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 8 files changed, 1477 insertions(+) create mode 100644 java/docs/algo/APropertyBFS.html create mode 100644 java/docs/algo/BreadthFirstSearch.html create mode 100644 java/docs/algo/DepthFirstSearch.html create mode 100644 java/docs/algo/DistanceMatrix.html create mode 100644 java/docs/algo/GeomDistanceMatrix.html create mode 100644 java/docs/algo/Morgan.html create mode 100644 java/docs/algo/bibliography.html create mode 100644 java/docs/algo/formulas/o_e+v.gif (limited to 'java/docs/algo') diff --git a/java/docs/algo/APropertyBFS.html b/java/docs/algo/APropertyBFS.html new file mode 100644 index 0000000..df26fb7 --- /dev/null +++ b/java/docs/algo/APropertyBFS.html @@ -0,0 +1,93 @@ +

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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