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joelib.desc.types
Class GraphPotentials  

java.lang.Object
  joelib.desc.SimpleDoubleAtomProperty
      joelib.desc.types.GraphPotentials

All Implemented Interfaces:

joelib.desc.Descriptor, joelib.util.PropertyAcceptor

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public class GraphPotentials

extends joelib.desc.SimpleDoubleAtomProperty

External rotational symmetry or graph potentials.

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Field Summary
static java.lang.String	DESC_KEY
private static org.apache.log4j.Category	logger           Obtain a suitable logger.

 

Fields inherited from class joelib.desc.SimpleDoubleAtomProperty

descInfo

 

Constructor Summary

GraphPotentials()

 

Method Summary
private static jmat.data.Matrix	cMatrix(joelib.molecule.JOEMol mol)           Construct the matrix C, which is simply a column vector consisting of the valence for each atom
double[]	getDoubleAtomProperties(joelib.molecule.JOEMol mol)           Gets the double atom property values.
private static jmat.data.Matrix	gMatrix(joelib.molecule.JOEMol mol)           Construct the matrix G, which puts each atoms valence+1 on the diagonal and and -1 on the off diagonal if two atoms are connected.
static double[]	graphPotentials(joelib.molecule.JOEMol mol)           Calculate the Graph Potentials of a molecule based on V.E.

 

Methods inherited from class joelib.desc.SimpleDoubleAtomProperty

acceptedProperties, calculate, calculate, calculate, calculate, clear, getDescInfo, getDescription, initialize, testDescriptor

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

logger

private static org.apache.log4j.Category logger

Obtain a suitable logger.

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DESC_KEY

public static final java.lang.String DESC_KEY

See Also:

Constant Field Values

Constructor Detail

GraphPotentials

public GraphPotentials()

Method Detail

getDoubleAtomProperties

public double[] getDoubleAtomProperties(joelib.molecule.JOEMol mol)

Description copied from class: joelib.desc.SimpleDoubleAtomProperty

Gets the double atom property values.

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graphPotentials

public static double[] graphPotentials(joelib.molecule.JOEMol mol)

Calculate the Graph Potentials of a molecule based on V.E. Rozenblit, A.B. Golender Logical and Combinatorial Algorithms for Drug Design for an example see:
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(5), 1015-1017

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cMatrix

private static jmat.data.Matrix cMatrix(joelib.molecule.JOEMol mol)

Construct the matrix C, which is simply a column vector consisting of the valence for each atom

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gMatrix

private static jmat.data.Matrix gMatrix(joelib.molecule.JOEMol mol)

Construct the matrix G, which puts each atoms valence+1 on the diagonal and and -1 on the off diagonal if two atoms are connected.

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> desc >> [ types overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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