org.openscience.cdk.signature

Class AtomSignature

java.lang.Object

signature.AbstractVertexSignature

org.openscience.cdk.signature.AtomSignature

public class AtomSignature
extends signature.AbstractVertexSignature

The signature [Faulon, J. L., Visco, D. P., and Pophale, R. S., The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies., Journal of Chemical Information and Computer Sciences, 2003, 43:707-720, Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences, Journal of Chemical Information and Computer Sciences, 2004, 44:427-436] for a molecule rooted at a particular atom.

A signature is a description of the connectivity of a molecule, in the form of a tree-like structure called a directed acyclic graph (DAG). This DAG can be written out as a string, for example ethane:

   [C]([C]([H][H][H])[H][H][H])
 

where each atom is represented by an atom symbol in square brackets. The branching of the tree is indicated by round brackets. When the molecule has a cycle, the signature string will have numbers after the atom symbol, like:

 [C]([C]([C,0])[C]([C,0]))
 

these are known as 'colors' and indicate ring closures, in a roughly similar way to SMILES notation. Note that the colors start from 0 in this implementation, in contrast to the examples in [Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences, Journal of Chemical Information and Computer Sciences, 2004, 44:427-436].

Multiple bonds are represented by symbols in front of the opening square bracket of an atom. Double bonds are '=', triple are '#'. Since there is a defined direction for the signature tree, only the child node will have the bond symbol, and the relevant bond is to the parent.

Author:

maclean

Source code:

master

Belongs to CDK module:

signature

Nested Class Summary

Nested classes/interfaces inherited from class signature.AbstractVertexSignature

signature.AbstractVertexSignature.InvariantType

Field Summary

Fields inherited from class signature.AbstractVertexSignature

END_BRANCH_SYMBOL, END_NODE_SYMBOL, START_BRANCH_SYMBOL, START_NODE_SYMBOL, TMP_COLORING_COUNT

Constructor Summary

Constructors

Constructor and Description
AtomSignature(IAtom atom, IAtomContainer molecule) Create an atom signature for the atom atom.
AtomSignature(IAtom atom, int height, signature.AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule) Create an atom signature for the atom atom, with maximum height of height, and using a particular invariant type.
AtomSignature(IAtom atom, int height, IAtomContainer molecule) Create an atom signature for the atom atom and with a maximum height of height.
AtomSignature(int atomIndex, IAtomContainer molecule) Create an atom signature starting at atomIndex.
AtomSignature(int atomIndex, int height, signature.AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule) Create an atom signature starting at atomIndex, with maximum height of height, and using a particular invariant type.
AtomSignature(int atomIndex, int height, IAtomContainer molecule) Create an atom signature starting at atomIndex and with a maximum height of height.

Method Summary

Methods

Modifier and Type	Method and Description
protected int	convertEdgeLabelToColor(String edgeLabel)
protected int[]	getConnected(int vertexIndex)
protected String	getEdgeLabel(int vertexIndex, int otherVertexIndex)
protected int	getIntLabel(int vertexIndex)
protected String	getVertexSymbol(int vertexIndex)

Methods inherited from class signature.AbstractVertexSignature

accept, canonize, create, createMaximumHeight, getCanonicalLabelling, getHeight, getOriginalVertexIndex, getVertexCount, parse, toCanonicalString, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomSignature

public AtomSignature(int atomIndex,
             IAtomContainer molecule)

Create an atom signature starting at atomIndex.

Parameters:

atomIndex - the index of the atom that roots this signature

molecule - the molecule to create the signature from

AtomSignature

public AtomSignature(IAtom atom,
             IAtomContainer molecule)

Create an atom signature for the atom atom.

Parameters:

atom - the atom to make the signature for

molecule - the molecule to create the signature from

AtomSignature

public AtomSignature(int atomIndex,
             int height,
             IAtomContainer molecule)

Create an atom signature starting at atomIndex and with a maximum height of height.

Parameters:

atomIndex - the index of the atom that roots this signature

height - the maximum height of the signature

molecule - the molecule to create the signature from

AtomSignature

public AtomSignature(IAtom atom,
             int height,
             IAtomContainer molecule)

Create an atom signature for the atom atom and with a maximum height of height.

Parameters:

atom - the index of the atom that roots this signature

height - the maximum height of the signature

molecule - the molecule to create the signature from

AtomSignature

public AtomSignature(int atomIndex,
             int height,
             signature.AbstractVertexSignature.InvariantType invariantType,
             IAtomContainer molecule)

Create an atom signature starting at atomIndex, with maximum height of height, and using a particular invariant type.

Parameters:

atomIndex - the index of the atom that roots this signature

height - the maximum height of the signature

invariantType - the type of invariant (int, string, ...)

molecule - the molecule to create the signature from

AtomSignature

public AtomSignature(IAtom atom,
             int height,
             signature.AbstractVertexSignature.InvariantType invariantType,
             IAtomContainer molecule)

Create an atom signature for the atom atom, with maximum height of height, and using a particular invariant type.

Parameters:

atom - the index of the atom that roots this signature

height - the maximum height of the signature

invariantType - the type of invariant (int, string, ...)

molecule - the molecule to create the signature from

Method Detail

getIntLabel

protected int getIntLabel(int vertexIndex)

Specified by:

getIntLabel in class signature.AbstractVertexSignature

getConnected

protected int[] getConnected(int vertexIndex)

Specified by:

getConnected in class signature.AbstractVertexSignature

getEdgeLabel

protected String getEdgeLabel(int vertexIndex,
                  int otherVertexIndex)

Specified by:

getEdgeLabel in class signature.AbstractVertexSignature

getVertexSymbol

protected String getVertexSymbol(int vertexIndex)

Specified by:

getVertexSymbol in class signature.AbstractVertexSignature

convertEdgeLabelToColor

protected int convertEdgeLabelToColor(String edgeLabel)

Specified by:

convertEdgeLabelToColor in class signature.AbstractVertexSignature