 -0.232 - 3.701 9.244 3.506 - 4.923 8.595 3.369 - 4.974 7.200 3.360 - 3.793 6.473 3.469 - 2.572 7.123 3.600 - 2.526 8.511 3.625 - 6.226 6.465 3.244 - 7.439 7.314 3.297 - 7.244 8.592 2.508 - 6.165 9.419 3.213 -2 a1aaaa2a1aa1a(a2)[C,N,O]CCC1 - 3.474 0.259 -1.427 - 4.628 0.122 -2.189 - 4.538 -0.261 -3.523 - 3.295 -0.510 -4.095 - 2.141 -0.374 -3.330 - 2.231 0.013 -1.999 - 1.077 0.151 -1.239 - -0.171 -0.100 -1.800 - -0.263 -0.488 -3.137 - 0.896 -0.625 -3.895 - -1.599 -0.770 -3.795 - -2.774 -0.194 -2.980 - -2.628 -0.641 -1.536 - -1.399 0.060 -0.929 - 7.474 4.259 -1.698 - 8.628 4.122 -0.936 - 8.538 3.739 0.399 - 7.295 3.490 0.970 - 6.141 3.626 0.205 - 6.231 4.012 -1.126 - 5.077 4.151 -1.886 - 3.829 3.901 -1.325 - 3.737 3.512 0.012 - 4.896 3.375 0.770 - 2.401 3.230 0.670 - 1.226 3.806 -0.145 - 1.372 3.359 -1.589 - 2.601 4.060 -2.196 -#modified cyclohexene to include oxygen -2 C1C=COCC1 - -1.726 2.105 -0.199 - -0.474 1.293 -0.051 - -0.515 -0.033 0.118 - -1.716 -0.794 0.093 - -2.883 -0.048 -0.321 - -2.907 1.311 0.359 - 2.255 6.064 1.686 - 3.517 5.279 1.889 - 3.493 3.965 2.135 - 2.297 3.216 2.304 - 1.099 4.022 2.381 - 1.124 5.106 1.315 -#naphthalene -1 a1a2a(aaa1)aaaa2 - -3.026 2.635 0.596 - -1.821 1.957 0.448 - -1.820 0.605 0.125 - -3.023 -0.069 -0.048 - -4.227 0.608 0.100 - -4.228 1.960 0.423 - -0.615 -0.072 -0.024 - 0.588 0.603 0.149 - 0.586 1.954 0.472 - -0.618 2.632 0.621 -#penicillin type ring system -2 C1[C@@H]2[C@H](CS1)NC(=O)N2 - 0.387 0.908 -2.127 - 1.874 1.142 -1.804 - 2.750 0.147 -2.605 - 1.874 -0.881 -3.323 - 0.283 -0.883 -2.452 - 3.588 -0.463 -1.583 - 3.269 -0.032 -0.319 - 3.806 -0.393 0.715 - 2.256 0.889 -0.423 - -2.405 0.599 -0.470 - -0.869 0.753 -0.470 - -0.204 -0.452 -1.171 - -1.249 -1.352 -1.816 - -2.685 -0.278 -2.054 - 0.557 -1.085 -0.114 - 0.580 -0.318 1.029 - 1.219 -0.560 2.039 - -0.232 0.777 0.829 -#anthracene -1 a1a2a(aaa1)aa1a(a2)aaaa1 - -3.186 2.722 -0.000 - -1.980 2.028 -0.000 - -1.980 0.638 0.000 - -3.185 -0.056 0.001 - -4.391 0.638 -0.000 - -4.391 2.028 -0.001 - -0.775 -0.056 0.000 - 0.431 0.637 -0.000 - 0.432 2.028 0.000 - -0.774 2.722 0.000 - 1.638 2.722 0.001 - 2.843 2.028 0.001 - 2.843 0.638 0.000 - 1.637 -0.056 0.000 -#phenothiazine -1 a1a2a(aaa1)[#16]a1a([#7]2)aaaa1 - -4.212 -2.391 -2.255 - -3.033 -1.710 -1.970 - -3.042 -0.740 -0.970 - -4.213 -0.463 -0.272 - -5.385 -1.148 -0.564 - -5.384 -2.116 -1.560 - -1.608 0.143 -0.567 - -0.335 -0.407 -1.607 - -0.560 -1.406 -2.552 - -1.851 -2.071 -2.763 - 0.495 -1.813 -3.363 - 1.754 -1.238 -3.240 - 1.971 -0.243 -2.296 - 0.925 0.170 -1.482 -#phenothiazine with extra ring attached -1 a12a(a3a(aa1)[#7]a1a([#16]3)aaaa1)aaaa2 - 2.352 0.659 -1.491 - 1.577 1.319 -0.548 - 0.460 0.704 0.005 - 0.094 -0.585 -0.374 - 0.880 -1.241 -1.322 - 2.001 -0.628 -1.879 - -1.095 -1.308 0.177 - -1.984 -0.668 1.196 - -1.781 0.616 1.704 - -0.453 1.591 1.175 - -2.647 1.150 2.653 - -3.730 0.413 3.114 - -3.942 -0.866 2.617 - -3.074 -1.398 1.667 - 1.914 2.607 -0.147 - 3.028 3.237 -0.689 - 3.806 2.577 -1.634 - 3.468 1.288 -2.035 -1 a1aa2a(aa1)aa1a(a2)nas1 - 2.478 1.933 -0.932 - 1.663 2.544 0.014 - 0.559 1.875 0.531 - 0.272 0.579 0.088 - 1.089 -0.029 -0.859 - 2.191 0.646 -1.369 - -0.828 -0.114 0.586 - -1.613 0.533 1.526 - -1.345 1.808 1.976 - -0.248 2.504 1.482 - -2.224 2.251 2.888 - -3.188 1.361 3.178 - -2.938 0.017 2.290 -#quinone -1 a1a2a(aaa1)[C^2](C=C[C^2]2) - -3.259 2.452 -0.001 - -2.059 1.749 -0.000 - -2.069 0.360 0.000 - -3.277 -0.329 -0.000 - -4.478 0.372 0.000 - -4.468 1.763 0.001 - -0.799 -0.369 0.001 - 0.471 0.366 -0.001 - 0.482 1.699 -0.002 - -0.773 2.460 0.000 -#carbazole -1 a12aaaaa1[a,A]a1a2aaaa1 - 0.583 -0.188 -0.205 - 1.840 -0.767 -0.252 - 2.565 -0.593 -1.430 - 2.036 0.132 -2.503 - 0.766 0.706 -2.434 - 0.054 0.527 -1.258 - -1.221 0.993 -0.936 - -1.445 0.530 0.362 - -0.355 -0.186 0.809 - -0.306 -0.763 2.067 - -1.424 -0.585 2.881 - -2.534 0.141 2.435 - -2.562 0.712 1.162 -1 a12a3aaaa1aaaa2CC3 - 0.267 0.324 -1.025 - 1.497 -0.266 -1.033 - 2.306 -0.159 -2.156 - 1.810 0.562 -3.248 - 0.544 1.160 -3.219 - -0.244 1.036 -2.079 - -1.515 1.584 -1.932 - -2.214 1.390 -0.734 - -1.666 0.659 0.327 - -0.396 0.125 0.151 - 0.425 -0.702 1.125 - 1.784 -0.983 0.276 -1 a12aaaaa1a1a(aa2)aaaa1 - 2.088 -0.303 -0.252 - 3.569 -0.384 -0.666 - 4.038 0.265 -1.981 - 3.026 0.996 -2.883 - 1.544 1.077 -2.469 - 1.076 0.428 -1.154 - -0.405 0.508 -0.740 - -0.874 -0.141 0.576 - 0.139 -0.872 1.477 - 1.620 -0.953 1.063 - -2.355 -0.060 0.989 - -3.368 0.670 0.088 - -2.899 1.320 -1.227 - -1.418 1.239 -1.641 -#anthracene-like ring where central not aromatic -1 a1a2a(aaa1)[A^2]a1a([A^2]2)aaaa1 - -3.102 2.015 0.447 - -1.892 1.342 0.299 - -1.885 -0.009 -0.022 - -3.089 -0.685 -0.196 - -4.299 -0.014 -0.049 - -4.306 1.339 0.273 - -0.600 -0.721 -0.179 - 0.678 -0.007 0.005 - 0.673 1.346 0.329 - -0.613 2.059 0.485 - 1.878 2.023 0.503 - 3.088 1.350 0.356 - 3.093 -0.002 0.033 - 1.889 -0.678 -0.142 -2 [a]12[A][a]3[a]([A][A][a]1[a][a][a][a]2)[a][a][a][a]3 - 0.227 1.258 0.377 - 0.842 1.371 -1.011 - -0.072 1.128 -2.173 - -0.759 -0.065 -2.331 - -0.611 -1.147 -1.352 - -1.322 -0.798 -0.052 - -0.733 0.322 0.791 - -1.207 0.376 2.099 - -0.749 1.327 3.001 - 0.208 2.243 2.596 - 0.684 2.201 1.293 - -1.582 -0.257 -3.436 - -1.725 0.748 -4.385 - -1.036 1.944 -4.230 - -0.209 2.129 -3.129 - 4.227 5.258 0.031 - 4.842 5.371 1.419 - 3.928 5.128 2.581 - 3.241 3.934 2.739 - 3.389 2.853 1.760 - 2.678 3.202 0.459 - 3.267 4.322 -0.383 - 2.793 4.376 -1.691 - 3.251 5.327 -2.593 - 4.208 6.244 -2.188 - 4.685 6.201 -0.885 - 2.418 3.743 3.843 - 2.275 4.748 4.792 - 2.964 5.944 4.638 - 3.791 6.129 3.536 -#spiro 56 system -2 [AX4]1[AX4]C2([AX4][AX4]C1)[$([ND2]),$(N=*),$(N[a])]CNC2 - -4.140 2.060 1.052 - -2.715 1.720 0.570 - -2.544 0.187 0.496 - -3.565 -0.364 -0.522 - -4.997 -0.038 -0.049 - -5.169 1.492 0.052 - -2.710 -0.495 1.832 - -1.512 -1.314 1.944 - -0.599 -1.127 0.889 - -1.179 -0.200 0.036 - -1.140 5.060 1.413 - 0.285 4.720 1.895 - 0.456 3.187 1.969 - -0.565 2.636 2.987 - -1.997 2.962 2.513 - -2.169 4.492 2.412 - 0.290 2.505 0.633 - 1.488 1.686 0.521 - 2.401 1.873 1.576 - 1.821 2.800 2.428 -#unsat steroid -1 C1CCCC2C1CCC1=C2CCC2C1CCC2 - 4.788 0.733 -0.073 - 5.885 0.544 -1.144 - 5.932 -0.942 -1.570 - 4.569 -1.362 -2.161 - 3.460 -1.108 -1.117 - 3.418 0.357 -0.670 - 2.335 0.469 0.385 - 0.971 0.213 -0.281 - 0.974 -0.988 -1.217 - 2.116 -1.593 -1.613 - 2.096 -2.814 -2.559 - 0.721 -3.040 -3.234 - -0.329 -2.892 -2.161 - -0.344 -1.493 -1.722 - -1.504 -1.448 -0.731 - -2.560 -2.366 -1.456 - -1.764 -2.978 -2.666 -#unsat steroid -1 C1CCCC2C=1CCC1C2CCC2C1CCC2 - 4.660 0.856 -0.309 - 5.958 0.453 -0.983 - 5.926 -1.013 -1.452 - 4.648 -1.231 -2.249 - 3.474 -1.116 -1.264 - 3.524 0.163 -0.445 - 2.293 0.634 0.303 - 0.976 0.236 -0.403 - 0.993 -1.220 -0.896 - 2.115 -1.364 -1.935 - 2.104 -2.810 -2.536 - 0.730 -3.084 -3.201 - -0.365 -2.903 -2.134 - -0.339 -1.528 -1.592 - -1.539 -1.559 -0.650 - -2.615 -2.296 -1.531 - -1.779 -2.921 -2.708 -#estrogen like steroid -1 c1cccc2c1CCC1C2CCC2C1CCC2 - 4.756 0.562 -0.057 - 5.913 0.077 -0.655 - 5.823 -0.838 -1.697 - 4.576 -1.265 -2.137 - 3.416 -0.780 -1.541 - 3.505 0.141 -0.496 - 2.270 0.692 0.200 - 0.957 0.365 -0.545 - 0.988 -1.093 -0.977 - 2.082 -1.260 -2.040 - 2.156 -2.730 -2.563 - 0.772 -3.127 -3.147 - -0.302 -2.925 -2.059 - -0.340 -1.512 -1.614 - -1.510 -1.546 -0.636 - -2.566 -2.397 -1.433 - -1.728 -3.061 -2.586 -#porphyrin -#1 c1cc2nc1cc1nc(cc1)cc1nc(cc1)cc1ccc(n1)c2 -1 c1cc2[#7]c1cc1[#7]c(cc1)cc1[#7]c(cc1)cc1ccc([#7]1)c2 - 3.332 -1.312 1.154 - 4.518 -1.237 0.440 - 4.201 -0.594 -0.748 - 2.908 -0.285 -0.790 - 2.373 -0.711 0.350 - 1.042 -0.592 0.730 - 0.060 0.003 -0.053 - 0.228 0.536 -1.259 - -0.959 0.988 -1.648 - -1.923 0.747 -0.679 - -1.262 0.108 0.356 - -1.246 1.621 -2.852 - -0.303 1.878 -3.841 - 0.990 1.572 -3.798 - 1.524 1.995 -4.940 - 0.563 2.588 -5.747 - -0.622 2.512 -5.034 - 2.856 1.880 -5.319 - 3.840 1.291 -4.533 - 5.164 1.192 -4.938 - 5.825 0.553 -3.902 - 4.859 0.306 -2.936 - 3.671 0.755 -3.328 - 5.144 -0.332 -1.734 diff --git a/java/joelib2/data/plain/torlib.txt b/java/joelib2/data/plain/torlib.txt deleted file mode 100644 index f3a95fb..0000000 --- a/java/joelib2/data/plain/torlib.txt +++ /dev/null @@ -1,28 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -SP3-SP3 60.0 -60.0 180.0 -SP2-SP2 0.0 180.0 -30.0 30.0 150.0 -150.0 -SP3-SP2 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0 - -#nitro -[aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0 diff --git a/java/joelib2/data/plain/types.txt b/java/joelib2/data/plain/types.txt deleted file mode 100644 index f06d012..0000000 --- a/java/joelib2/data/plain/types.txt +++ /dev/null @@ -1,209 +0,0 @@ -VENDOR: http://joelib.sf.net -RELEASE_VERSION: $Revision: 1.2 $ -RELEASE_DATE: $Date: 2005/01/07 07:18:15 $ - -######################################################################### -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -######################################################################## - -183 18 -INT ATN HYB MMD MM2 XYZ ALC HAD MCML C3D SYB MOL MAP DRE XED DOK M3D IDX -Xx 0 0 62 0 X Du 0 X 0 Du 26 X X 21 25 un.0 0 -Mn 25 0 62 0 Mn Du 0 M 258 Mn 26 Mn Mn 20 25 Mn.0 1 -Fe 26 0 62 0 Fe Du 0 M 266 Fe 26 Fe Fe 20 25 Fe.6 2 -Du 0 0 61 0 Du Du 0 Z 0 Du 26 Du Du 20 25 un.0 3 -C3 6 3 3 1 C C3 4 C 64 C.3 1 C3 C_3 1 5 C.4 4 -C2 6 2 2 2 C C2 3 C 63 C.2 2 C2 C_2 2 1 C.3 5 -C2 6 2 2 38 C C2 3 C 63 C.2 2 C2 C_2 2 1 C.3 6 -C1 6 1 1 4 C C1 2 C 62 C.1 4 C1 C_1 4 1 C.2 7 -Cac 6 2 2 3 C C2 0 C 63 C.2 2 C2 C_2 2 1 C.3 8 -Cbl 6 2 2 3 C C2 3 C 63 C.2 2 C2 C_2 2 1 C.3 9 -C- 6 2 10 27 C C3 4 C 64 C.3 1 C3 C_3 1 1 C.4 10 -N3+ 7 3 32 39 N N3+ 4 N 79 N.4 31 N3 N_3 5 9 N.4 11 -N3 7 3 26 8 N N3 3 N 73 N.3 5 N3 N_3 6 10 N.4 12 -N2 7 2 25 9 N NPL3 2 N 72 N.2 19 N2 N_2 8 8 N.3 13 -Npl 7 2 25 9 N NPL3 3 N 72 N.pl3 19 N2 N_2 9 8 N.3 14 -Naz 7 2 25 37 N N2 0 N 72 N.2 6 N2 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Wegner -// Version: $Revision: 1.1.1.1 $ -// $Date: 2004/12/06 15:32:05 $ -// $Author: wegner $ -// -// Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany -// -// This program is free software; you can redistribute it and/or modify -// it under the terms of the GNU General Public License as published by -// the Free Software Foundation version 2 of the License. -// -// This program is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -// GNU General Public License for more details. -/////////////////////////////////////////////////////////////////////////////// - -#include -#include -#include - -using namespace std; - -int main(int argc,char **argv) -{ - char *buffer = new char[10000]; - char *title = new char[1000]; - int i,n; - char ch; - int line=1; - int end; - char *attribute = "MOL_TITLE"; - - if(argc>1)attribute=argv[1]; - for(;;) - { - end=0; - for( i = 0; ((ch = getchar()) != EOF) && (ch != '\n'); i++ ) - { - buffer[i] = (char)ch; - if(i<4) - { - end|=(end<<1); - if(ch=='$')end|=1; - } - } - - if(end!=15) - { - buffer[i] = '\0'; - //printf( "line %i:%s\n",line, buffer ); - printf( "%s\n", buffer ); - } - if(line==1) - { - for( n = 0; n<=i; n++ ) - { - title[n]=buffer[n]; - } - } - - if(ch==EOF || end==15) - { - break; - } - - line++; - } - - //write simple data entry - printf( "> <%s>\n",attribute); - printf( "%s\n", title ); - printf( "\n$$$$" ); -} diff --git a/java/log4j.jar b/java/log4j.jar deleted file mode 100644 index be4a917..0000000 Binary files a/java/log4j.jar and /dev/null differ diff --git a/java/log4j.properties b/java/log4j.properties deleted file mode 100644 index 96ea876..0000000 --- a/java/log4j.properties +++ /dev/null @@ -1,104 +0,0 @@ -############################################################################## -# Copyright OELIB: OpenEye Scientific Software, Santa Fe, -# U.S.A., 1999,2000,2001 -# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of -# Tuebingen, Germany, 2001,2002,2003,2004,2005 -# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, -# 2003,2004,2005 -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation version 2 of the License. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -############################################################################## -############################################################################## -# Set root defaults and appenders -############################################################################## -log4j.rootCategory=INFO, A1 - -############################################################################## -# Configure verbosity of specific packages/classes -############################################################################## -log4j.category.joelib=INFO - -log4j.category.joelib=INFO -log4j.category.joelib2.algo.contribution.GCPredictor=ERROR -log4j.category.joelib2.data.BasicAromaticityTyper=INFO -log4j.category.joelib2.data.BasicTransformationRulesHolder=INFO -log4j.category.joelib2.data.BasicAtomTyper=INFO -log4j.category.joelib2.feature.data.MoleculesDescriptorMatrix=ERROR -log4j.category.joelib2.feature.ResultFactory=INFO -log4j.category.joelib2.feature.SMARTSCounter=ERROR -log4j.category.joelib2.feature.result.DynamicArrayResult=INFO -log4j.category.joelib2.feature.types.bondlabel.BondKekuleType=ERROR -log4j.category.joelib2.feature.types.Autocorrelation=ERROR -log4j.category.joelib2.feature.types.ElectrotopologicalState=INFO -log4j.category.joelib2.feature.types.IntrinsicState=INFO -log4j.category.joelib2.feature.types.GeometricalDiameter=ERROR -log4j.category.joelib2.feature.types.GeometricalRadius=ERROR -log4j.category.joelib2.feature.types.SSKey3DS=ERROR -log4j.category.joelib2.feature.types.TopologicalDiameter=ERROR -log4j.category.joelib2.feature.types.TopologicalRadius=ERROR -log4j.category.joelib2.io.JOEFileFormat=INFO -log4j.category.joelib2.io.types.ChemicalMarkupLanguage=INFO -log4j.category.joelib2.io.types.ClearTextFormat=INFO -log4j.category.joelib2.io.types.cml.CMLCoreModule=INFO -log4j.category.joelib2.io.types.cml.MoleculeFileCDO=INFO -log4j.category.joelib2.io.types.MDLSD=INFO 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a/java/resources/logP.mr.txt +++ /dev/null @@ -1 +0,0 @@ -Oc1ccccc1OC 1.40(logP) 34.66(mr) diff --git a/java/resources/multiple.mol b/java/resources/multiple.mol deleted file mode 100644 index d31160e..0000000 --- a/java/resources/multiple.mol +++ /dev/null @@ -1,296 +0,0 @@ -test1 - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 26 27 0 0 0 0 0 0 0 0 1 V2000 - 10.8454 -4.8462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -4.2790 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8454 -6.5298 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 9.0538 -8.2222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -3.1268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -7.1328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -9.3566 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 7.8475 -8.2222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8454 -9.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.2803 -7.1328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0649 -7.6730 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 - 8.4507 -2.5775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 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Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 12.0388 -5.3472 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 4 7 1 0 0 0 0 - 5 1 2 0 0 0 0 - 6 5 1 0 0 0 0 - 7 3 1 0 0 0 0 - 8 2 1 0 0 0 0 - 9 4 1 0 0 0 0 - 10 3 1 0 0 0 0 - 11 9 2 0 0 0 0 - 12 6 1 0 0 0 0 - 13 8 2 0 0 0 0 - 14 12 2 0 0 0 0 - 15 9 1 0 0 0 0 - 16 11 1 0 0 0 0 - 8 10 1 0 0 0 0 - 6 4 2 0 0 0 0 - 14 11 1 0 0 0 0 -M END -> (1111) -1111 - -> (1111) -123 - -$$$$ -test3 - TestMolecule 3 - - 26 27 0 0 0 0 0 0 0 0 1 V2000 - 8.0184 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2232 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8059 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -4.7206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5858 -7.0083 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8059 -4.1181 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2232 -8.7240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5858 -5.8568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.3810 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5858 -4.7206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8059 -2.9514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -5.8568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.6481 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -9.3111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -9.3111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.3810 -5.2620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1837 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.3810 -4.1181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -2.4024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.6481 -5.2620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8759 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -10.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -10.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8759 -5.8568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2232 -11.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 4 1 1 0 0 0 0 - 5 2 1 0 0 0 0 - 6 3 1 0 0 0 0 - 7 4 1 0 0 0 0 - 8 2 1 0 0 0 0 - 9 6 1 0 0 0 0 - 10 6 1 0 0 0 0 - 11 7 1 0 0 0 0 - 12 7 1 0 0 0 0 - 13 5 2 0 0 0 0 - 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0 0 0 0 0 0 0 0 0 - 1.8430 5.2920 -1.0750 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.5800 -1.4250 0.3370 H 0 0 0 0 0 0 0 0 0 0 0 0 - -1.9900 1.5400 -0.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 - -1.3480 2.8750 0.1250 H 0 0 0 0 0 0 0 0 0 0 0 0 - -0.8910 2.7360 -1.5900 H 0 0 0 0 0 0 0 0 0 0 0 0 - -0.8520 -1.9540 -0.2790 H 0 0 0 0 0 0 0 0 0 0 0 0 - -1.9570 -0.6600 0.2420 H 0 0 0 0 0 0 0 0 0 0 0 0 - -1.4930 -0.7990 -1.4710 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.8590 6.8280 0.0100 H 0 0 0 0 0 0 0 0 0 0 0 0 - 3.3800 5.3780 1.9280 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.6530 3.0260 1.9290 H 0 0 0 0 0 0 0 0 0 0 0 0 - 0.8870 3.5810 -1.9260 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.6180 5.9310 -1.9170 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 7 1 0 0 0 0 - 1 2 4 0 0 0 0 - 1 5 4 0 0 0 0 - 2 8 1 0 0 0 0 - 2 3 4 0 0 0 0 - 3 15 1 0 0 0 0 - 3 4 4 0 0 0 0 - 4 5 4 0 0 0 0 - 4 6 2 0 0 0 0 - 5 12 4 0 0 0 0 - 7 17 1 0 0 0 0 - 7 16 1 0 0 0 0 - 7 18 1 0 0 0 0 - 8 20 1 0 0 0 0 - 8 19 1 0 0 0 0 - 8 21 1 0 0 0 0 - 9 22 1 0 0 0 0 - 9 10 4 0 0 0 0 - 9 14 4 0 0 0 0 - 10 23 1 0 0 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end of file diff --git a/java/resources/patty.txt b/java/resources/patty.txt deleted file mode 100644 index 73e1ee4..0000000 --- a/java/resources/patty.txt +++ /dev/null @@ -1,4 +0,0 @@ -O=C hbacceptor1 -a aromat -c1ccccc1 benzol -[Cl;Br;I] hal \ No newline at end of file diff --git a/java/resources/psa.txt b/java/resources/psa.txt deleted file mode 100644 index c3761cc..0000000 --- a/java/resources/psa.txt +++ /dev/null @@ -1,20 +0,0 @@ -COCCc1ccc(OCC(O)CNC(C)C)cc1 metoprolol 102 50.72 -O=C3CN=C(c1ccccc1)c2cc(Cl)ccc2N3 nordiazepam 99 41.46 -CN3C(=O)CN=C(c1ccccc1)c2cc(Cl)ccc23 diazepam 97 32.67 -C=CCOc1ccccc1OCC(O)CNC(C)C oxprenolol 97 50.72 -Cc2cc(=O)n(c1ccccc1)n2C phenazone 97 26.94 -O=C3Nc1ccc(Cl)cc1C(c2ccccc2)=NC3O oxazepam 97 61.69 -C=CCc1ccccc1OCC(O)CNC(C)C alprenolol 96 41.49 -CC(=O)Nc1ccc(OCC(O)CNC(C)C)cc1 practolol 95 70.59 -CC(C)NCC(O)COc1cccc2[nH]ccc12 pindolol 92 57.28 -O=C(O)c4cn(C1CC1)c3cc(N2CCNCC2)c(F)cc3c4=O ciprofloxacin 69 74.57 -Cc1ccccc1N3C(=O)c2cc(S(N)(=O)=O)c(Cl)cc2NC3C metolazone 64 92.5 (+8.38 missed [S](-*)(-*)(=*)=*) -NCC1CCC(C(=O)O)CC1 tranexamic acid 55 63.32 -CC(C)NCC(O)COc1ccc(CC(N)=O)cc1 atenolol 54 84.58 -CCN1CCCC1CNC(=O)c2cc(S(N)(=O)=O)ccc2OC sulpiride 36 101.73 (+8.38 missed [S](-*)(-*)(=*)=*) -OCC(O)C(O)C(O)C(O)CO mannitol 26 121.37 -O=C(O)P(=O)(O)O foscarnet 17 94.83 (+9,81 missed [P](-*)(-*)(=*)=*) -O=C(O)c3cc(N=Nc2ccc(S(=O)(=O)Nc1ccccn1)cc2)ccc3O sulfasalazine 12 141.32 (+8.38 missed [S](-*)(-*)(=*)=*) -O=C(O)c2cc(N=Nc1ccc(O)c(C(=O)O)c1)ccc2O olsalazine 2.3 139.78 -O=C(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO lactulose 0.6 197.36 -OCC3OC(OCC2OC(OC1(CO)OC(CO)C(O)C1O)C(O)C(O)C2O)C(O)C(O)C3O raffinose 0.3 268.68 diff --git a/java/resources/renumbered.sdf b/java/resources/renumbered.sdf deleted file mode 100644 index 32a9738..0000000 --- a/java/resources/renumbered.sdf +++ /dev/null @@ -1,120 +0,0 @@ -phenanzone.mol2 - -ISIS- 3D -null - 26 27 0 0 0 0 0 0 0 0 1 V2000 - 0.0250 1.3500 -0.3100 N 0 0 0 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0 0 0 0 0 0 0 - 1.8100 4.7580 -1.4750 H 0 0 0 0 0 0 0 0 0 0 0 0 - 0.0550 -3.8510 -0.0190 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 4 0 0 0 0 - 1 4 4 0 0 0 0 - 1 3 4 0 0 0 0 - 2 5 4 0 0 0 0 - 2 6 4 0 0 0 0 - 3 8 1 0 0 0 0 - 3 7 4 0 0 0 0 - 4 9 4 0 0 0 0 - 4 10 2 0 0 0 0 - 5 15 1 0 0 0 0 - 5 11 4 0 0 0 0 - 6 16 1 0 0 0 0 - 6 12 4 0 0 0 0 - 7 13 1 0 0 0 0 - 7 9 4 0 0 0 0 - 8 18 1 0 0 0 0 - 8 17 1 0 0 0 0 - 8 19 1 0 0 0 0 - 9 20 1 0 0 0 0 - 11 21 1 0 0 0 0 - 11 14 4 0 0 0 0 - 12 22 1 0 0 0 0 - 12 14 4 0 0 0 0 - 13 24 1 0 0 0 0 - 13 23 1 0 0 0 0 - 13 25 1 0 0 0 0 - 14 26 1 0 0 0 0 -M END - -$$$$ \ No newline at end of file diff --git a/java/resources/smartsEvaluation/2-phenylnaphtho-oxazole.mol b/java/resources/smartsEvaluation/2-phenylnaphtho-oxazole.mol deleted file mode 100644 index 0aca844..0000000 --- a/java/resources/smartsEvaluation/2-phenylnaphtho-oxazole.mol +++ /dev/null @@ -1,46 +0,0 @@ -2-phenylnaphtho[1,2-d][1,3]oxazole - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 19 22 0 0 0 0 0 0 0 0 1 V2000 - 27.8297 -11.1277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 27.8297 -12.5046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 26.6372 -13.1931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 25.4448 -12.5046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 25.4448 -11.1277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 26.6372 -10.4392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.2523 -13.1931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 22.9943 -12.6330 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 22.0730 -13.6563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 22.7615 -14.8488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 22.0730 -16.0413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.6960 -16.0413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.0075 -14.8488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.6306 -14.8488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.9421 -13.6563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.6306 -12.4638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.0075 -12.4638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.6960 -13.6563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.1083 -14.5625 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 1 6 2 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 2 0 0 0 0 - 4 7 1 0 0 0 0 - 5 6 1 0 0 0 0 - 7 8 2 0 0 0 0 - 7 19 1 0 0 0 0 - 8 9 1 0 0 0 0 - 9 10 2 0 0 0 0 - 9 18 1 0 0 0 0 - 10 11 1 0 0 0 0 - 10 19 1 0 0 0 0 - 11 12 2 0 0 0 0 - 12 13 1 0 0 0 0 - 13 14 2 0 0 0 0 - 13 18 1 0 0 0 0 - 14 15 1 0 0 0 0 - 15 16 2 0 0 0 0 - 16 17 1 0 0 0 0 - 17 18 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/2H-chromen-2-one.mol b/java/resources/smartsEvaluation/2H-chromen-2-one.mol deleted file mode 100644 index 5043954..0000000 --- a/java/resources/smartsEvaluation/2H-chromen-2-one.mol +++ /dev/null @@ -1,28 +0,0 @@ -2H-chromen-2-one - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 11 12 0 0 0 0 0 0 0 0 1 V2000 - 15.3484 -4.8980 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 16.0134 -3.7462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0134 -6.0498 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 17.3434 -3.7462 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 15.3484 -7.2016 0.0000 O 0 0 0 1 0 0 1 0 0 0 0 0 - 17.3434 -6.0498 0.0000 O 0 0 0 1 0 0 1 0 0 0 0 0 - 18.0084 -4.8980 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 18.0084 -2.5943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.3384 -4.8980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.3384 -2.5943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.0034 -3.7462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 2 0 0 0 0 - 1 3 1 0 0 0 0 - 2 4 1 0 0 0 0 - 3 5 2 0 0 0 0 - 3 6 1 0 0 0 0 - 4 7 2 0 0 0 0 - 4 8 1 0 0 0 0 - 6 7 1 0 0 0 0 - 7 9 1 0 0 0 0 - 8 10 2 0 0 0 0 - 9 11 2 0 0 0 0 - 10 11 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/3-hydroxy-4-iminocyclohexa-2,5-dien-1-one.mol b/java/resources/smartsEvaluation/3-hydroxy-4-iminocyclohexa-2,5-dien-1-one.mol deleted file mode 100644 index df06e7e..0000000 --- a/java/resources/smartsEvaluation/3-hydroxy-4-iminocyclohexa-2,5-dien-1-one.mol +++ /dev/null @@ -1,23 +0,0 @@ -3-hydroxy-4-iminocyclohexa-2,5-dien-1-one - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 9 9 0 0 0 0 0 0 0 0 1 V2000 - 16.6868 -5.8657 -0.4523 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.8457 -4.6103 -0.4926 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.4075 -6.0656 -0.2358 N 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8127 -3.6875 -0.3296 O 0 0 0 0 0 0 0 0 0 0 0 0 - 17.8498 -4.2016 -0.6653 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.6496 -5.1278 -0.7891 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.4670 -6.3600 -0.7451 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.3888 -6.9904 -0.5576 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.3679 -6.8545 -1.6433 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 2 0 0 0 0 - 4 2 1 0 0 0 0 - 5 2 2 0 0 0 0 - 6 5 1 0 0 0 0 - 7 6 1 0 0 0 0 - 8 7 2 0 0 0 0 - 8 1 1 0 0 0 0 - 9 6 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/4-(methylimino)cyclohexa-2,5-dien-1-one.mol b/java/resources/smartsEvaluation/4-(methylimino)cyclohexa-2,5-dien-1-one.mol deleted file mode 100644 index 2acceac..0000000 --- a/java/resources/smartsEvaluation/4-(methylimino)cyclohexa-2,5-dien-1-one.mol +++ /dev/null @@ -1,23 +0,0 @@ -4-(methylimino)cyclohexa-2,5-dien-1-one - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 9 9 0 0 0 0 0 0 0 0 1 V2000 - 17.0888 -6.8970 -0.2894 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.9513 -5.6389 -0.3235 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8764 -7.3987 -0.3337 N 0 0 0 0 0 0 0 0 0 0 0 0 - 14.4666 -6.5683 -0.4165 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.8439 -5.0005 -0.2968 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.8479 -5.7083 -0.2352 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.9567 -6.9496 -0.2028 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.0430 -7.8213 -0.2253 C 0 0 0 0 0 0 0 0 0 0 0 0 - 21.0621 -6.9571 -0.6842 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 2 0 0 0 0 - 4 3 1 0 0 0 0 - 5 2 2 0 0 0 0 - 6 5 1 0 0 0 0 - 7 6 1 0 0 0 0 - 8 7 2 0 0 0 0 - 8 1 1 0 0 0 0 - 9 6 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/4-chlorpyrimidin.mol b/java/resources/smartsEvaluation/4-chlorpyrimidin.mol deleted file mode 100644 index a1f088f..0000000 --- a/java/resources/smartsEvaluation/4-chlorpyrimidin.mol +++ /dev/null @@ -1,19 +0,0 @@ -4-chlorpyrimidin - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 7 7 0 0 0 0 0 0 0 0 1 V2000 - 12.4065 -4.8406 0.4940 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.4533 -6.0573 0.4671 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4366 -4.2077 0.3623 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.4991 -4.7834 0.2069 N 0 0 0 0 0 0 0 0 0 0 0 0 - 14.5549 -6.0012 0.1835 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.5194 -6.6277 0.3136 N 0 0 0 0 0 0 0 0 0 0 0 0 - 13.3923 -2.6943 0.3907 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 2 0 0 0 0 - 3 1 1 0 0 0 0 - 4 3 2 0 0 0 0 - 5 4 1 0 0 0 0 - 6 5 2 0 0 0 0 - 6 2 1 0 0 0 0 - 7 3 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/4-chlorpyrimidin_h.mol b/java/resources/smartsEvaluation/4-chlorpyrimidin_h.mol deleted file mode 100644 index 2473f33..0000000 --- a/java/resources/smartsEvaluation/4-chlorpyrimidin_h.mol +++ /dev/null @@ -1,25 +0,0 @@ -4-chlorpyrimidin_h - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 10 10 0 0 0 0 0 0 0 0 1 V2000 - 14.5058 -5.0464 0.3676 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.5546 -6.4262 0.3240 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.6762 -4.3264 0.2263 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.8812 -4.9799 0.0436 N 0 0 0 0 0 0 0 0 0 0 0 0 - 16.9301 -6.3597 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.7596 -7.0792 0.1412 N 0 0 0 0 0 0 0 0 0 0 0 0 - 15.6340 -2.6078 0.2781 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 13.6340 -4.5747 0.4998 H 0 0 0 0 0 0 0 0 0 0 0 0 - 13.7123 -6.9556 0.4253 O 0 0 0 0 0 0 0 0 0 0 0 0 - 17.8018 -6.8316 -0.1321 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 2 0 0 0 0 - 3 1 1 0 0 0 0 - 4 3 2 0 0 0 0 - 5 4 1 0 0 0 0 - 6 5 2 0 0 0 0 - 6 2 1 0 0 0 0 - 7 3 1 0 0 0 0 - 8 1 1 0 0 0 0 - 9 2 1 0 0 0 0 - 10 5 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane.mol b/java/resources/smartsEvaluation/5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane.mol deleted file mode 100644 index 5a0d35f..0000000 --- a/java/resources/smartsEvaluation/5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane.mol +++ /dev/null @@ -1,49 +0,0 @@ -5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 21 23 0 0 0 0 0 0 0 0 1 V2000 - 14.4588 -9.9742 0.1275 O 0 0 0 0 0 0 0 0 0 0 0 0 - 14.0084 -9.0071 0.1648 S 0 0 0 0 0 0 0 0 0 0 0 0 - 14.9065 -7.4627 -0.3333 O 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8063 -7.8254 -0.5992 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.6675 -7.1375 -0.9800 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.1948 -8.7445 -0.6210 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7874 -6.5911 -1.4328 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.8956 -4.9493 -1.3257 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.6846 -4.3295 -1.6733 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.3954 -3.9491 -1.2754 N 0 0 0 0 0 0 0 0 0 0 0 0 - 18.0849 -5.4216 -1.6781 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.8313 -5.8972 -1.8774 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.9739 -4.9793 -2.0385 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.5343 -4.5242 -0.5636 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4972 -4.7288 -0.1811 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.6782 -3.1645 -0.7588 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.8767 -2.5753 -0.4658 P 0 0 0 0 0 0 0 0 0 0 0 0 - 12.5866 -3.8311 0.0233 N 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8387 -2.9265 -0.0507 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.7675 -3.8872 -1.9869 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.3640 -11.6660 0.1275 H 0 0 0 0 0 0 0 0 0 0 0 0 - 3 2 1 0 0 0 0 - 4 3 1 0 0 0 0 - 5 4 1 0 0 0 0 - 6 4 1 0 0 0 0 - 7 5 1 0 0 0 0 - 8 5 1 0 0 0 0 - 9 8 1 0 0 0 0 - 10 8 1 0 0 0 0 - 10 9 1 0 0 0 0 - 11 7 1 0 0 0 0 - 12 7 1 0 0 0 0 - 13 12 1 0 0 0 0 - 13 11 1 0 0 0 0 - 14 5 1 0 0 0 0 - 15 14 1 0 0 0 0 - 16 14 1 0 0 0 0 - 17 16 1 0 0 0 0 - 18 15 1 0 0 0 0 - 19 18 1 0 0 0 0 - 19 17 1 0 0 0 0 - 1 2 1 0 0 0 0 - 20 9 1 0 0 0 0 - 21 1 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/5-cyclobutyl-2-cycloheptylphosphinane.mol b/java/resources/smartsEvaluation/5-cyclobutyl-2-cycloheptylphosphinane.mol deleted file mode 100644 index c23c0da..0000000 --- a/java/resources/smartsEvaluation/5-cyclobutyl-2-cycloheptylphosphinane.mol +++ /dev/null @@ -1,41 +0,0 @@ -5-cyclobutyl-2-cycloheptylphosphinane - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 17 19 0 0 0 0 0 0 0 0 1 V2000 - 11.5601 -7.2473 -0.7307 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.9182 -5.7812 -0.8202 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8945 -6.3064 -0.7134 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.0579 -5.1632 -0.7910 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.1518 -6.8939 -0.2466 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.9384 -7.7871 -0.0697 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.1751 -6.6864 -0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.6125 -7.4850 0.2722 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.6013 -8.5627 0.2967 P 0 0 0 0 0 0 0 0 0 0 0 0 - 15.4289 -8.6482 0.5263 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.3401 -9.4580 0.7129 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.3497 -10.0100 0.6071 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0690 -10.3513 1.1261 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.7372 -10.8208 0.6625 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0702 -11.4419 1.4078 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.2826 -11.6494 1.0131 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.1815 -11.8748 1.2967 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 4 3 1 0 0 0 0 - 4 2 1 0 0 0 0 - 5 3 1 0 0 0 0 - 6 5 1 0 0 0 0 - 7 5 1 0 0 0 0 - 8 7 1 0 0 0 0 - 9 6 1 0 0 0 0 - 10 9 1 0 0 0 0 - 10 8 1 0 0 0 0 - 11 10 1 0 0 0 0 - 12 11 1 0 0 0 0 - 13 11 1 0 0 0 0 - 14 12 1 0 0 0 0 - 15 13 1 0 0 0 0 - 16 14 1 0 0 0 0 - 17 16 1 0 0 0 0 - 17 15 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/6-iminocyclohexa-1,4-diene-1,3-diol.mol b/java/resources/smartsEvaluation/6-iminocyclohexa-1,4-diene-1,3-diol.mol deleted file mode 100644 index 6f6efa2..0000000 --- a/java/resources/smartsEvaluation/6-iminocyclohexa-1,4-diene-1,3-diol.mol +++ /dev/null @@ -1,23 +0,0 @@ -6-iminocyclohexa-1,4-diene-1,3-diol - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 9 9 0 0 0 0 0 0 0 0 1 V2000 - 16.6868 -5.8657 -0.4523 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.8457 -4.6103 -0.4926 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.4075 -6.0656 -0.2358 N 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8127 -3.6875 -0.3296 O 0 0 0 0 0 0 0 0 0 0 0 0 - 17.8498 -4.2016 -0.6653 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.6496 -5.1278 -0.7891 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.4670 -6.3600 -0.7451 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.3888 -6.9904 -0.5576 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.3679 -6.8545 -1.6433 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 2 0 0 0 0 - 4 2 1 0 0 0 0 - 5 2 2 0 0 0 0 - 6 5 1 0 0 0 0 - 7 6 1 0 0 0 0 - 8 7 2 0 0 0 0 - 8 1 1 0 0 0 0 - 9 6 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-ol.mol b/java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-ol.mol deleted file mode 100644 index dcdd2f5..0000000 --- a/java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-ol.mol +++ /dev/null @@ -1,59 +0,0 @@ -8-amino-3H-phenoxazin-3-ol - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 26 28 0 0 0 0 0 0 0 0 1 V2000 - 16.8415 -3.7720 1.2970 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.1621 -4.9129 0.4191 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.6179 -3.5988 1.7103 N 0 0 0 0 0 0 0 0 0 0 0 0 - 14.5595 -4.5433 1.2954 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.1962 -5.8402 0.1447 O 0 0 0 0 0 0 0 0 0 0 0 0 - 14.8956 -5.6437 0.5182 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.9131 -6.5367 0.1216 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.2428 -4.3348 1.6732 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.2609 -5.2278 1.2743 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.5962 -6.3278 0.5003 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.9197 -5.0165 1.6539 N 0 0 0 0 0 0 0 0 0 0 0 0 - 10.6484 -4.1408 2.2622 H 0 0 0 0 0 0 0 0 0 0 0 0 - 18.3892 -5.0377 -0.1119 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.5065 -4.0278 0.1541 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.1387 -2.9584 1.1825 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.9047 -2.8440 1.7003 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.6402 -4.7288 0.6407 O 0 0 0 0 0 0 0 0 0 0 0 0 - 21.3144 -4.0532 0.7439 H 0 0 0 0 0 0 0 0 0 0 0 0 - 14.1539 -7.3305 -0.4368 H 0 0 0 0 0 0 0 0 0 0 0 0 - 13.0016 -3.5417 2.2326 H 0 0 0 0 0 0 0 0 0 0 0 0 - 11.8866 -6.9719 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0 - 10.0839 -5.5356 1.4752 H 0 0 0 0 0 0 0 0 0 0 0 0 - 18.4680 -5.8534 -0.6849 H 0 0 0 0 0 0 0 0 0 0 0 0 - 19.7493 -3.5846 -0.7088 H 0 0 0 0 0 0 0 0 0 0 0 0 - 19.7634 -2.2697 1.5506 H 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7828 -2.1002 2.3575 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 2 0 0 0 0 - 4 3 1 0 0 0 0 - 5 2 1 0 0 0 0 - 6 5 1 0 0 0 0 - 6 4 1 0 0 0 0 - 7 6 2 0 0 0 0 - 8 4 2 0 0 0 0 - 9 8 1 0 0 0 0 - 10 7 1 0 0 0 0 - 10 9 2 0 0 0 0 - 11 9 1 0 0 0 0 - 12 11 1 0 0 0 0 - 13 2 2 0 0 0 0 - 14 13 1 0 0 0 0 - 15 14 1 0 0 0 0 - 16 15 2 0 0 0 0 - 16 1 1 0 0 0 0 - 17 14 1 0 0 0 0 - 18 17 1 0 0 0 0 - 19 7 1 0 0 0 0 - 20 8 1 0 0 0 0 - 21 10 1 0 0 0 0 - 22 11 1 0 0 0 0 - 23 13 1 0 0 0 0 - 24 14 1 0 0 0 0 - 25 15 1 0 0 0 0 - 26 16 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-one.mol b/java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-one.mol deleted file mode 100644 index 949aa97..0000000 --- a/java/resources/smartsEvaluation/8-amino-3H-phenoxazin-3-one.mol +++ /dev/null @@ -1,41 +0,0 @@ -8-amino-3H-phenoxazin-3-one - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 17 19 0 0 0 0 0 0 0 0 1 V2000 - 16.6868 -5.8657 -0.4523 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.8457 -4.6103 -0.4926 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.4075 -6.0656 -0.2358 N 0 0 0 0 0 0 0 0 0 0 0 0 - 14.2465 -4.9240 -0.0538 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8127 -3.6875 -0.3296 O 0 0 0 0 0 0 0 0 0 0 0 0 - 14.7171 -3.7269 -0.1457 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.8801 -2.9037 -0.0145 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.9789 -4.8871 0.1583 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.3559 -3.8400 0.2511 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.0668 -2.6003 0.1185 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0367 -4.9626 0.4844 N 0 0 0 0 0 0 0 0 0 0 0 0 - 11.1267 -5.7337 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0 - 17.8498 -4.2016 -0.6653 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.6496 -5.1278 -0.7891 C 0 0 0 0 0 0 0 0 0 0 0 0 - 18.4670 -6.3600 -0.7451 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.3888 -6.9904 -0.5576 C 0 0 0 0 0 0 0 0 0 0 0 0 - 20.3679 -6.8545 -1.6433 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 2 0 0 0 0 - 4 3 1 0 0 0 0 - 5 2 1 0 0 0 0 - 6 5 1 0 0 0 0 - 6 4 1 0 0 0 0 - 7 6 2 0 0 0 0 - 8 4 2 0 0 0 0 - 9 8 1 0 0 0 0 - 10 7 1 0 0 0 0 - 10 9 2 0 0 0 0 - 11 9 1 0 0 0 0 - 12 11 1 0 0 0 0 - 13 2 2 0 0 0 0 - 14 13 1 0 0 0 0 - 15 14 1 0 0 0 0 - 16 15 2 0 0 0 0 - 16 1 1 0 0 0 0 - 17 14 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/9,10-dihydroxyphenanthrene.mol b/java/resources/smartsEvaluation/9,10-dihydroxyphenanthrene.mol deleted file mode 100644 index a63ee84..0000000 --- a/java/resources/smartsEvaluation/9,10-dihydroxyphenanthrene.mol +++ /dev/null @@ -1,39 +0,0 @@ -9,10-dihydroxyphenanthrene - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 16 18 0 0 0 0 0 0 0 0 1 V2000 - 30.1198 -12.7631 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 23.0621 -16.8379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 23.0621 -24.9874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 30.1198 -29.0622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0043 -29.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0043 -37.2118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9466 -41.2866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.8889 -37.2118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.8889 -29.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9466 -24.9874 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9466 -16.8379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.8889 -12.7631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.8889 -4.6136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9466 -0.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0043 -4.6135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.0043 -12.7631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 2 16 1 0 0 0 0 - 3 4 1 0 0 0 0 - 3 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 5 10 1 0 0 0 0 - 6 7 1 0 0 0 0 - 7 8 2 0 0 0 0 - 8 9 1 0 0 0 0 - 9 10 2 0 0 0 0 - 10 11 1 0 0 0 0 - 11 12 2 0 0 0 0 - 11 16 1 0 0 0 0 - 12 13 1 0 0 0 0 - 13 14 2 0 0 0 0 - 14 15 1 0 0 0 0 - 15 16 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/TEST_1.mol b/java/resources/smartsEvaluation/TEST_1.mol deleted file mode 100644 index 64363b1..0000000 --- a/java/resources/smartsEvaluation/TEST_1.mol +++ /dev/null @@ -1,31 +0,0 @@ -TEST_1 - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 13 13 0 0 0 0 0 0 0 0 1 V2000 - 3.9852 0.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1152 0.7487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.2552 0.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.2552 -0.7513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.3884 -1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.5199 -0.7474 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 1.3864 -2.2448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1152 -1.2513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9852 -0.7513 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8507 0.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8503 1.7444 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9805 2.2448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 5.7205 0.2492 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 4 0 0 0 0 - 9 1 4 0 0 0 0 - 1 10 1 0 0 0 0 - 2 3 4 0 0 0 0 - 3 4 4 0 0 0 0 - 4 5 1 0 0 0 0 - 4 8 4 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 2 0 0 0 0 - 8 9 4 0 0 0 0 - 10 11 1 0 0 0 0 - 10 13 2 0 0 0 0 - 11 12 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/TEST_1_H.mol b/java/resources/smartsEvaluation/TEST_1_H.mol deleted file mode 100644 index 4c514f4..0000000 --- a/java/resources/smartsEvaluation/TEST_1_H.mol +++ /dev/null @@ -1,40 +0,0 @@ -TEST_1_H - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 17 17 0 0 0 0 0 0 0 0 1 V2000 - 3.9852 0.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1152 0.7487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.2552 0.2487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.2552 -0.7513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.3884 -1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.5199 -0.7474 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 - 1.3864 -2.2448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1152 -1.2513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9852 -0.7513 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8507 0.7496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8503 1.7444 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9805 2.2448 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 - 5.7205 0.2492 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1125 1.8102 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.3351 0.7781 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1125 -2.3128 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 5.7115 2.2427 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 4 0 0 0 0 - 9 1 4 0 0 0 0 - 1 10 1 0 0 0 0 - 2 3 4 0 0 0 0 - 2 14 1 0 0 0 0 - 3 4 4 0 0 0 0 - 3 15 1 0 0 0 0 - 4 5 1 0 0 0 0 - 4 8 4 0 0 0 0 - 5 6 1 0 0 0 0 - 5 7 2 0 0 0 0 - 8 9 4 0 0 0 0 - 8 16 1 0 0 0 0 - 10 11 1 0 0 0 0 - 10 13 2 0 0 0 0 - 11 12 1 0 0 0 0 - 11 17 1 0 0 0 0 -M END -$$$$ diff --git a/java/resources/smartsEvaluation/TEST_2.mol b/java/resources/smartsEvaluation/TEST_2.mol deleted file mode 100644 index b4f0bb5..0000000 --- a/java/resources/smartsEvaluation/TEST_2.mol +++ /dev/null @@ -1,36 +0,0 @@ -TEST_2 - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 15 16 0 0 0 0 0 0 0 0999V2000 - 14.0242 -6.4270 0.0000 P 0 0 0 1 0 0 1 0 0 0 0 0 - 14.0242 -5.1384 0.0000 O 0 0 0 1 0 0 1 0 0 0 0 0 - 12.7356 -6.4270 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 14.0242 -7.7156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 15.3129 -6.4270 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 15.9572 -5.3110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.9572 -7.5430 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 17.2458 -5.3110 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 15.3129 -8.6590 0.0000 O 0 0 0 1 0 0 1 0 0 0 0 0 - 17.2458 -7.5430 0.0000 O 0 0 0 1 0 0 1 0 0 0 0 0 - 17.8901 -6.4270 0.0000 C 0 0 0 1 0 0 1 0 0 0 0 0 - 17.8901 -4.1950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.1788 -6.4270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.1788 -4.1950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.8231 -5.3110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 2 0 0 0 0 - 1 3 1 0 0 0 0 - 1 4 1 0 0 0 0 - 1 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 5 7 1 0 0 0 0 - 6 8 1 0 0 0 0 - 7 9 2 0 0 0 0 - 7 10 1 0 0 0 0 - 8 11 2 0 0 0 0 - 8 12 1 0 0 0 0 - 10 11 1 0 0 0 0 - 11 13 1 0 0 0 0 - 12 14 2 0 0 0 0 - 13 15 2 0 0 0 0 - 14 15 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/TEST_3.mol b/java/resources/smartsEvaluation/TEST_3.mol deleted file mode 100644 index 8ae9ba8..0000000 --- a/java/resources/smartsEvaluation/TEST_3.mol +++ /dev/null @@ -1,41 +0,0 @@ -TEST_3 - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 17 19 0 0 0 0 0 0 0 0999V2000 - 0.0021 -0.0041 0.0000 O 0 0 0 1 0 0 0 0 0 0 0 0 - -0.0144 1.2129 0.0000 C 0 0 0 1 0 0 0 0 0 0 0 0 - 1.2363 1.9914 0.0000 C 0 0 0 1 0 0 0 0 0 0 0 0 - -1.1838 1.8973 0.0000 O 0 0 0 1 0 0 0 0 0 0 0 0 - 1.1895 3.2632 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - 2.4979 1.4237 0.0000 C 0 0 0 1 0 0 0 0 0 0 0 0 - -1.2660 3.0272 0.0000 C 0 0 0 1 0 0 0 0 0 0 0 0 - -0.0979 3.7491 0.0000 C 0 0 0 1 0 0 0 0 0 0 0 0 - 2.6117 1.1165 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - 3.5742 1.1891 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - -2.4855 3.4804 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - -0.1779 4.9167 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - 3.7890 0.5876 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - 4.7464 0.6598 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - -2.5381 4.6346 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - -1.3930 5.3460 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - 4.8552 0.3624 0.0000 C 0 0 0 2 0 0 0 0 0 0 0 0 - 1 2 2 0 0 0 0 - 2 3 1 0 0 0 0 - 2 4 1 0 0 0 0 - 3 5 2 0 0 0 0 - 3 6 1 0 0 0 0 - 4 7 1 0 0 0 0 - 5 8 1 0 0 0 0 - 6 9 4 0 0 0 0 - 6 10 4 0 0 0 0 - 7 11 4 0 0 0 0 - 7 8 4 0 0 0 0 - 8 12 4 0 0 0 0 - 9 13 4 0 0 0 0 - 10 14 4 0 0 0 0 - 11 15 4 0 0 0 0 - 12 16 4 0 0 0 0 - 13 17 4 0 0 0 0 - 14 17 4 0 0 0 0 - 15 16 4 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/ab_unsat_carbonyl.mol b/java/resources/smartsEvaluation/ab_unsat_carbonyl.mol deleted file mode 100644 index 67ab7fd..0000000 --- a/java/resources/smartsEvaluation/ab_unsat_carbonyl.mol +++ /dev/null @@ -1,16 +0,0 @@ -ab_unsat_carbonyl - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 6 5 0 0 0 0 0 0 0 0 1 V2000 - -0.0180 1.0970 -0.0040 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.1070 1.7400 0.2500 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.2490 3.1690 0.4210 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.2890 3.9340 0.3380 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2.6340 3.7420 0.7120 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.3500 1.7460 -0.1600 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 2 0 0 0 0 - 1 6 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 5 1 0 0 0 0 - 3 4 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/ab_unsat_carbonyl_h.mol b/java/resources/smartsEvaluation/ab_unsat_carbonyl_h.mol deleted file mode 100644 index 05db536..0000000 --- a/java/resources/smartsEvaluation/ab_unsat_carbonyl_h.mol +++ /dev/null @@ -1,32 +0,0 @@ -ab_unsat_carbonyl_h - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 14 13 0 0 0 0 0 0 0 0 1 V2000 - 15.0105 -5.3202 0.2014 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.1808 -4.7218 0.4759 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.2843 -3.2566 0.5938 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.2980 -2.5681 0.4621 O 0 0 0 0 0 0 0 0 0 0 0 0 - 17.6207 -2.6145 0.8782 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.7424 -4.5178 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.0800 -6.3164 0.1494 H 0 0 0 0 0 0 0 0 0 0 0 0 - 16.9519 -5.3483 0.5892 H 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7554 -2.5498 1.8670 H 0 0 0 0 0 0 0 0 0 0 0 0 - 17.6417 -1.6981 0.4783 H 0 0 0 0 0 0 0 0 0 0 0 0 - 18.3492 -3.1709 0.4783 H 0 0 0 0 0 0 0 0 0 0 0 0 - 13.3575 -4.2743 0.8903 H 0 0 0 0 0 0 0 0 0 0 0 0 - 13.0796 -5.0652 -0.5111 H 0 0 0 0 0 0 0 0 0 0 0 0 - 13.9533 -3.6845 -0.5111 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 2 0 0 0 0 - 1 6 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 5 1 0 0 0 0 - 3 4 2 0 0 0 0 - 7 1 1 0 0 0 0 - 8 2 1 0 0 0 0 - 9 5 1 0 0 0 0 - 10 5 1 0 0 0 0 - 11 5 1 0 0 0 0 - 12 6 1 0 0 0 0 - 13 6 1 0 0 0 0 - 14 6 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/actinides.mol b/java/resources/smartsEvaluation/actinides.mol deleted file mode 100644 index a92d50f..0000000 --- a/java/resources/smartsEvaluation/actinides.mol +++ /dev/null @@ -1,53 +0,0 @@ -actinides - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 21 26 0 0 0 0 0 0 0 0 2 V2000 - 17.7518 -1.0541 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 17.8648 -3.2578 0.0000 Np 0 0 0 0 0 0 0 0 0 0 0 0 - 10.9341 -3.4481 0.0000 Ac 0 0 0 0 0 0 0 0 0 0 0 0 - 10.9341 -4.5662 0.0000 Am 0 0 0 0 0 0 0 0 0 0 0 0 - 11.1165 -5.6922 0.0000 Md 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8056 -5.6922 0.0000 No 0 5 0 0 0 0 0 0 0 0 0 0 - 12.8056 -4.5662 0.0000 Cm 0 5 0 0 0 0 0 0 0 0 0 0 - 12.9959 -3.4481 0.0000 Th 0 5 0 0 0 0 0 0 0 0 0 0 - 14.6770 -3.4481 0.0000 Pa 0 0 0 0 0 0 0 0 0 0 0 0 - 14.8673 -4.5662 0.0000 Bk 0 5 0 0 0 0 0 0 0 0 0 0 - 14.8673 -5.5099 0.0000 Lr 0 0 0 0 0 0 0 0 0 0 0 0 - 16.3660 -3.4481 0.0000 U 0 0 0 0 0 0 0 0 0 0 0 0 - 16.1757 -4.3838 0.0000 Cf 0 0 0 0 0 0 0 0 0 0 0 0 - 18.0472 -4.3838 0.0000 Es 0 0 0 0 0 0 0 0 0 0 0 0 - 19.5459 -3.0675 0.0000 Pu 0 0 0 0 0 0 0 0 0 0 0 0 - 19.7363 -4.3838 0.0000 Fm 0 0 0 0 0 0 0 0 0 0 0 0 - 9.5532 -2.5937 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 20.7043 -1.7954 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 20.9759 -5.2509 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 14.8673 -1.7954 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 15.3854 -7.3449 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 4 7 1 0 0 0 0 - 3 8 1 0 0 0 0 - 8 7 1 0 0 0 0 - 7 6 1 0 0 0 0 - 8 9 1 0 0 0 0 - 7 10 1 0 0 0 0 - 6 11 1 0 0 0 0 - 10 11 1 0 0 0 0 - 9 12 1 0 0 0 0 - 10 13 1 0 0 0 0 - 9 10 1 0 0 0 0 - 12 13 1 0 0 0 0 - 13 14 1 0 0 0 0 - 2 14 1 0 0 0 0 - 2 15 1 0 0 0 0 - 14 16 1 0 0 0 0 - 15 16 1 0 0 0 0 - 17 3 1 0 0 0 0 - 18 15 1 0 0 0 0 - 19 16 1 0 0 0 0 - 20 9 1 0 0 0 0 - 21 11 1 0 0 0 0 -M CHG 4 6 -1 7 -1 8 -1 10 -1 -M END diff --git a/java/resources/smartsEvaluation/alkali_elements.mol b/java/resources/smartsEvaluation/alkali_elements.mol deleted file mode 100644 index ea0c7ea..0000000 --- a/java/resources/smartsEvaluation/alkali_elements.mol +++ /dev/null @@ -1,17 +0,0 @@ -alkali_elements - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 6 5 0 0 0 0 0 0 0 0 2 V2000 - 4.7880 -3.8887 0.0000 Li 0 0 0 0 0 0 0 0 0 0 0 0 - 6.5867 -3.5847 0.0000 Na 0 5 0 0 0 0 0 0 0 0 0 0 - 8.9807 -3.5847 0.0000 K 0 5 0 0 0 0 0 0 0 0 0 0 - 11.9700 -3.5847 0.0000 Rb 0 5 0 0 0 0 0 0 0 0 0 0 - 14.9593 -3.8887 0.0000 Cs 0 5 0 0 0 0 0 0 0 0 0 0 - 17.0493 -3.8887 0.0000 Fr 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 - 5 6 1 0 0 0 0 -M CHG 4 2 -1 3 -1 4 -1 5 -1 -M END diff --git a/java/resources/smartsEvaluation/boron_group.mol b/java/resources/smartsEvaluation/boron_group.mol deleted file mode 100644 index 482e7a7..0000000 --- a/java/resources/smartsEvaluation/boron_group.mol +++ /dev/null @@ -1,15 +0,0 @@ -boron_group - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 5 4 0 0 0 0 0 0 0 0 2 V2000 - 7.1820 -3.8887 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 - 8.6767 -3.8887 0.0000 Al 0 3 0 0 0 0 0 0 0 0 0 0 - 11.0707 -3.8887 0.0000 Ga 0 3 0 0 0 0 0 0 0 0 0 0 - 14.3640 -3.8887 0.0000 In 0 3 0 0 0 0 0 0 0 0 0 0 - 17.0493 -3.8887 0.0000 Tl 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 1 0 0 0 0 - 3 4 1 0 0 0 0 - 4 5 1 0 0 0 0 -M CHG 3 2 1 3 1 4 1 -M END diff --git a/java/resources/smartsEvaluation/butan.mol b/java/resources/smartsEvaluation/butan.mol deleted file mode 100644 index e881f05..0000000 --- a/java/resources/smartsEvaluation/butan.mol +++ /dev/null @@ -1,12 +0,0 @@ -butan - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 4 3 0 0 0 0 0 0 0 0 1 V2000 - 5.1807 -5.5480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.4100 -4.2813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.0693 -6.1813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8047 -4.7120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 2 1 0 0 0 0 - 4 3 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/butene.mol b/java/resources/smartsEvaluation/butene.mol deleted file mode 100644 index 94a6355..0000000 --- a/java/resources/smartsEvaluation/butene.mol +++ /dev/null @@ -1,12 +0,0 @@ -butene - -ISIS- 2D - - 4 3 0 0 0 0 0 0 0 0 1 V2000 - 17.9805 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.5581 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.2325 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.8035 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 3 4 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/cis_butene.mol b/java/resources/smartsEvaluation/cis_butene.mol deleted file mode 100644 index cc7f500..0000000 --- a/java/resources/smartsEvaluation/cis_butene.mol +++ /dev/null @@ -1,12 +0,0 @@ -cis-butene - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 4 3 0 0 0 0 0 0 0 0 1 V2000 - 16.8836 -2.6538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.2185 -3.8056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.8885 -3.8056 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.2235 -2.6538 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 3 4 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/di_halogen_ethyl.mol b/java/resources/smartsEvaluation/di_halogen_ethyl.mol deleted file mode 100644 index 3bee9c2..0000000 --- a/java/resources/smartsEvaluation/di_halogen_ethyl.mol +++ /dev/null @@ -1,42 +0,0 @@ -di_halogen_ethyl - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 19 18 0 0 0 0 0 0 0 0 1 V2000 - 6.2827 -8.6767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3727 -9.5760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2720 -7.7773 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0813 -11.9700 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 - 7.4860 -5.6873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.1607 -4.4840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.5867 -15.5547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3727 -14.9593 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 14.0600 -3.2933 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4647 -6.8780 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 - 6.5867 -17.0493 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 - 10.7667 -10.1713 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4753 -17.0493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.4647 -15.8587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.9593 -16.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8587 -15.2633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.1627 -13.4647 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 16.7580 -16.7580 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 17.3533 -14.9593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 2 1 0 0 0 0 - 4 2 1 0 0 0 0 - 5 1 1 0 0 0 0 - 6 5 1 0 0 0 0 - 7 1 1 0 0 0 0 - 8 7 1 0 0 0 0 - 9 6 1 0 0 0 0 - 10 6 1 0 0 0 0 - 11 7 1 0 0 0 0 - 12 2 1 0 0 0 0 - 13 7 1 0 0 0 0 - 14 13 1 0 0 0 0 - 15 14 1 0 0 0 0 - 16 15 1 0 0 0 0 - 17 16 1 0 0 0 0 - 18 16 1 0 0 0 0 - 19 16 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/earth_alkanline.mol b/java/resources/smartsEvaluation/earth_alkanline.mol deleted file mode 100644 index 7b31a0d..0000000 --- a/java/resources/smartsEvaluation/earth_alkanline.mol +++ /dev/null @@ -1,12 +0,0 @@ -earth_alkanline - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 6 0 0 0 0 0 0 0 0 0 2 V2000 - 6.2827 -3.5847 0.0000 Be 0 2 0 0 0 0 0 0 0 0 0 0 - 8.0813 -3.5847 0.0000 Mg 0 2 0 0 0 0 0 0 0 0 0 0 - 9.8800 -3.5847 0.0000 Ca 0 2 0 0 0 0 0 0 0 0 0 0 - 11.9700 -3.5847 0.0000 Sr 0 2 0 0 0 0 0 0 0 0 0 0 - 13.7687 -3.5847 0.0000 Ba 0 2 0 0 0 0 0 0 0 0 0 0 - 15.8587 -3.5847 0.0000 Ra 0 2 0 0 0 0 0 0 0 0 0 0 -M CHG 6 1 2 2 2 3 2 4 2 5 2 6 2 -M END diff --git a/java/resources/smartsEvaluation/ethan.mol b/java/resources/smartsEvaluation/ethan.mol deleted file mode 100644 index 49fd26b..0000000 --- a/java/resources/smartsEvaluation/ethan.mol +++ /dev/null @@ -1,8 +0,0 @@ -ethan - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 2 1 0 0 0 0 0 0 0 0 1 V2000 - 6.9667 -5.9407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.0193 -5.9407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/evaluation.txt b/java/resources/smartsEvaluation/evaluation.txt deleted file mode 100644 index 6e7eec7..0000000 --- a/java/resources/smartsEvaluation/evaluation.txt +++ /dev/null @@ -1,130 +0,0 @@ -#################################################################################################################### -# SMARTS evaluation definitions: -# SMARTSpattern SMARTSdescription moleculeList -# -# where moleculeList can be of type: -# mol1 mol2 mol3 which means that this SMARTSpattern should NOT occure in these molecules -# mol1#1#5#22 which means that this SMARTSpattern should occure at atoms 1,5 and 22 of this molecule -# mol1#1 mol2#8 which means that this SMARTSpattern should occure at molecule1/atom 1 and molecule2/atom 8 -# mol1#1 mol2 which means that this SMARTSpattern should occure at molecule1/atom 1 and NOT in molecule2 -# mol1#-1 mol2#-1 which means that this SMARTSpattern should occure at molecule1 and in molecule2, in both with undefined atom positions -# mol1#-1 mol2 which means that this SMARTSpattern should occure at molecule1 and NOT in molecule2 -# -#################################################################################################################### -############################### -## cis/trans detection -############################### -CC=CC a_carbon_in_abcd_with_trans butene#1#4 trans-butene#1#4 cis-butene#1#4 -C\C=C/C a_carbon_in_abcd_with_trans butene trans-butene -C/C=C\C a_carbon_in_abcd_with_trans butene trans-butene -C/C=C/C a_carbon_in_abcd_with_trans butene trans-butene#1#4 -C/?C=C/?C a_carbon_in_abcd_with_trans butene#1#4 trans-butene#1#4 -C\C=C\C a_carbon_in_abcd_with_cis butene cis-butene -C/C=C/C a_carbon_in_abcd_with_cis butene cis-butene -C/C=C\C a_carbon_in_abcd_with_cis butene cis-butene#1 -C\C=C/C a_carbon_in_abcd_with_cis butene cis-butene#4 -C/?C=C\?C a_carbon_in_abcd_with_cis butene#1#4 cis-butene#1 -C\?C=C/?C a_carbon_in_abcd_with_cis butene#1#4 cis-butene#4 -# this can not be found for MDL SDF import, because JOELib's auto-assign method assign C/C=C/C !!! -C\C=C\C a_carbon_in_abcd_with_trans butene trans-butene -############################### -## misc -############################### -[#8][#1] hydroxy_group_explicit_h 8-amino-3H-phenoxazin-3-ol#17 -[#8;H1] hydroxy_group 8-amino-3H-phenoxazin-3-ol#17 6-iminocyclohexa-1,4-diene-1,3-diol#4#9 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#1 -[*;!#6;r3] heteroatoms_in_3-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#10 -[*;r3] 3_ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#8#9#10 -[*;r4] 4_ring 5-cyclobutyl-2-cycloheptylphosphinane#1#2#3#4 -[*;r7] 7_ring 5-cyclobutyl-2-cycloheptylphosphinane#11#12#13#14#15#16#17 -[*;!#6;r6] hetero_in_6-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#17#18 -[#7;!#6;r6] N_in_6-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#18 -[#15;!#6;r6] P_in_6-ring 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#17 -[*;!#6;H1] het_atoms_with_H 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#1#10#18#17 -[#7][#1] N_explicit_h 8-amino-3H-phenoxazin-3-ol#11 8-amino-3H-phenoxazin-3-one#11 -[#7]:c N_in_aromatic_bonds_with_C pyridine#6 8-amino-3H-phenoxazin-3-one#3 -[n] aromatic_N pyridine#6 -[a] aromatic pyridine#1#2#3#4#5#6 8-amino-3H-phenoxazin-3-one#1#2#3#4#5#6#7#8#9#10#13#14#15#16 -[a] aromatic pyridine#-1 8-amino-3H-phenoxazin-3-one#-1 phenol#-1 -*@*!@*@* ring_nbr_of_non-ring_bonds_that_connect_rings 5-cyclobutyl-2-cycloheptylphosphinane#1#4#6#7#8#9#12#13 -[*;r]!@[*;r] non-ring_bonds_that_connect_rings 5-cyclobutyl-2-cycloheptylphosphinane#3#5#10#11 -O!:a:a O_in_non-aromatic_bonds_to_an_a phenol#7 8-amino-3H-phenoxazin-3-one#17 -[*;!#6;!#1]~[*;!#6;!#1] het-het_bonds 5-[1-cyclobutyl-2-[(hydroxythio)oxy]-1-(3-methylaziridin-2-yl)propyl]-1,3-azaphosphinane#1#2#3 8-amino-3H-phenoxazin-3-ol -[*;!#6;!#1]~[*;!#6;!#1] het-het_bonds {(Z)-1-(1-hydrazinopropyl)-2-[(hydroxythio)oxy]-2-sulfinovinyl}(oxo)sulfonium#2#3#4#5#6#7#12#13#14#15 -[O]-[O] peroxide_NoKey peroxide#1#2 -[OH1]-[OH1] hydroperoxide_NoKey peroxide#1#2 -[*;r4] atoms_in_4_ring_Key11 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#1#2#3#4 -[#7](~[#8])(~[#6])~[#6] N_connected_to_1_O_and_2_C_Key13 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#5 -[#16]-[#16] S_atoms_in_S-S_groups_Key14 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#8#9 -[#6](~[#8])(~[#8])~[#8] C_connected_to_3_O_Key15 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#10 -[*;!#6;!#1;r3] heteroatoms_in_3-membered_rings_Key16 {[[hydroxy(oxetan-3-yl)amino](oxaziridin-3-yl)methyl]dithio}methanetriol#15#16 -############################### -## ALTANA Pharma, Germany Tests -############################### -[#6][NH][OH,O-] hydroxylamin hydroxylamin#1 TEST_1#10 -[#6][NH][OH,O-] hydroxylamin hydroxylamin_H#1 TEST_1_H#10 -[*;!#1;!#5;!#6;!#14;!#7;!#15;!#8;!#16;!#9;!#17;!#35;!#53] metal hydroxylamin phenol pyridine 5-cyclobutyl-2-cycloheptylphosphinane 8-amino-3H-phenoxazin-3-ol -[#1] explicit_hydrogen water#2#3 -[OH2] water water#1 -[*;!#1] all_except_hydrogen water#1 8-amino-3H-phenoxazin-3-ol#1#2#3#4#5#6#7#8#9#10#11#13#14#15#16#17 -O=[$(C);$(C-[*!r!N!O])]-[$(C);$(C-[*!r!N!O!S])]=[$(C);$(C-[*!r!N!O!S])] ab_unsat_carbonyl ab_unsat_carbonyl_h#4 -O=[$(C);$(C-[*!r!N!O])]-[$(C);$(C-[*!r!N!O!S])]=[$(C);$(C-[*!r!N!O!S])] ab_unsat_carbonyl ab_unsat_carbonyl#4 -[#6]1(~[*!r!G7])~[#6]([*!r!G7])~[#6](~[G7])~[#7]~[#6](~[#7]1)[*!r!G7] pyrimidin_derivat_with_nonHalogen_at_2_5_6_and_halogen_at_4_explicit_nbr pyrimidin_derivat#2 -C[$([CH1]),$(CC)]([G7])([G7]) di_halogen_ethyl_connected_to_H_or_C di_halogen_ethyl#1#5#13 -[$([#6]);$(*~[*!r!G7]),$([*!H0])]1~[$([#6]);$(*~[*!r!G7]),$([*!H0])]~[#6](~[G7])~[#7]~[$([#6]);$(*~[*!r!G7]),$([*!H0])]~[#7]1 pyrimidin_derivat_with_nonHalogen_at_2_5_6_and_halogen_at_4_h_allowed pyrimidin_derivat#2 4-chlorpyrimidin#2 -[$(c);$(*~[*!r!G7]),$([*!H0])]1~[$(c);$(*~[*!r!G7]),$([*!H0])]~c(~[G7])~n~[$([c]);$(*~[*!r!G7]),$([*!H0])]~n1 pyrimidin_with_nonHalogen_at_2_5_6_and_halogen_at_4_h_allowed pyrimidin_derivat#2 4-chlorpyrimidin#2 -[*!r!G7,#1] notHalogenOrH 4-chlorpyrimidin 4-chlorpyrimidin_h#8#9#10 -[$(C);!$(C~[*;R,N,O])] Knock65CNonRNO knockout65#1 -############################### -#### recognize explicite hydrogens flag : FALSE #### -# joelib.smarts.ParseSmart.ParseSmart.anyRecognizesExpliciteHydrogens=false -* all_atoms hydroxylamin_H#1#2#3#4 -#### recognize explicite hydrogens flag :TRUE #### -# joelib.smarts.ParseSmart.ParseSmart.anyRecognizesExpliciteHydrogens=true -#* all_atoms hydroxylamin_H#1#2#3#4#5#6#7#8#9#10#11 -############################### -############################### -## Stephen Jelfs -############################### -[CH3Q1] terminal_methyl ethan#1#2 -[CH3Q1] terminal_methyl propan#1#3 -[CH3Q1] terminal_methyl butan#1#4 -[CH3]C terminal_ethyl ethan#1#2 -[CH3]C terminal_ethyl propan#1#3 -[CH3]C terminal_ethyl butan#1#4 -############################### -############################### -## aromaticity model -############################### -### inner ring problem -[a] aromatic pyrene-4,5-diol#2#3#5#6#7#8#9#10#11#12#13#14#15#16#17#18 -[a] aromatic 9,10-dihydroxyphenanthrene#2#3#5#6#7#8#9#10#11#12#13#14#15#16 -###misc -c1ccc2c(c1)C=CC(=O)O2 2H-chromen-2-one TEST_3 -*!@* 2H-chromen-2-one TEST_3#1#2#3#6 -[#6rQ3]=!@[!#6] 2H-chromen-2-one TEST_3#2 -c1ccc2c(c1)C=CC(=O)O2 2H-chromen-2-one TEST_2 -c1ccc2c(c1)C=CC(=O)O2 2H-chromen-2-one 2H-chromen-2-one -c1ccc2ocnc2c1 c1ccc2ocnc2c1 2-phenylnaphtho[1,2-d][1,3]oxazole#13 -############################### -## RECAP-SMARTS pattern -############################### -[$([NX3]~*);!$([NX3]C=[G6]);!$([NX3]S(=O)=O)]~* amine-bond recap#1#7 -[$([OD2;H0](C)C);!$([OD2](*)C=O)] etherO-bond recap#8 -[NX4]~* quatN-bond recap#11 -n-C nC-bond recap#19 -c-c biphenyl-bond recap#25#26 -[$([NX3]C=[G6]);!$([NX3]C(=O)[NX3])]C=O amideN-bond recap#35#56 -[OD2]C=O esterO-bond recap#42 -[NX3]C(=O)[NX3] ureaC-bond recap#47#49 -C=C olefin-bond recap#52#53 -[N;r6]([C;r6]=O)C lactamN-bond recap#56 -[NX3]S(=O)=O sulphonamide-bond recap#65 -############################### -## groups -############################### -[#89,#90,#91,#92,#93,#94,#95,#96,#97,#98,#99,#100,#101,#102,#103] Actinides_Key4 actinides#2#3#4#5#6#7#8#9#10#11#12#13#14#15#16 -[#57,#58,#59,#60,#61,#62,#63,#64,#65,#66,#67,#68,#69,#70,#71] Lanthanides_Key6 lanthanides#1#2#3#4#5#6#7#8#9#10#11#12#13#14#15 lanthanides2#1#2#3#4#5#6#7#8#9#10#11#12#13#14#15 -[#4,#12,#20,#38,#56,#88] alkaline_earth_elements_Key10 earth_alkanline#1#2#3#4#5#6 -[#5,#13,#31,#49,#81] group_IIIA_elements_Key18 boron_group#1#2#3#4#5 -[#3,#11,#19,#37,#55,#87] alkali_(group_IA)_elements_Key35 alkali_elements#1#2#3#4#5#6 -[#2,#10,#18,#36,#54,#85,#86] other_elements_(He,Ne,Ar,Kr,Xe,Rn,At)_Key44 he_group#1#2#3#4#5#6 diff --git a/java/resources/smartsEvaluation/he_group.mol b/java/resources/smartsEvaluation/he_group.mol deleted file mode 100644 index 1e31a76..0000000 --- a/java/resources/smartsEvaluation/he_group.mol +++ /dev/null @@ -1,11 +0,0 @@ -he_group - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 6 0 0 0 0 0 0 0 0 0 1 V2000 - 5.6873 -5.9787 0.0000 He 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3727 -5.9787 0.0000 Ne 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0707 -5.9787 0.0000 Ar 0 0 0 0 0 0 0 0 0 0 0 0 - 13.7687 -5.6873 0.0000 Kr 0 0 0 0 0 0 0 0 0 0 0 0 - 15.8587 -5.6873 0.0000 Xe 0 0 0 0 0 0 0 0 0 0 0 0 - 19.1520 -5.6873 0.0000 Rn 0 0 0 0 0 0 0 0 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/hydroxylamin.mol b/java/resources/smartsEvaluation/hydroxylamin.mol deleted file mode 100644 index ff13a0f..0000000 --- a/java/resources/smartsEvaluation/hydroxylamin.mol +++ /dev/null @@ -1,12 +0,0 @@ -hydroxylamin - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 4 3 0 0 0 0 0 0 0 0 1 V2000 - 6.5867 -8.3727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.6873 -6.8780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3727 -8.3727 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8800 -8.6767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 4 3 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/hydroxylamin_H.mol b/java/resources/smartsEvaluation/hydroxylamin_H.mol deleted file mode 100644 index 7e28ce7..0000000 --- a/java/resources/smartsEvaluation/hydroxylamin_H.mol +++ /dev/null @@ -1,27 +0,0 @@ -hydroxylamin_H - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 11 10 0 0 0 0 0 0 0 0 1 V2000 - 6.5867 -8.3727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.6873 -6.8780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3727 -8.3727 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8800 -8.6767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 6.2741 -8.9255 0.8981 H 0 0 0 0 0 0 0 0 0 0 0 0 - 6.3452 -8.7998 -0.9845 H 0 0 0 0 0 0 0 0 0 0 0 0 - 4.6095 -7.0980 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 5.9427 -6.2965 0.8981 H 0 0 0 0 0 0 0 0 0 0 0 0 - 5.9426 -6.2968 -0.8984 H 0 0 0 0 0 0 0 0 0 0 0 0 - 8.4318 -7.7810 -0.8410 H 0 0 0 0 0 0 0 0 0 0 0 0 - 10.0194 -9.6568 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 1 5 1 0 0 0 0 - 1 6 1 0 0 0 0 - 2 7 1 0 0 0 0 - 2 8 1 0 0 0 0 - 2 9 1 0 0 0 0 - 4 3 1 0 0 0 0 - 3 10 1 0 0 0 0 - 4 11 1 0 0 0 0 -M END -$$$$ diff --git a/java/resources/smartsEvaluation/knockout65.mol b/java/resources/smartsEvaluation/knockout65.mol deleted file mode 100644 index 73d4612..0000000 --- a/java/resources/smartsEvaluation/knockout65.mol +++ /dev/null @@ -1,29 +0,0 @@ -knockout65 - MOE2002 2D - - 12 11 0 0 0 0 0 0 0 0 1 V2000 - -0.6310 0.3380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.0480 1.0550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1930 0.3310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.0450 -0.3760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.8720 1.0550 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - -2.3760 0.1810 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - -2.3760 1.9290 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - -0.6380 1.7690 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 0.6100 -0.3860 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 0.1080 -1.2610 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1.6190 -0.3830 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - -0.6410 -1.0900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 1 3 2 0 0 0 0 - 1 4 1 0 0 0 0 - 1 2 1 0 0 0 0 - 2 5 1 0 0 0 0 - 2 8 2 0 0 0 0 - 3 9 1 0 0 0 0 - 4 12 3 0 0 0 0 - 5 7 1 0 0 0 0 - 5 6 1 0 0 0 0 - 9 11 1 0 0 0 0 - 9 10 1 0 0 0 0 -M END -$$$$ diff --git a/java/resources/smartsEvaluation/lanthanides.mol b/java/resources/smartsEvaluation/lanthanides.mol deleted file mode 100644 index 3d7984a..0000000 --- a/java/resources/smartsEvaluation/lanthanides.mol +++ /dev/null @@ -1,48 +0,0 @@ -lanthanides - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 18 24 0 0 0 0 0 0 0 0 2 V2000 - 3.5847 -3.5847 0.0000 La 0 0 0 0 0 0 0 0 0 0 0 0 - 3.2933 -5.3833 0.0000 Tb 0 0 0 0 0 0 0 0 0 0 0 0 - 5.6873 -3.5847 0.0000 Ce 0 0 0 0 0 0 0 0 0 0 0 0 - 5.6873 -5.3833 0.0000 Dy 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0813 -3.5847 0.0000 Pr 0 0 0 0 0 0 0 0 0 0 0 0 - 7.7773 -5.3833 0.0000 Ho 0 0 0 0 0 0 0 0 0 0 0 0 - 10.1713 -3.5847 0.0000 Nd 0 0 0 0 0 0 0 0 0 0 0 0 - 10.1713 -5.3833 0.0000 Er 0 0 0 0 0 0 0 0 0 0 0 0 - 12.5653 -3.5847 0.0000 Pm 0 0 0 0 0 0 0 0 0 0 0 0 - 12.5653 -5.3833 0.0000 Tm 0 0 0 0 0 0 0 0 0 0 0 0 - 14.9593 -3.2933 0.0000 Sm 0 5 0 0 0 0 0 0 0 0 0 0 - 15.5547 -5.3833 0.0000 Yb 0 5 0 0 0 0 0 0 0 0 0 0 - 17.0493 -2.9893 0.0000 Eu 0 5 0 0 0 0 0 0 0 0 0 0 - 18.2527 -5.0920 0.0000 Lu 0 0 0 0 0 0 0 0 0 0 0 0 - 19.4433 -2.9893 0.0000 Gd 0 0 0 0 0 0 0 0 0 0 0 0 - 2.6980 -2.3940 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2.0900 -5.9787 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 21.2420 -2.3940 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 1 3 1 0 0 0 0 - 2 4 1 0 0 0 0 - 3 4 1 0 0 0 0 - 3 5 1 0 0 0 0 - 5 6 1 0 0 0 0 - 4 6 1 0 0 0 0 - 5 7 1 0 0 0 0 - 7 8 1 0 0 0 0 - 6 8 1 0 0 0 0 - 7 9 1 0 0 0 0 - 9 10 1 0 0 0 0 - 8 10 1 0 0 0 0 - 9 11 1 0 0 0 0 - 11 12 1 0 0 0 0 - 10 12 1 0 0 0 0 - 11 13 1 0 0 0 0 - 13 14 1 0 0 0 0 - 12 14 1 0 0 0 0 - 13 15 1 0 0 0 0 - 15 14 1 0 0 0 0 - 16 1 1 0 0 0 0 - 17 2 1 0 0 0 0 - 18 15 1 0 0 0 0 -M CHG 3 11 -1 12 -1 13 -1 -M END diff --git a/java/resources/smartsEvaluation/lanthanides2.mol b/java/resources/smartsEvaluation/lanthanides2.mol deleted file mode 100644 index fa23d8c..0000000 --- a/java/resources/smartsEvaluation/lanthanides2.mol +++ /dev/null @@ -1,22 +0,0 @@ -lanthanides2 - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 15 0 0 0 0 0 0 0 0 0 3 V2000 - 3.5847 -3.5847 0.0000 La 0 1 0 0 0 0 0 0 0 0 0 0 - 5.6873 -3.5847 0.0000 Ce 0 1 0 0 0 0 0 0 0 0 0 0 - 8.0813 -3.5847 0.0000 Pr 0 1 0 0 0 0 0 0 0 0 0 0 - 10.1713 -3.5847 0.0000 Nd 0 1 0 0 0 0 0 0 0 0 0 0 - 12.5653 -3.5847 0.0000 Pm 0 1 0 0 0 0 0 0 0 0 0 0 - 14.9593 -3.2933 0.0000 Sm 0 2 0 0 0 0 0 0 0 0 0 0 - 17.0493 -2.9893 0.0000 Eu 0 2 0 0 0 0 0 0 0 0 0 0 - 19.4433 -2.9893 0.0000 Gd 0 1 0 0 0 0 0 0 0 0 0 0 - 3.2933 -5.3833 0.0000 Tb 0 1 0 0 0 0 0 0 0 0 0 0 - 5.6873 -5.3833 0.0000 Dy 0 1 0 0 0 0 0 0 0 0 0 0 - 7.7773 -5.3833 0.0000 Ho 0 1 0 0 0 0 0 0 0 0 0 0 - 10.1713 -5.3833 0.0000 Er 0 1 0 0 0 0 0 0 0 0 0 0 - 12.5653 -5.3833 0.0000 Tm 0 1 0 0 0 0 0 0 0 0 0 0 - 15.5547 -5.3833 0.0000 Yb 0 2 0 0 0 0 0 0 0 0 0 0 - 18.2527 -5.0920 0.0000 Lu 0 1 0 0 0 0 0 0 0 0 0 0 -M CHG 8 1 3 2 3 3 3 4 3 5 3 6 2 7 2 8 3 -M CHG 7 9 3 10 3 11 3 12 3 13 3 14 2 15 3 -M END diff --git a/java/resources/smartsEvaluation/peroxide.mol b/java/resources/smartsEvaluation/peroxide.mol deleted file mode 100644 index 86b6725..0000000 --- a/java/resources/smartsEvaluation/peroxide.mol +++ /dev/null @@ -1,10 +0,0 @@ -peroxide - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 3 2 0 0 0 0 0 0 0 0 1 V2000 - 6.8780 -8.3727 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4753 -8.0813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 11.6660 -6.2827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 2 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/phenol.mol b/java/resources/smartsEvaluation/phenol.mol deleted file mode 100644 index 7dbb177..0000000 --- a/java/resources/smartsEvaluation/phenol.mol +++ /dev/null @@ -1,19 +0,0 @@ -phenol - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 7 7 0 0 0 0 0 0 0 0 1 V2000 - 6.5867 -6.5867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.5867 -8.9807 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.4860 -5.0920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8800 -6.2827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.8800 -8.6767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9807 -10.4753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2720 -12.8693 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 2 0 0 0 0 - 3 1 1 0 0 0 0 - 4 3 2 0 0 0 0 - 5 4 1 0 0 0 0 - 6 5 2 0 0 0 0 - 2 6 1 0 0 0 0 - 7 6 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/propan.mol b/java/resources/smartsEvaluation/propan.mol deleted file mode 100644 index c922539..0000000 --- a/java/resources/smartsEvaluation/propan.mol +++ /dev/null @@ -1,10 +0,0 @@ -propan - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 3 2 0 0 0 0 0 0 0 0 1 V2000 - 6.3713 -6.9287 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9047 -5.4973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.4380 -7.1313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 2 1 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/pyrene-4,5-diol.mol b/java/resources/smartsEvaluation/pyrene-4,5-diol.mol deleted file mode 100644 index 28363fc..0000000 --- a/java/resources/smartsEvaluation/pyrene-4,5-diol.mol +++ /dev/null @@ -1,44 +0,0 @@ -pyrene-4,5-diol - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 18 21 0 0 0 0 0 0 0 0 1 V2000 - 11.0010 -19.9618 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 13.2430 -16.0786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0010 -12.1953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.5170 -12.1953 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 13.2430 -8.3120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.0010 -4.4288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.2430 -0.5455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7270 -0.5455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.9690 -4.4288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.4530 -4.4288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 26.6950 -8.3120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.4530 -12.1953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 26.6950 -16.0786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 24.4530 -19.9618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.9690 -19.9618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7270 -16.0786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 19.9690 -12.1953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 17.7270 -8.3120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 2 16 1 0 0 0 0 - 3 4 1 0 0 0 0 - 3 5 1 0 0 0 0 - 5 6 2 0 0 0 0 - 5 18 1 0 0 0 0 - 6 7 1 0 0 0 0 - 7 8 2 0 0 0 0 - 8 9 1 0 0 0 0 - 9 10 2 0 0 0 0 - 9 18 1 0 0 0 0 - 10 11 1 0 0 0 0 - 11 12 2 0 0 0 0 - 12 13 1 0 0 0 0 - 12 17 1 0 0 0 0 - 13 14 2 0 0 0 0 - 14 15 1 0 0 0 0 - 15 16 2 0 0 0 0 - 16 17 1 0 0 0 0 - 17 18 2 0 0 0 0 -M END diff --git a/java/resources/smartsEvaluation/pyridine.mol b/java/resources/smartsEvaluation/pyridine.mol deleted file mode 100644 index 203b9c9..0000000 --- a/java/resources/smartsEvaluation/pyridine.mol +++ /dev/null @@ -1,17 +0,0 @@ -pyridine - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 6 6 0 0 0 0 0 0 0 0 1 V2000 - 7.4860 -5.9787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.1820 -8.6767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.5760 -4.7880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.3747 -6.2827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.3747 -8.9807 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.9807 -10.4753 0.0000 N 0 0 0 0 0 0 0 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0 0 0 - 15 14 1 0 0 0 0 - 16 15 1 0 0 0 0 - 14 16 1 0 0 0 0 -M END diff --git a/java/resources/test.mol b/java/resources/test.mol deleted file mode 100644 index 7b8096e..0000000 --- a/java/resources/test.mol +++ /dev/null @@ -1,66 +0,0 @@ -title for test molecule 1 - TestMolecule 1 - - 26 27 0 0 0 0 0 0 0 0 1 V2000 - 10.8454 -4.8462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -4.2790 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8454 -6.5298 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 9.0538 -8.2222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -3.1268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -7.1328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.6570 -9.3566 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 7.8475 -8.2222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8454 -9.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.2803 -7.1328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.0649 -7.6730 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 - 8.4507 -2.5775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8454 -11.0581 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 9.0538 -5.9626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.8454 -2.5775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 7.8475 -5.9626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8766 -7.1328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.0158 -9.3566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 13.2221 -9.9417 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 12.0158 -3.1268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.7061 -7.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.8766 -5.9626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.4105 -9.3566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.5178 -7.1328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.7061 -5.4313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.5178 -5.9626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 2 0 0 0 0 - 4 6 1 0 0 0 0 - 5 2 1 0 0 0 0 - 6 3 1 0 0 0 0 - 7 4 1 0 0 0 0 - 8 4 2 0 0 0 0 - 9 7 1 0 0 0 0 - 10 16 2 0 0 0 0 - 11 10 1 0 0 0 0 - 12 5 2 0 0 0 0 - 13 9 2 0 0 0 0 - 14 6 2 0 0 0 0 - 15 5 1 0 0 0 0 - 16 14 1 0 0 0 0 - 17 11 1 0 0 0 0 - 18 9 1 0 0 0 0 - 19 18 1 0 0 0 0 - 20 15 1 0 0 0 0 - 21 17 1 0 0 0 0 - 22 17 2 0 0 0 0 - 23 19 1 0 0 0 0 - 24 21 2 0 0 0 0 - 25 22 1 0 0 0 0 - 26 25 2 0 0 0 0 - 10 8 1 0 0 0 0 - 26 24 1 0 0 0 0 -M ISO 1 1 13 -M END -> (1111) -1111 - -> (1111) -123 - -$$$$ \ No newline at end of file diff --git a/java/resources/test2.mol b/java/resources/test2.mol deleted file mode 100644 index 1c08b41..0000000 --- a/java/resources/test2.mol +++ /dev/null @@ -1,46 +0,0 @@ - - TestMolecule 2 - - 16 18 0 0 0 0 0 0 0 0 1 V2000 - 5.8468 -3.5866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5999 -2.9800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 5.8468 -4.7659 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3151 -4.7659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.0852 -2.9800 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 8.3151 -3.5866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 7.0852 -5.3472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9851 -4.1679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.5535 -5.3472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.5999 -5.3472 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.7919 -4.7659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.5535 -2.9800 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.7467 -4.1679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 - 10.7919 -3.5866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.5535 -6.5351 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 12.0388 -5.3472 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 4 7 1 0 0 0 0 - 5 1 2 0 0 0 0 - 6 5 1 0 0 0 0 - 7 3 1 0 0 0 0 - 8 2 1 0 0 0 0 - 9 4 1 0 0 0 0 - 10 3 1 0 0 0 0 - 11 9 2 0 0 0 0 - 12 6 1 0 0 0 0 - 13 8 2 0 0 0 0 - 14 12 2 0 0 0 0 - 15 9 1 0 0 0 0 - 16 11 1 0 0 0 0 - 8 10 1 0 0 0 0 - 6 4 2 0 0 0 0 - 14 11 1 0 0 0 0 -M END -> (1111) -1111 - -> (1111) -123 - -$$$$ diff --git a/java/resources/test3.mol b/java/resources/test3.mol deleted file mode 100644 index 9a68bc6..0000000 --- a/java/resources/test3.mol +++ /dev/null @@ -1,66 +0,0 @@ - - TestMolecule 3 - - 26 27 0 0 0 0 0 0 0 0 1 V2000 - 8.0184 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2232 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8059 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -4.7206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5858 -7.0083 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8059 -4.1181 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2232 -8.7240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5858 -5.8568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.3810 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 5.5858 -4.7206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 6.8059 -2.9514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -5.8568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.6481 -7.5650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -9.3111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -9.3111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.3810 -5.2620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.1837 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.3810 -4.1181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -2.4024 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 11.6481 -5.2620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8759 -7.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 10.4585 -10.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 8.0184 -10.4627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 12.8759 -5.8568 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 9.2232 -11.0423 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2 1 1 0 0 0 0 - 3 1 1 0 0 0 0 - 4 1 1 0 0 0 0 - 5 2 1 0 0 0 0 - 6 3 1 0 0 0 0 - 7 4 1 0 0 0 0 - 8 2 1 0 0 0 0 - 9 6 1 0 0 0 0 - 10 6 1 0 0 0 0 - 11 7 1 0 0 0 0 - 12 7 1 0 0 0 0 - 13 5 2 0 0 0 0 - 14 5 1 0 0 0 0 - 15 8 1 0 0 0 0 - 16 8 1 0 0 0 0 - 17 9 1 0 0 0 0 - 18 10 1 0 0 0 0 - 19 11 1 0 0 0 0 - 20 12 1 0 0 0 0 - 21 13 1 0 0 0 0 - 22 14 2 0 0 0 0 - 23 15 1 0 0 0 0 - 24 16 1 0 0 0 0 - 25 22 1 0 0 0 0 - 26 24 1 0 0 0 0 - 26 23 1 0 0 0 0 - 25 21 2 0 0 0 0 -M END -> (1111) -1111 - -> (1111) -123 - -$$$$ - diff --git a/java/resources/trans_butene.mol b/java/resources/trans_butene.mol deleted file mode 100644 index 5739624..0000000 --- a/java/resources/trans_butene.mol +++ /dev/null @@ -1,12 +0,0 @@ -trans-butene - -ISIS- 2D -Used JOELib chemistry kernel (expert systems) ID is 715333816 - 4 3 0 0 0 0 0 0 0 0 1 V2000 - 16.8848 -2.5852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 16.2197 -3.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.8896 -3.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 14.2246 -4.8890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1 2 1 0 0 0 0 - 2 3 2 0 0 0 0 - 3 4 1 0 0 0 0 -M END diff --git a/java/sgt.jar b/java/sgt.jar deleted file mode 100644 index 6d5e6f9..0000000 Binary files a/java/sgt.jar and /dev/null differ diff --git a/java/vecmath.jar b/java/vecmath.jar deleted file mode 100644 index 6d8b3a1..0000000 Binary files a/java/vecmath.jar and /dev/null differ diff --git a/java/weka.jar b/java/weka.jar deleted file mode 100644 index e8efc2f..0000000 Binary files a/java/weka.jar and /dev/null differ diff --git a/java/windows/title2data.cpp b/java/windows/title2data.cpp deleted file mode 100644 index 01276a0..0000000 --- a/java/windows/title2data.cpp +++ /dev/null @@ -1,82 +0,0 @@ -/////////////////////////////////////////////////////////////////////////////// -// Filename: $RCSfile: title2data.cpp,v $ -// Purpose: Externl program example. -// Language: Java -// Compiler: GCC -// Authors: Joerg K. Wegner -// Version: $Revision: 1.1.1.1 $ -// $Date: 2004/12/06 15:33:04 $ -// $Author: wegner $ -// -// Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany -// -// This program is free software; you can redistribute it and/or modify -// it under the terms of the GNU General Public License as published by -// the Free Software Foundation version 2 of the License. -// -// This program is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -// GNU General Public License for more details. -/////////////////////////////////////////////////////////////////////////////// - -#include -#include -#include - -using namespace std; - -int main(int argc,char **argv) -{ - char *buffer = new char[10000]; - char *title = new char[1000]; - int i,n; - char ch; - int line=1; - int end; - char *attribute = "MOL_TITLE"; - - if(argc>1)attribute=argv[1]; - cout<<"CPP: start"< <%s>\n\r",attribute); - printf( "%s\n\r", title ); - printf( "\n\r$$$$" ); - //cout << "fini"<