public class McGregorChecks
extends java.lang.Object
Modifier and Type | Method and Description |
---|---|
protected static boolean |
case1(int G1_atom,
int G3_atom,
int G4_atom,
int row_atom1,
int row_atom2,
int column_atom3,
int column_atom4) |
protected static boolean |
case2(int G2_atom,
int G3_atom,
int G4_atom,
int row_atom1,
int row_atom2,
int column_atom3,
int column_atom4) |
protected static boolean |
case3(int G1_atom,
int G3_atom,
int G2_atom,
int row_atom1,
int row_atom2,
int column_atom3,
int column_atom4) |
protected static boolean |
case4(int G1_atom,
int G2_atom,
int G4_atom,
int row_atom1,
int row_atom2,
int column_atom3,
int column_atom4) |
protected static boolean |
cases(int G1_atom,
int G2_atom,
int G3_atom,
int G4_atom,
int row_atom1,
int row_atom2,
int column_atom3,
int column_atom4) |
protected static int |
changeCharBonds(int corresponding_atom,
java.lang.String new_symbol,
int neighbor_bondnum,
org.openscience.cdk.interfaces.IAtomContainer atomContainer,
java.util.List<java.lang.String> c_bond_neighbors) |
protected static int |
changeCharBonds(int corresponding_atom,
java.lang.String new_symbol,
int neighbor_bondnum,
java.util.List<java.lang.Integer> i_bond_neighbors,
java.util.List<java.lang.String> c_bond_neighbors) |
protected static int |
countArcsLeft(java.util.List<java.lang.Integer> TEMPMARCS,
int neighborBondNumA,
int neighborBondNumB) |
protected static java.util.List<java.lang.String> |
generateCSetCopy(int bond_number,
java.util.List<java.lang.String> c_set) |
protected static java.util.List<java.lang.String> |
generateCTabCopy(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
protected static boolean |
isAtomMatch(java.lang.String G1A,
java.lang.String G2A,
java.lang.String G1B,
java.lang.String G2B) |
protected static boolean |
isFurtherMappingPossible(org.openscience.cdk.interfaces.IAtomContainer source,
org.openscience.cdk.interfaces.IAtomContainer target,
int neighborBondNumA,
int neighborBondNumB,
java.util.List<java.lang.Integer> i_bond_neighbor_atoms_A,
java.util.List<java.lang.Integer> i_bond_neighbor_atoms_B,
java.util.List<java.lang.String> cBondNeighborsA,
java.util.List<java.lang.String> cBondNeighborsB,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType) |
protected static boolean |
isMatchFeasible(org.openscience.cdk.interfaces.IBond bondA1,
org.openscience.cdk.interfaces.IBond bondA2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType) |
protected static java.util.List<java.lang.Integer> |
removeRecurringMappings(java.util.List<java.lang.Integer> atom_mapping) |
protected static void |
removeRedundantArcs(int row,
int column,
java.util.List<java.lang.Integer> MARCS,
McgregorHelper mcGregorHelper)
The function is called in function partsearch.
|
protected static int |
removeTreeStructure(BinaryTree cur_struc) |
protected static int |
searchCorrespondingAtom(int mappedAtomsSize,
int atomFromOtherMolecule,
int molecule,
java.util.List<java.lang.Integer> mapped_atoms_org) |
protected static java.util.List<java.lang.Integer> |
setArcs(org.openscience.cdk.interfaces.IAtomContainer source,
org.openscience.cdk.interfaces.IAtomContainer target,
int neighborBondNumA,
int neighborBondNumB,
java.util.List<java.lang.Integer> i_bond_neighbor_atoms_A,
java.util.List<java.lang.Integer> i_bond_neighbor_atoms_B,
java.util.List<java.lang.String> cBondNeighborsA,
java.util.List<java.lang.String> cBondNeighborsB,
java.util.List<java.lang.Integer> modifiedARCS,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType) |
protected static boolean isFurtherMappingPossible(org.openscience.cdk.interfaces.IAtomContainer source, org.openscience.cdk.interfaces.IAtomContainer target, int neighborBondNumA, int neighborBondNumB, java.util.List<java.lang.Integer> i_bond_neighbor_atoms_A, java.util.List<java.lang.Integer> i_bond_neighbor_atoms_B, java.util.List<java.lang.String> cBondNeighborsA, java.util.List<java.lang.String> cBondNeighborsB, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType)
source
- target
- neighborBondNumA
- neighborBondNumB
- i_bond_neighbor_atoms_A
- i_bond_neighbor_atoms_B
- cBondNeighborsA
- cBondNeighborsB
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- protected static boolean isMatchFeasible(org.openscience.cdk.interfaces.IBond bondA1, org.openscience.cdk.interfaces.IBond bondA2, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType)
bondA1
- bondA2
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- protected static int searchCorrespondingAtom(int mappedAtomsSize, int atomFromOtherMolecule, int molecule, java.util.List<java.lang.Integer> mapped_atoms_org)
mappedAtomsSize
- atomFromOtherMolecule
- molecule
- mapped_atoms_org
- protected static boolean isAtomMatch(java.lang.String G1A, java.lang.String G2A, java.lang.String G1B, java.lang.String G2B)
G1A
- G2A
- G1B
- G2B
- protected static int removeTreeStructure(BinaryTree cur_struc)
cur_struc
- protected static java.util.List<java.lang.Integer> removeRecurringMappings(java.util.List<java.lang.Integer> atom_mapping)
atom_mapping
- protected static void removeRedundantArcs(int row, int column, java.util.List<java.lang.Integer> MARCS, McgregorHelper mcGregorHelper)
row
- column
- MARCS
- mcGregorHelper
- protected static java.util.List<java.lang.String> generateCSetCopy(int bond_number, java.util.List<java.lang.String> c_set)
bond_number
- c_set
- protected static java.util.List<java.lang.String> generateCTabCopy(org.openscience.cdk.interfaces.IAtomContainer atomContainer) throws java.io.IOException
atomContainer
- java.io.IOException
protected static boolean case1(int G1_atom, int G3_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4)
G1_atom
- G3_atom
- G4_atom
- row_atom1
- row_atom2
- column_atom3
- column_atom4
- protected static boolean case2(int G2_atom, int G3_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4)
G2_atom
- G3_atom
- G4_atom
- row_atom1
- row_atom2
- column_atom3
- column_atom4
- protected static boolean case3(int G1_atom, int G3_atom, int G2_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4)
G1_atom
- G3_atom
- G2_atom
- row_atom1
- row_atom2
- column_atom3
- column_atom4
- protected static boolean case4(int G1_atom, int G2_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4)
G1_atom
- G2_atom
- G4_atom
- row_atom1
- row_atom2
- column_atom3
- column_atom4
- protected static boolean cases(int G1_atom, int G2_atom, int G3_atom, int G4_atom, int row_atom1, int row_atom2, int column_atom3, int column_atom4)
G1_atom
- G2_atom
- G3_atom
- G4_atom
- row_atom1
- row_atom2
- column_atom3
- column_atom4
- protected static java.util.List<java.lang.Integer> setArcs(org.openscience.cdk.interfaces.IAtomContainer source, org.openscience.cdk.interfaces.IAtomContainer target, int neighborBondNumA, int neighborBondNumB, java.util.List<java.lang.Integer> i_bond_neighbor_atoms_A, java.util.List<java.lang.Integer> i_bond_neighbor_atoms_B, java.util.List<java.lang.String> cBondNeighborsA, java.util.List<java.lang.String> cBondNeighborsB, java.util.List<java.lang.Integer> modifiedARCS, boolean shouldMatchBonds, boolean shouldMatchRings, boolean matchAtomType)
source
- target
- neighborBondNumA
- neighborBondNumB
- i_bond_neighbor_atoms_A
- i_bond_neighbor_atoms_B
- cBondNeighborsA
- cBondNeighborsB
- modifiedARCS
- shouldMatchBonds
- shouldMatchRings
- matchAtomType
- protected static int countArcsLeft(java.util.List<java.lang.Integer> TEMPMARCS, int neighborBondNumA, int neighborBondNumB)
TEMPMARCS
- neighborBondNumA
- neighborBondNumB
- protected static int changeCharBonds(int corresponding_atom, java.lang.String new_symbol, int neighbor_bondnum, org.openscience.cdk.interfaces.IAtomContainer atomContainer, java.util.List<java.lang.String> c_bond_neighbors)
corresponding_atom
- new_symbol
- neighbor_bondnum
- atomContainer
- c_bond_neighbors
- protected static int changeCharBonds(int corresponding_atom, java.lang.String new_symbol, int neighbor_bondnum, java.util.List<java.lang.Integer> i_bond_neighbors, java.util.List<java.lang.String> c_bond_neighbors)
corresponding_atom
- new_symbol
- neighbor_bondnum
- i_bond_neighbors
- c_bond_neighbors
-