org.openscience.cdk.smsd.algorithm.mcgregor

Class McGregorChecks

java.lang.Object

org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks

Deprecated.

SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

@Deprecated
public class McGregorChecks
extends Object

Class to perform check/methods for McGregor class.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
McGregorChecks() Deprecated.

Method Summary

Modifier and Type	Method and Description
protected static boolean	case1(int g1Atom, int g3Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4) Deprecated.
protected static boolean	case2(int g2Atom, int g3Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4) Deprecated.
protected static boolean	case3(int g1Atom, int g3Atom, int g2Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4) Deprecated.
protected static boolean	case4(int g1Atom, int g2Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4) Deprecated.
protected static boolean	cases(int g1Atom, int g2Atom, int g3Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4) Deprecated.
protected static int	changeCharBonds(int correspondingAtom, String newSymbol, int neighborBondNum, IAtomContainer atomContainer, List<String> cBondNeighbors) Deprecated.
protected static int	changeCharBonds(int correspondingAtom, String newSymbol, int neighborBondNum, List<Integer> iBondNeighbors, List<String> cBondNeighbors) Deprecated.
protected static int	countArcsLeft(List<Integer> tempmarcs, int neighborBondNumA, int neighborBondNumB) Deprecated.
protected static List<String>	generateCSetCopy(int bondNumber, List<String> cSet) Deprecated.
protected static List<String>	generateCTabCopy(IAtomContainer atomContainer) Deprecated.
protected static boolean	isAtomMatch(String g1A, String g2A, String g1B, String g2B) Deprecated.
protected static boolean	isFurtherMappingPossible(IAtomContainer source, IAtomContainer target, int neighborBondNumA, int neighborBondNumB, List<Integer> iBondNeighborAtomsA, List<Integer> iBondNeighborAtomsB, List<String> cBondNeighborsA, List<String> cBondNeighborsB, boolean shouldMatchBonds) Deprecated.
protected static boolean	isMatchFeasible(IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds) Deprecated.
protected static List<Integer>	removeRecurringMappings(List<Integer> atomMapping) Deprecated.
protected static void	removeRedundantArcs(int row, int column, List<Integer> marcs, McgregorHelper mcGregorHelper) Deprecated. The function is called in function partsearch.
protected static int	removeTreeStructure(BinaryTree curStruc) Deprecated.
protected static int	searchCorrespondingAtom(int mappedAtomsSize, int atomFromOtherMolecule, int molecule, List<Integer> mappedAtomsOrg) Deprecated.
protected static List<Integer>	setArcs(IAtomContainer source, IAtomContainer target, int neighborBondNumA, int neighborBondNumB, List<Integer> iBondNeighborAtomsA, List<Integer> iBondNeighborAtomsB, List<String> cBondNeighborsA, List<String> cBondNeighborsB, List<Integer> modifiedARCS, boolean shouldMatchBonds) Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

McGregorChecks

public McGregorChecks()

Deprecated.

Method Detail

isFurtherMappingPossible

protected static boolean isFurtherMappingPossible(IAtomContainer source,
                                                  IAtomContainer target,
                                                  int neighborBondNumA,
                                                  int neighborBondNumB,
                                                  List<Integer> iBondNeighborAtomsA,
                                                  List<Integer> iBondNeighborAtomsB,
                                                  List<String> cBondNeighborsA,
                                                  List<String> cBondNeighborsB,
                                                  boolean shouldMatchBonds)

Deprecated.

Parameters:

source -

target -

neighborBondNumA -

neighborBondNumB -

iBondNeighborAtomsA -

iBondNeighborAtomsB -

cBondNeighborsA -

cBondNeighborsB -

shouldMatchBonds -

Returns:

isMatchFeasible

protected static boolean isMatchFeasible(IAtomContainer ac1,
                                         IBond bondA1,
                                         IAtomContainer ac2,
                                         IBond bondA2,
                                         boolean shouldMatchBonds)

Deprecated.

searchCorrespondingAtom

protected static int searchCorrespondingAtom(int mappedAtomsSize,
                                             int atomFromOtherMolecule,
                                             int molecule,
                                             List<Integer> mappedAtomsOrg)

Deprecated.

Parameters:

mappedAtomsSize -

atomFromOtherMolecule -

molecule -

mappedAtomsOrg -

Returns:

isAtomMatch

protected static boolean isAtomMatch(String g1A,
                                     String g2A,
                                     String g1B,
                                     String g2B)

Deprecated.

Parameters:

g1A -

g2A -

g1B -

g2B -

Returns:

removeTreeStructure

protected static int removeTreeStructure(BinaryTree curStruc)

Deprecated.

removeRecurringMappings

protected static List<Integer> removeRecurringMappings(List<Integer> atomMapping)

Deprecated.

Parameters:

atomMapping -

Returns:

removeRedundantArcs

protected static void removeRedundantArcs(int row,
                                          int column,
                                          List<Integer> marcs,
                                          McgregorHelper mcGregorHelper)

Deprecated.

The function is called in function partsearch. The function is given a temporary matrix and a position (row/column) within this matrix. First the function sets all entries to zero, which can be exlcuded in respect to the current atom by atom matching. After this the function replaces all entries in the same row and column of the current position by zeros. Only the entry of the current position is set to one. Return value "count_arcsleft" counts the number of arcs, which are still in the matrix.

Parameters:

row -

column -

marcs -

mcGregorHelper -

generateCSetCopy

protected static List<String> generateCSetCopy(int bondNumber,
                                               List<String> cSet)

Deprecated.

Parameters:

bondNumber -

cSet -

Returns:

generateCTabCopy

protected static List<String> generateCTabCopy(IAtomContainer atomContainer)
                                        throws IOException

Deprecated.

Parameters:

atomContainer -

Returns:

Throws:

IOException

case1

protected static boolean case1(int g1Atom,
                               int g3Atom,
                               int g4Atom,
                               int rowAtom1,
                               int rowAtom2,
                               int columnAtom3,
                               int columnAtom4)

Deprecated.

Parameters:

g1Atom -

g3Atom -

g4Atom -

rowAtom1 -

rowAtom2 -

columnAtom3 -

columnAtom4 -

Returns:

case2

protected static boolean case2(int g2Atom,
                               int g3Atom,
                               int g4Atom,
                               int rowAtom1,
                               int rowAtom2,
                               int columnAtom3,
                               int columnAtom4)

Deprecated.

Parameters:

g2Atom -

g3Atom -

g4Atom -

rowAtom1 -

rowAtom2 -

columnAtom3 -

columnAtom4 -

Returns:

case3

protected static boolean case3(int g1Atom,
                               int g3Atom,
                               int g2Atom,
                               int rowAtom1,
                               int rowAtom2,
                               int columnAtom3,
                               int columnAtom4)

Deprecated.

Parameters:

g1Atom -

g3Atom -

g2Atom -

rowAtom1 -

rowAtom2 -

columnAtom3 -

columnAtom4 -

Returns:

case4

protected static boolean case4(int g1Atom,
                               int g2Atom,
                               int g4Atom,
                               int rowAtom1,
                               int rowAtom2,
                               int columnAtom3,
                               int columnAtom4)

Deprecated.

Parameters:

g1Atom -

g2Atom -

g4Atom -

rowAtom1 -

rowAtom2 -

columnAtom3 -

columnAtom4 -

Returns:

cases

protected static boolean cases(int g1Atom,
                               int g2Atom,
                               int g3Atom,
                               int g4Atom,
                               int rowAtom1,
                               int rowAtom2,
                               int columnAtom3,
                               int columnAtom4)

Deprecated.

Parameters:

g1Atom -

g2Atom -

g3Atom -

g4Atom -

rowAtom1 -

rowAtom2 -

columnAtom3 -

columnAtom4 -

Returns:

setArcs

protected static List<Integer> setArcs(IAtomContainer source,
                                       IAtomContainer target,
                                       int neighborBondNumA,
                                       int neighborBondNumB,
                                       List<Integer> iBondNeighborAtomsA,
                                       List<Integer> iBondNeighborAtomsB,
                                       List<String> cBondNeighborsA,
                                       List<String> cBondNeighborsB,
                                       List<Integer> modifiedARCS,
                                       boolean shouldMatchBonds)

Deprecated.

Parameters:

source -

target -

neighborBondNumA -

neighborBondNumB -

iBondNeighborAtomsA -

iBondNeighborAtomsB -

cBondNeighborsA -

cBondNeighborsB -

modifiedARCS -

shouldMatchBonds -

Returns:

countArcsLeft

protected static int countArcsLeft(List<Integer> tempmarcs,
                                   int neighborBondNumA,
                                   int neighborBondNumB)

Deprecated.

Parameters:

tempmarcs -

neighborBondNumA -

neighborBondNumB -

Returns:

changeCharBonds

protected static int changeCharBonds(int correspondingAtom,
                                     String newSymbol,
                                     int neighborBondNum,
                                     IAtomContainer atomContainer,
                                     List<String> cBondNeighbors)

Deprecated.

Parameters:

correspondingAtom -

newSymbol -

neighborBondNum -

atomContainer -

cBondNeighbors -

Returns:

changeCharBonds

protected static int changeCharBonds(int correspondingAtom,
                                     String newSymbol,
                                     int neighborBondNum,
                                     List<Integer> iBondNeighbors,
                                     List<String> cBondNeighbors)

Deprecated.

Parameters:

correspondingAtom -

newSymbol -

neighborBondNum -

iBondNeighbors -

cBondNeighbors -

Returns: