Blue Obelisk ChemoInformatics Dictionary

Christian Hoppe, Christoph Steinbeck, Egon Willighagen and Peter Murray-Rust

This dictionary is started to cluster available open source chemoinformatics algorithm implementations. This document contains MathML [MATHML] equations and can best be viewed with a MathML aware browser, like Mozilla and FireFox [Mozilla] .

[Entries] [Bibliography] [Final Notes]

Table of Contents

Atom Type Perception

Entries

Atom Type Perception based on HOSE codes (atomTypePerceptionWithHOSECodes)

• Definition
  Identifies a predefined atom type for a given atom.

  Description
  The implementation is free to choose a set of atom types, which are then assigned to given atoms of a molecule.To describe the environment of an atom, HOSE codes are used [BREM78] . Further descriptors used by the implementation are: Valence electrons, Formal Charge, Hybridisation

  Classification
  This algorithm is classified as: Atom Type Perception
  Implementations
  Search implementations on Google.com

Contributed by: Christian Hoppe. Created on: 2005-08-15.

Calculate 3D Center of Mass (calculate3DCenterOfMass)

• Definition
  Calculates the 3D center of mass.

  Description
  The algorithm is defined for the x coordinate as $x_{\mathrm{com}}=\frac{$ \sum $ x_{a_i}{m}_{a_i}$$}{$ \sum m_{a_i}$}$ where $a_i$ is the i-th atom, and $m_{a_i}$ its mass. And similarly equations can be written down for the y and z coordinates.

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-27.

Calculate Adjecency Matrix (calculateAdjecencyMatrix)

• Definition
  Calculates the adjecency matrix as defined in the book Chemical Graph Theory [TRI92] .

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-27.

Calculate Connectivity Matrix (calculateConnectivityMatrix)

• Definition
  Calculates the connectivity matrix as defined in the book Chemical Graph Theory [TRI92] .

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-27.

Calculate Orthogonalisation Matrix (calculateOrthogonalisationMatrix)

• Definition
  Algorithm to calculate the orthogonalisation matrix from ????.

  Classification
  This algorithm is classified as: Crystallography
  Implementations
  Search implementations on Google.com

Contributed by: Peter Murray-Rust. Created on: 2005-04-17.

Convert Cartesian Into Fractional Coordinates (convertCartesianIntoFractionalCoordinates)

• Definition
  Converts cartesian atomic coordinates into fractional coordinates using the unit cell parameters.

  Classification
  This algorithm is classified as: Crystallography
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-28.

Convert Cartesian Into Notional Coordinates (convertCartesianIntoNotionalCoordinates)

• Definition
  Converts cartesian unit cell parameters into the notional parameters alpha, beta, gamma and the unit axes lengths.

  Classification
  This algorithm is classified as: Crystallography
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-28.

Convert Cartesian Into Z-matrix Coordinates (cartesianCoordinatesIntoZmatrixCoordinates)

• Definition
  Converts cartesian atomic coordinates into Z-matrix coordinates.

  Classification
  This algorithm is classified as: 3D Geometry
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-22.

Convert Fractional Into Cartesian Coordinates (convertFractionIntoCartesianCoordinates)

• Definition
  Converts fractional atomic coordinates into cartesian coordinates using the unit cell parameters.

  Description
  The implementation is free to choose how to orient the unit cell axis when calculation the cartesian coordinates. A common approach is the place the a axis on the x axis and the b axis in the xy plane.

  Classification
  This algorithm is classified as: Crystallography
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-28.

Convert Notional Into Cartesian Coordinates (convertNotionalIntoCartesianCoordinates)

• Definition
  Converts notional unit cell parameters into cartesian coordinates.

  Description
  The implementation is free to choose how to orient the unit cell axis when calculation the cartesian coordinates. A common approach is the place the a axis on the x axis and the b axis in the xy plane.

  Classification
  This algorithm is classified as: Crystallography
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-28.

Convert Z-matrix Into Cartesian Coordinates (zmatrixCoordinatesIntoCartesianCoordinates)

• Definition
  Converts Z-matrix atomic coordinates into cartesian coordinates.

  Classification
  This algorithm is classified as: 3D Geometry
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-22.

Create a 2D atomic coordinates for a molecular diagram (layoutMolecule)

• Definition
  Calculates 2D atomic coordinates to create a visual attractive 2D diagram.

  Description
  The implementation is free to use templates for certain substructures.

  Classification
  This algorithm is classified as: 2D Layout
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-22.

Determine Spanning Tree (graphSpanningTree)

• Definition
  Algorithm that calculates the spanning tree from a graph.

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-21.

Find Smallest Set of Smallest Rings (findSmallestSetOfSmallestRings)

• Definition
  Algorithm that finds the smallest set of smallest rings starting with a molecular graph.

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-21.

Find Smallest Set of Smallest Rings (Berger Algorithm) (findSmallestSetOfSmallestRings_Berger)

• Definition
  Algorithm to find the smallest set of smallest rings starting with a molecular graph [BGdV04a] .

  Relations
  Is a: Find Smallest Set of Smallest Rings
  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-22.

Find Smallest Set of Smallest Rings (Figueras Algorithm) (findSmallestSetOfSmallestRings_Figueras)

• Definition
  Figueras algorithm to find the smallest set of smallest rings starting with a molecular graph [FIG96] .

  Relations
  Is a: Find Smallest Set of Smallest Rings
  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-22.

Graph Partitioning (graphPartitioning)

• Definition
  Repartitions a disconnected graphs into two or more distinct fully connected graphs.

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-21.

Kabsch Alignment (alignmentKabsch)

• Definition
  Aligns two molecules using the Kabsch algorithm [KAB76] .

  Classification
  This algorithm is classified as: 3D Geometry
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-21.

Perceives Graph Symmetry (perceiveGraphSymmetry)

• Definition
  Finds symmetries in the graph.

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-06-22.

Rebond from 3D Coordinates (rebondFrom3DCoordinates)

• Definition
  Calculates the connectivity based on the 3D coordinates of the atoms in the structure. It assumes that covalent radii of the atoms are known.

  Classification
  This algorithm is classified as: Chemical Graph Theory
  Implementations
  Search implementations on Google.com

Contributed by: Egon Willighagen. Created on: 2005-04-27.

Bibliography

[BGdV04a] Berger, F. and Gritzmann, P. and De Vries, S.. Minimum cycle bases for network graphs, Algorithmica. no. 1, . 2004, pp. 51-62.
[BREM78] Bremser, W.. HOSE- A Novel Substructure Code, Analytica Chimica Acta. vol. 103. 1978, pp. 355-365.
[FIG96] Figueras, J.. Ring Perception Using Breadth-First Search, J. Chem. Inf. Comput Sci.. vol. 36. 1996, pp. 986-991.
[KAB76] Kabsch, W.. A Solution for the Best Rotation to Relate Two Sets of Vectors, Acta Cryst.. vol. A32. 1976, pp. 922-923.
[MATHML] W3C Math Home, http://www.w3.org/Math/.
[Mozilla] Mozilla - Home of the FireFox browser, http://www.mozilla.org/.
[TRI92] Trinijastic, N.. Chemical Graph Theory, CRC Press. 1992,

Final Notes

This dictionary [$Revision: 1.12 $] was last modified by [$Author: egonw $] on [$Date: 2005/09/12 14:50:32 $]. The XML source can be found in CVS

Additions to this dictionary can be send to the QSAR project developers list (qsar-devel). If you find an error on this page, please post a bug report then on this page. In Category you can select the dictionary which contains the error.