java.lang.Object
- org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks

```
@Deprecated
public class McGregorChecks
extends Object
```
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

Class to perform check/methods for McGregor class.

Author:

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

Source code:
main

Belongs to CDK module:
smsd

Constructor Summary

Constructors
Constructor Description

McGregorChecks()
Deprecated.

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	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, List<Integer> iBondNeighbors, List<String> cBondNeighbors)`	Deprecated.
`protected static int`	`changeCharBonds(int correspondingAtom, String newSymbol, int neighborBondNum, IAtomContainer atomContainer, 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:

Class McGregorChecks

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

McGregorChecks

Method Detail

isFurtherMappingPossible

isMatchFeasible

searchCorrespondingAtom

isAtomMatch

removeTreeStructure

removeRecurringMappings

removeRedundantArcs

generateCSetCopy

generateCTabCopy

case1

case2

case3

case4

cases

setArcs

countArcsLeft

changeCharBonds

changeCharBonds