From e77cc376aaff8ca481fdace6d5795c5b5feb0e87 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Mon, 20 Feb 2012 14:45:20 +0100 Subject: Added pc descriptor calc service --- java/docs/algo/APropertyBFS.html | 93 +++ java/docs/algo/BreadthFirstSearch.html | 122 +++ java/docs/algo/DepthFirstSearch.html | 137 ++++ java/docs/algo/DistanceMatrix.html | 102 +++ java/docs/algo/GeomDistanceMatrix.html | 84 ++ java/docs/algo/Morgan.html | 157 ++++ java/docs/algo/bibliography.html | 782 ++++++++++++++++++ java/docs/algo/formulas/o_e+v.gif | Bin 0 -> 2058 bytes java/docs/feature/APropertyBFS.html | 93 +++ java/docs/feature/APropertyDistanceMatrix.html | 93 +++ java/docs/feature/AcidicGroups.html | 93 +++ java/docs/feature/AliphaticOHGroups.html | 93 +++ java/docs/feature/AromaticBonds.html | 93 +++ java/docs/feature/AromaticOHGroups.html | 93 +++ java/docs/feature/AtomBondOrderSum.html | 3 + java/docs/feature/AtomENAllredRochow.html | 3 + java/docs/feature/AtomENPauling.html | 3 + 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java/docs/feature/AtomIsSulfur.html | 3 + java/docs/feature/AtomIsUnsaturated.html | 3 + java/docs/feature/AtomKekuleBondOrderSum.html | 3 + java/docs/feature/AtomMass.html | 93 +++ java/docs/feature/AtomPartialCharge.html | 3 + java/docs/feature/AtomType.html | 3 + java/docs/feature/AtomValence.html | 93 +++ java/docs/feature/AtomValenceSum.html | 3 + java/docs/feature/AtomVanDerWaalsVolume.html | 93 +++ java/docs/feature/Autocorrelation.html | 168 ++++ java/docs/feature/BCUT.html | 3 + java/docs/feature/BasicGroups.html | 93 +++ java/docs/feature/BondInAromaticSystem.html | 3 + java/docs/feature/BondInRing.html | 3 + java/docs/feature/BondIsAmide.html | 3 + java/docs/feature/BondIsCarbonyl.html | 3 + java/docs/feature/BondIsClosure.html | 3 + java/docs/feature/BondIsEster.html | 3 + java/docs/feature/BondIsPrimaryAmide.html | 3 + java/docs/feature/BondIsRotor.html | 3 + java/docs/feature/BondKekuleType.html | 3 + java/docs/feature/BurdenEigenvalues.html | 3 + java/docs/feature/BurdenModifiedEigenvalues.html | 96 +++ java/docs/feature/CompressedFeatureMatrix.html | 3 + java/docs/feature/ConjElectroTopolState.html | 173 ++++ .../feature/ConjugatedTopologicalDistance.html | 117 +++ java/docs/feature/DistanceDistanceMatrix.html | 3 + java/docs/feature/DistanceMatrix.html | 111 +++ java/docs/feature/Dummy.html | 3 + java/docs/feature/ElectrogeometricalState.html | 139 ++++ java/docs/feature/ElectrotopologicalState.html | 139 ++++ java/docs/feature/FractionRotatableBonds.html | 93 +++ java/docs/feature/GeomDistanceMatrix.html | 93 +++ java/docs/feature/GeometricalDiameter.html | 93 +++ java/docs/feature/GeometricalRadius.html | 93 +++ java/docs/feature/GeometricalShapeCoefficient.html | 93 +++ .../docs/feature/GlobalTopologicalChargeIndex.html | 96 +++ java/docs/feature/GraphPotentials.html | 131 +++ java/docs/feature/GraphShapeCoefficient.html | 93 +++ java/docs/feature/HBA1.html | 94 +++ java/docs/feature/HBA2.html | 94 +++ 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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.

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

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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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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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Descriptor

Atom masss

Atom mass.

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Descriptor

Valence

Valence.

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

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

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 new file mode 100644 index 0000000..6deea0d --- /dev/null +++ b/java/docs/feature/ConjugatedTopologicalDistance.html @@ -0,0 +1,117 @@ +

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

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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\ No newline at end of file diff --git a/java/docs/feature/Dummy.html b/java/docs/feature/Dummy.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/Dummy.html @@ -0,0 +1,3 @@ + +Dummy + \ No newline at end of file diff --git a/java/docs/feature/ElectrogeometricalState.html b/java/docs/feature/ElectrogeometricalState.html new file mode 100644 index 0000000..d25b39a --- /dev/null +++ b/java/docs/feature/ElectrogeometricalState.html @@ -0,0 +1,139 @@ +

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 new file mode 100644 index 0000000..6de0bf2 --- /dev/null +++ b/java/docs/feature/ElectrotopologicalState.html @@ -0,0 +1,139 @@ +

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 new file mode 100644 index 0000000..a34080c --- /dev/null +++ b/java/docs/feature/FractionRotatableBonds.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..ff8cc05 --- /dev/null +++ b/java/docs/feature/GeomDistanceMatrix.html @@ -0,0 +1,93 @@ +

Descriptor

Geometrical distance matrix

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

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\ No newline at end of file diff --git a/java/docs/feature/GeometricalDiameter.html b/java/docs/feature/GeometricalDiameter.html new file mode 100644 index 0000000..242edc6 --- /dev/null +++ b/java/docs/feature/GeometricalDiameter.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..76a2596 --- /dev/null +++ b/java/docs/feature/GeometricalRadius.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..e1401be --- /dev/null +++ b/java/docs/feature/GeometricalShapeCoefficient.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..63e2715 --- /dev/null +++ b/java/docs/feature/GlobalTopologicalChargeIndex.html @@ -0,0 +1,96 @@ +

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 new file mode 100644 index 0000000..a192e96 --- /dev/null +++ b/java/docs/feature/GraphPotentials.html @@ -0,0 +1,131 @@ +

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 new file mode 100644 index 0000000..735e913 --- /dev/null +++ b/java/docs/feature/GraphShapeCoefficient.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..6dcb012 --- /dev/null +++ b/java/docs/feature/HBA1.html @@ -0,0 +1,94 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/HBA2.html b/java/docs/feature/HBA2.html new file mode 100644 index 0000000..4ad7747 --- /dev/null +++ b/java/docs/feature/HBA2.html @@ -0,0 +1,94 @@ +

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 new file mode 100644 index 0000000..58922cf --- /dev/null +++ b/java/docs/feature/HBD1.html @@ -0,0 +1,93 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/HBD2.html b/java/docs/feature/HBD2.html new file mode 100644 index 0000000..a66a20f --- /dev/null +++ b/java/docs/feature/HBD2.html @@ -0,0 +1,94 @@ +

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 new file mode 100644 index 0000000..c460fba --- /dev/null +++ b/java/docs/feature/HeavyBonds.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..d1e124f --- /dev/null +++ b/java/docs/feature/HeteroCycles.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..020d78c --- /dev/null +++ b/java/docs/feature/HydrophobicGroups.html @@ -0,0 +1,93 @@ +

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 new file mode 100644 index 0000000..82c8c76 --- /dev/null +++ b/java/docs/feature/IntrinsicState.html @@ -0,0 +1,145 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/KierShape1.html b/java/docs/feature/KierShape1.html new file mode 100644 index 0000000..9690413 --- /dev/null +++ b/java/docs/feature/KierShape1.html @@ -0,0 +1,176 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/KierShape2.html b/java/docs/feature/KierShape2.html new file mode 100644 index 0000000..d3117b2 --- /dev/null +++ b/java/docs/feature/KierShape2.html @@ -0,0 +1,131 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/KierShape3.html b/java/docs/feature/KierShape3.html new file mode 100644 index 0000000..7b760b5 --- /dev/null +++ b/java/docs/feature/KierShape3.html @@ -0,0 +1,131 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/LogP.html b/java/docs/feature/LogP.html new file mode 100644 index 0000000..914533b --- /dev/null +++ b/java/docs/feature/LogP.html @@ -0,0 +1,96 @@ +

Descriptor

Octanol/Water partition coefficient (logP)

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

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\ No newline at end of file diff --git a/java/docs/feature/MolarRefractivity.html b/java/docs/feature/MolarRefractivity.html new file mode 100644 index 0000000..88757de --- /dev/null +++ b/java/docs/feature/MolarRefractivity.html @@ -0,0 +1,96 @@ +

Descriptor

Molar refractivity (MR)

Molar refractivity (MR) [wc99].

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\ No newline at end of file diff --git a/java/docs/feature/MolecularWeight.html b/java/docs/feature/MolecularWeight.html new file mode 100644 index 0000000..e463e1c --- /dev/null +++ b/java/docs/feature/MolecularWeight.html @@ -0,0 +1,93 @@ +

Descriptor

Molecular weight (MW)

Molecular weight (MW).

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\ No newline at end of file diff --git a/java/docs/feature/MoleculeHashcode.html b/java/docs/feature/MoleculeHashcode.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/MoleculeHashcode.html @@ -0,0 +1,3 @@ + +Dummy + \ No newline at end of file diff --git a/java/docs/feature/NO2Groups.html b/java/docs/feature/NO2Groups.html new file mode 100644 index 0000000..6fa91d4 --- /dev/null +++ b/java/docs/feature/NO2Groups.html @@ -0,0 +1,97 @@ +

Descriptor

Number of -NO2 groups

Number of -NO2 groups.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfAtoms.html b/java/docs/feature/NumberOfAtoms.html new file mode 100644 index 0000000..f79063f --- /dev/null +++ b/java/docs/feature/NumberOfAtoms.html @@ -0,0 +1,93 @@ +

Descriptor

Number of atoms

Number of atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfB.html b/java/docs/feature/NumberOfB.html new file mode 100644 index 0000000..fd7e2e4 --- /dev/null +++ b/java/docs/feature/NumberOfB.html @@ -0,0 +1,93 @@ +

Descriptor

Number of boron atoms

Number of boron atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfBonds.html b/java/docs/feature/NumberOfBonds.html new file mode 100644 index 0000000..22dfb7e --- /dev/null +++ b/java/docs/feature/NumberOfBonds.html @@ -0,0 +1,93 @@ +

Descriptor

Number of bonds

Number of bonds.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfBr.html b/java/docs/feature/NumberOfBr.html new file mode 100644 index 0000000..5807bb9 --- /dev/null +++ b/java/docs/feature/NumberOfBr.html @@ -0,0 +1,93 @@ +

Descriptor

Number of bromine atoms

Number of bromine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfC.html b/java/docs/feature/NumberOfC.html new file mode 100644 index 0000000..a1b224e --- /dev/null +++ b/java/docs/feature/NumberOfC.html @@ -0,0 +1,93 @@ +

Descriptor

Number of carbon atoms

Number of carbon atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfCl.html b/java/docs/feature/NumberOfCl.html new file mode 100644 index 0000000..04892d5 --- /dev/null +++ b/java/docs/feature/NumberOfCl.html @@ -0,0 +1,93 @@ +

Descriptor

Number of chlorine atoms

Number of chlorine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfF.html b/java/docs/feature/NumberOfF.html new file mode 100644 index 0000000..c12b2f5 --- /dev/null +++ b/java/docs/feature/NumberOfF.html @@ -0,0 +1,93 @@ +

Descriptor

Number of fluorine atoms

Number of fluorine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfHal.html b/java/docs/feature/NumberOfHal.html new file mode 100644 index 0000000..11df356 --- /dev/null +++ b/java/docs/feature/NumberOfHal.html @@ -0,0 +1,93 @@ +

Descriptor

Number of halogen atoms

Number of halogen atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfI.html b/java/docs/feature/NumberOfI.html new file mode 100644 index 0000000..0580e12 --- /dev/null +++ b/java/docs/feature/NumberOfI.html @@ -0,0 +1,93 @@ +

Descriptor

Number of iodine atoms

Number of iodine atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfN.html b/java/docs/feature/NumberOfN.html new file mode 100644 index 0000000..bd65ada --- /dev/null +++ b/java/docs/feature/NumberOfN.html @@ -0,0 +1,93 @@ +

Descriptor

Number of nitrogen atoms

Number of nitrogen atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfO.html b/java/docs/feature/NumberOfO.html new file mode 100644 index 0000000..7ecbe0a --- /dev/null +++ b/java/docs/feature/NumberOfO.html @@ -0,0 +1,93 @@ +

Descriptor

Number of oxygen atoms

Number of oxygen atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfP.html b/java/docs/feature/NumberOfP.html new file mode 100644 index 0000000..3669e91 --- /dev/null +++ b/java/docs/feature/NumberOfP.html @@ -0,0 +1,93 @@ +

Descriptor

Number of phosphorus atoms

Number of phosphorus atoms.

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\ No newline at end of file diff --git a/java/docs/feature/NumberOfS.html b/java/docs/feature/NumberOfS.html new file mode 100644 index 0000000..b735ee5 --- /dev/null +++ b/java/docs/feature/NumberOfS.html @@ -0,0 +1,93 @@ +

Descriptor

Number of sulfur atoms

Number of sulfur atoms.

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\ No newline at end of file diff --git a/java/docs/feature/OSOGroups.html b/java/docs/feature/OSOGroups.html new file mode 100644 index 0000000..ca49ebf --- /dev/null +++ b/java/docs/feature/OSOGroups.html @@ -0,0 +1,93 @@ +

Descriptor

Number of -OSO atoms

Number of -OSO atoms.

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\ No newline at end of file diff --git a/java/docs/feature/PolarSurfaceArea.html b/java/docs/feature/PolarSurfaceArea.html new file mode 100644 index 0000000..357056f --- /dev/null +++ b/java/docs/feature/PolarSurfaceArea.html @@ -0,0 +1,96 @@ +

Descriptor

Polar surface area (PSA)

Polar surface area (PSA) [ers00].

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\ No newline at end of file diff --git a/java/docs/feature/RadialDistributionFunction.html b/java/docs/feature/RadialDistributionFunction.html new file mode 100644 index 0000000..09d9600 --- /dev/null +++ b/java/docs/feature/RadialDistributionFunction.html @@ -0,0 +1,230 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/RotatableBonds.html b/java/docs/feature/RotatableBonds.html new file mode 100644 index 0000000..42ef0d9 --- /dev/null +++ b/java/docs/feature/RotatableBonds.html @@ -0,0 +1,94 @@ +

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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\ No newline at end of file diff --git a/java/docs/feature/SMILESMolecule.html b/java/docs/feature/SMILESMolecule.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/SMILESMolecule.html @@ -0,0 +1,3 @@ + +Dummy + \ No newline at end of file diff --git a/java/docs/feature/SO2Groups.html b/java/docs/feature/SO2Groups.html new file mode 100644 index 0000000..e4cd9a7 --- /dev/null +++ b/java/docs/feature/SO2Groups.html @@ -0,0 +1,97 @@ +

Descriptor

Number of -SO2 atoms

Number of -SO2 atoms.

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\ No newline at end of file diff --git a/java/docs/feature/SOGroups.html b/java/docs/feature/SOGroups.html new file mode 100644 index 0000000..fd3e45a --- /dev/null +++ b/java/docs/feature/SOGroups.html @@ -0,0 +1,93 @@ +

Descriptor

Number of -SO groups

Number of -SO groups.

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\ No newline at end of file diff --git a/java/docs/feature/SSKey3DS.html b/java/docs/feature/SSKey3DS.html new file mode 100644 index 0000000..fad741d --- /dev/null +++ b/java/docs/feature/SSKey3DS.html @@ -0,0 +1,779 @@ +

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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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/TopologicalAtomPair.html b/java/docs/feature/TopologicalAtomPair.html new file mode 100644 index 0000000..32731b0 --- /dev/null +++ b/java/docs/feature/TopologicalAtomPair.html @@ -0,0 +1,93 @@ +

Descriptor

Valence

Atom pair descriptor using topological distances.

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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/TopologicalDiameter.html b/java/docs/feature/TopologicalDiameter.html new file mode 100644 index 0000000..660bbb6 --- /dev/null +++ b/java/docs/feature/TopologicalDiameter.html @@ -0,0 +1,93 @@ +

Descriptor

Topological diameter

Topological diameter.

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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/TopologicalRadius.html b/java/docs/feature/TopologicalRadius.html new file mode 100644 index 0000000..07299fa --- /dev/null +++ b/java/docs/feature/TopologicalRadius.html @@ -0,0 +1,93 @@ +

Descriptor

Topological radius

Topological radius.

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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenEigenvalues.html b/java/docs/feature/WeightedBurdenEigenvalues.html new file mode 100644 index 0000000..0d10a46 --- /dev/null +++ b/java/docs/feature/WeightedBurdenEigenvalues.html @@ -0,0 +1,3 @@ + +Dummy + \ No newline at end of file diff --git a/java/docs/feature/WeightedBurdenModifiedEigenvalues.html b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html new file mode 100644 index 0000000..0e93938 --- /dev/null +++ b/java/docs/feature/WeightedBurdenModifiedEigenvalues.html @@ -0,0 +1,93 @@ +

Descriptor

Weighted burden modified eigenvalues

Accepts six different weighted atom properties to calculate BCUT values.

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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/ZagrebIndex1.html b/java/docs/feature/ZagrebIndex1.html new file mode 100644 index 0000000..130990f --- /dev/null +++ b/java/docs/feature/ZagrebIndex1.html @@ -0,0 +1,123 @@ +

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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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/ZagrebIndex2.html b/java/docs/feature/ZagrebIndex2.html new file mode 100644 index 0000000..735a797 --- /dev/null +++ b/java/docs/feature/ZagrebIndex2.html @@ -0,0 +1,143 @@ +

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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  Bibliography
\ No newline at end of file diff --git a/java/docs/feature/bibliography.html b/java/docs/feature/bibliography.html new file mode 100644 index 0000000..0770682 --- /dev/null +++ b/java/docs/feature/bibliography.html @@ -0,0 +1,911 @@ +Bibliography
Prev 

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.

[ml91] E. C. Meng and R. A. Lewis, {D}etermination of {M}olecular {T}opology and {A}tomic {H}ybridisation {S}tates from {H}eavy {A}tom {C}oordinates, J. Comp. Chem., 12, 891-898, 1991.

[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.

[msg99] M. C. Hemmer, V. Steinhauer, and J. Gasteiger, Deriving the 3D Structure of Organic Molecules from their Infrared Spectra, Vibrat. Spect., 19, 63-67, 1999.

[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.

[wz03] J. K. Wegner and A. Zell, Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method, J. Chem. Inf. Comput. Sci., 43, 1077-1084, 2003.

[wfz04a] J. K. Wegner, H. Froehlich, and A. Zell, Feature Selection for Descriptor based Classification Models. 1. Theory and GA-SEC Algorithm, J. Chem. Inf. Comput. Sci., 44, ASAP alert, 2004.

[wfz04b] J. K. Wegner, H. Froehlich, and A. Zell, Feature Selection for Descriptor based Classification Models. 2. Human Intestinal Absorption, J. Chem. Inf. Comput. Sci., 44, ASAP alert, 2004.

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

PrevHome 
Bibliography  
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Böhm & G. Klebe, Development of New Hydrogen--Bond Descriptors and Their Application to Comparative Molecular Field Analyses , J. Med. Chem., 2002 , 45 , 1585-1597. +Article (bmv84), P. Broto; G. Moreau & C. Vandycke, Molecular Structures: Perception, Autocorrelation Descriptor and SAR Studies , Eur. J. Med. Chem., 1984 , 19 , 66-70. +Book (br90), D. Bonchev & D. H. Rouvray, D. Bonchev & D. H. Rouvray (ed.), Chemical Graph Theory: Introduction and Fundamentals , Gordon and Breach Science Publishers, 1990 , 1. +Article (bs93), B.L.Bush & R.P.Sheridan, PATTY: A Programmable Atom Typer and Language for Automatic Classification of Atoms in Molecular Databases. , J. Chem. Inf. Comput. Sci., 1993 , 33 , 756-762. +Inbook (clr98bfs), T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.2, MIT--Press, 1998 , 469-477. +Inbook (clr98complexity), T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 2, MIT--Press, 1998 , 23-41. +Inbook (clr98dfs), T. H. Cormen; C. E. Leiserson & R. L. Rivest, Introduction to Algorithms , 23.3, MIT--Press, 1998 , 477-483. +Incollection (dhl90), A.N. Davies; H. Hilling & M. Linscheid, J. Gasteiger (ed.), JCAMP--DX, a standard ? , Springer--Verlag, 1990 , 147-156. +Article (dl93), A. N. Davies & P. Lampen, JCAMP--DX for NMR , Appl. Spec., 1993 , 47 , 1093-1099. +Article (dw88), R. S. Mc Donald & Paul A. Wilks, JCAMP--DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form , Appl. Spec., 1988 , 42 , 151-162 . Article (ers00), P. Ertl; B. Rohde & 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. 2000, 43, 3714-3717, 2000 , 43 , 3714-3717. +Article (fig96), J. Figueras, Ring Perception Using Breadth--First Search , J. Chem. Inf. Comput. Sci., 1996 , 36 , 986-991. +Article (ghhjs91), J. Gasteiger; B. M. P. Hendriks; P. Hoever; C. Jochum & H. Somberg, JCAMP--CS: A Standard Format for Chemical Structure Information in Computer Readable Form , Appl. Spec., 1991 , 45 , 4-11. +Article (gm78), J. Gasteiger & M. Marsili, A New Model for Calculating Atomic Charges in Molecules , Tetrahedron Lett., 1978 , 3181-3184. +Article (gmrw01), G. V. Gkoutos; P. Murray--Rust; S. Rzepa & M. Wright, Chemical Markup, XML, and the World--Wide Web. 3. Toward a Signed Semantic Chemical Web of Trust , J. Chem. Inf. Comput. Sci., 2001 , 41 , 1295-1300 . DOI: 10.1021/ci000406v. +Article (gwb98), J. Gillet; P. Willett & J. Bradshaw, Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms , J. Chem. Inf. Comput. Sci., 1998 , 38 , 165-179. +Article (gxsb00), L. Xue; F. L. Stahura; J. W. Godden & J. Bajorath, Searching for molecules with similar biological activity: analysis by fingerprint profiling , Pac. Symp. Biocomput., 2000 , 8 , 566-575. +Misc (jwd00), C. A. James; D. Weininger & J. Delany, Daylight Theory Manual. +Article (lhdl94), P. Lampen; H. Hillig; A. N. Davies & Michael Linscheid, JCAMP--DX for Mass Spectrometry , Appl. Spec., 1994 , 48 , 1545-1552. +Article (lldf01), C. A. Lipinski; F. Lombardo; B. W. Dominy & P. J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , Adv. Drug Delivery Reviews, 2001 , 46 , 3-26. +Misc (mdlMolFormat), MDL Information Systems, Inc., MDL CTfile Formats. +Article (ml91), E. C. Meng & R. A. Lewis, Determination of Molecular Topology and Atomic Hybridisation States from Heavy Atom Coordinates , J. Comp. Chem., 1991 , 12 , 891-898. +Article (mor65), H. L. Morgan, The Generation of a Unique Machine Description for Chemical Structures -- A Technique Developed at Chemical Abstracts Service. , J. Chem. Doc., 1965 , 5 , 107-113. +Article (mr01), P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 2. Information Objects and the CMLDOM , J. Chem. Inf. Comput. Sci., 2001 , 41 , 1113-1123 . DOI: 10.1021/ci000404a. +Article (mr03), P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML and the World--Wide Web. 4. CML Schema , J. Chem. Inf. Comput. Sci., 2003 , 43 , 757-772 . DOI: 10.1021/ci0256541. +Article (mrww04), P. Murray--Rust; H. S. Rzepa; J. Williamson & E. L. Willighagen, Chemical Markup, XML and the World--Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators , J. Chem. Inf. Comput. Sci., 2004 , 44 , 462-469 . DOI: 10.1021/ci034244p. +Article (odtl01), T. I. Oprea; A. M. Davis; S. J. Teague & P. D. Leeson, Is There a Difference between Leads and Drugs? A Historical Perspective , J. Chem. Inf. Comput. Sci., 2001 , 41 , 1308-1315 . DOI: 10.1021/ci010366a. +Misc (pdbFormat), Protein Data Bank (PDB) File Format , 2002. +Misc (povray), POV--Team, Persistence of Vision Raytracer (POVRay). +Article (rr99b), P. Murray--Rust & H. S. Rzepa, Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles , J. Chem. Inf. Comput. Sci., 1999 , 39 , 928-942 . DOI: 10.1021/ci990052b. +Manual (smarts), Daylight Chemical Information Systems, Inc., Smiles ARbitrary Target Specification (SMARTS). +Manual (smilesFormat), Daylight Chemical Information Systems, Inc., Simplified Molecular Input Line Entry System (SMILES). +Manual (sybylmol2), Tripos, Tripos Mol2 File Format. +Inbook (tc00kiershape), R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , K, Wiley--VCH, 2000 , 248-250. +Inbook (tc00zagrebgroup), R. Todeschini & V. Consonni, Handbook of Molecular Descriptors , Z, Wiley--VCH, 2000 , 509. +Book (tri92), N. Trinajsti, Chemical Graph Theory , CRC Press, Florida, U.S.A., 1992. +Article (wc99), S. A. Wildman & G. M. Crippen, Prediction of Physicochemical Parameters by Atomic Contributions , J. Chem. Inf. Comput. Sci., 1999 , 39 , 868-873. +Article (wei88), D. Weininger, SMILES, a Chemical Language for Information Systems. 1. Introduction to Methodology and Encoding Rules. , J. Chem. Inf. Comput. Sci., 1988 , 28 , 31-36. +Article (wfz04a), Wegner, J. K.; Fröhlich, H. & Zell, A., Feature selection for Descriptor based Classification Models. 1. Theory and GA--SEC Algorithm , J. Chem. Inf. Comput. Sci., 2004 , 44 . DOI: 10.1021/ci0342324. +Article (wfz04b), J. K. Wegner; H. Fröhlich & A. Zell, Feature selection for Descriptor based Classification Models. 2. Human Intestinal Absorption (HIA) , J. Chem. Inf. Comput. Sci., 2004 , 44 . DOI: 10.1021/ci034233w. +Article (wil01), E. L. Willighagen, Processing CML Conventions in Java , Internet Journal of Chemistry, 2001 , 4 , 4. +Article (www89), D. Weininger; A. Weininger & J. L. Weininger, Algorithm for generation of unique SMILES notation , J. Chem. Inf. Comput. Sci., 1989 , 29 , 97-101. +Article (wy96), W. P. Walters & S. H. Yalkowsky, ESCHER--A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology , J. Chem. Inf. Comput. Sci., 1996 , 36 , 1015-1017. +Article (wz03), Wegner, J. K. & Zell, A., Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method , J. Chem. Inf. Comput. Sci., 2003 , 43 , 1077-1084 . DOI: 10.1021/ci034006u. +Inbook (zup89c), J. 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 new file mode 100644 index 0000000..1befd3f --- /dev/null +++ b/java/docs/literature.tex @@ -0,0 +1,34 @@ +% +% 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. Wegner, 2003\end{html} +%%tth:\begin{html}\end{html} +%------------------------------------------------------------------------------------------- + +%%% TITLE ---------------------------------------------------------------- +%%% ---------------------------------------------------------------------- +\begin{document} +% ------------------------------------------------------------------------ +\nocite{*} +% ------------------------------------------------------------------------ +\bibliographystyle{angewandte_chemie} +\bibliography{literature} +\end{document} +% ------------------------------------------------------------------------ -- cgit v1.2.3