org.openscience.cdk.smsd

Class Isomorphism

java.lang.Object

org.openscience.cdk.smsd.interfaces.AbstractMCS

org.openscience.cdk.smsd.Isomorphism

All Implemented Interfaces:

Serializable

Deprecated.

A more recent version of SMSD is available at http://github.com/asad/smsd

@Deprecated
public final class Isomorphism
extends AbstractMCS
implements Serializable

This class implements the Isomorphism- a multipurpose structure comparison tool. It allows users to, i) find the maximal common substructure(s) (MCS); ii) perform the mapping of a substructure in another structure, and; iii) map two isomorphic structures.

It also comes with various published algorithms. The user is free to choose his favorite algorithm to perform MCS or substructure search. For example 0: Isomorphism algorithm, 1: MCSPlus, 2: VFLibMCS, 3: CDKMCS, 4: Substructure

It also has a set of robust chemical filters (i.e. bond energy, fragment count, stereo & bond match) to sort the reported MCS solutions in a chemically relevant manner. Each comparison can be made with or without using the bond sensitive mode and with implicit or explicit hydrogens.

If you are using Isomorphism, please cite Rahman et.al. 2009 [Rahman, S.A. and Bashton, M. and Holliday, G.L. and Schrader, R. and Thornton, J.M. , Small Molecule Subgraph Detector (SMSD) Toolkit, Journal of Cheminformatics, 2009, 1:12, doi:10.1186/1758-2946-1-12]. The Isomorphism algorithm is described in this paper.

An example for Substructure search:

SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  // Benzene
  IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1");
  // Napthalene
  IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2");
  //Turbo mode search
  //Bond Sensitive is set true
  Isomorphism comparison = new Isomorphism(Algorithm.SubStructure, true);
  // set molecules, remove hydrogens, clean and configure molecule
  comparison.init(A1, A2, true, true);
  // set chemical filter true
  comparison.setChemFilters(false, false, false);
  if (comparison.isSubgraph()) {
  //Get similarity score
   System.out.println("Tanimoto coefficient:  " + comparison.getTanimotoSimilarity());
   System.out.println("A1 is a subgraph of A2:  " + comparison.isSubgraph());
  //Get Modified AtomContainer
   IAtomContainer Mol1 = comparison.getReactantMolecule();
   IAtomContainer Mol2 = comparison.getProductMolecule();
  // Print the mapping between molecules
   System.out.println(" Mappings: ");
   for (Map.Entry <Integer, Integer> mapping : comparison.getFirstMapping().entrySet()) {
      System.out.println((mapping.getKey() + 1) + " " + (mapping.getValue() + 1));

      IAtom eAtom = Mol1.getAtom(mapping.getKey());
      IAtom pAtom = Mol2.getAtom(mapping.getValue());
      System.out.println(eAtom.getSymbol() + " " + pAtom.getSymbol());
   }
   System.out.println("");
  }
  

An example for MCS search:

SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  // Benzene
  IAtomContainer A1 = sp.parseSmiles("C1=CC=CC=C1");
  // Napthalene
  IAtomContainer A2 = sp.parseSmiles("C1=CC2=C(C=C1)C=CC=C2");
  //{ 0: Default Isomorphism Algorithm, 1: MCSPlus Algorithm, 2: VFLibMCS Algorithm, 3: CDKMCS Algorithm}
  //Bond Sensitive is set true
  Isomorphism comparison = new Isomorphism(Algorithm.DEFAULT, true);
  // set molecules, remove hydrogens, clean and configure molecule
  comparison.init(A1, A2, true, true);
  // set chemical filter true
  comparison.setChemFilters(true, true, true);

  //Get similarity score
  System.out.println("Tanimoto coefficient:  " + comparison.getTanimotoSimilarity());
  System.out.println("A1 is a subgraph of A2:  " + comparison.isSubgraph());
  //Get Modified AtomContainer
  IAtomContainer Mol1 = comparison.getReactantMolecule();
  IAtomContainer Mol2 = comparison.getProductMolecule();
  // Print the mapping between molecules
  System.out.println(" Mappings: ");
  for (Map.Entry <Integer, Integer> mapping : comparison.getFirstMapping().entrySet()) {
      System.out.println((mapping.getKey() + 1) + " " + (mapping.getValue() + 1));

      IAtom eAtom = Mol1.getAtom(mapping.getKey());
      IAtom pAtom = Mol2.getAtom(mapping.getValue());
      System.out.println(eAtom.getSymbol() + " " + pAtom.getSymbol());
  }
  System.out.println("");
  

Author:

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

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

smsd

Requires:

java1.5+

Constructor Summary

Constructors

Constructor and Description
Isomorphism(Algorithm algorithmType, boolean bondTypeFlag) Deprecated. This is the algorithm factory and entry port for all the MCS algorithm in the Isomorphism supported algorithm Algorithm types: 0: Default, 1: MCSPlus, 2: VFLibMCS, 3: CDKMCS, 4: SubStructure

Method Summary

Methods

Modifier and Type	Method and Description
List<Map<IAtom,IAtom>>	getAllAtomMapping() Deprecated. Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
List<Map<IBond,IBond>>	getAllBondMaps() Deprecated.
List<Map<Integer,Integer>>	getAllMapping() Deprecated. Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e.
double	getBondInSensitiveTimeOut() Deprecated. get timeout in mins for bond insensitive searches
double	getBondSensitiveTimeOut() Deprecated. get timeout in mins for bond sensitive searches
Double	getEnergyScore(int key) Deprecated. Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
double	getEuclideanDistance() Deprecated. Returns Euclidean Distance between query and target molecule.
Map<IAtom,IAtom>	getFirstAtomMapping() Deprecated. Returns one of the best matches with atoms mapped.
Map<IBond,IBond>	getFirstBondMap() Deprecated.
Map<Integer,Integer>	getFirstMapping() Deprecated. Returns one of the best matches with atom indexes mapped.
Integer	getFragmentSize(int key) Deprecated. Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
IAtomContainer	getProductMolecule() Deprecated. Returns modified target molecule on which mapping was performed.
IAtomContainer	getReactantMolecule() Deprecated. Returns modified query molecule on which mapping was performed.
Integer	getStereoScore(int key) Deprecated. Returns a number which denotes the quality of the mcs.
double	getTanimotoAtomSimilarity() Deprecated.
double	getTanimotoBondSimilarity() Deprecated.
double	getTanimotoSimilarity() Deprecated. Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
void	init(IAtomContainer reactant, IAtomContainer product, boolean removeHydrogen, boolean cleanAndConfigureMolecule) Deprecated. initialize query and target molecules.
void	init(IQueryAtomContainer reactant, IAtomContainer product) Deprecated. initialize query and target molecules.
void	init(String sourceMolFileName, String targetMolFileName, boolean removeHydrogen, boolean cleanAndConfigureMolecule) Deprecated. Initialize the query and targetAtomCount mol via mol files
boolean	isMatchBonds() Deprecated.
boolean	isStereoMisMatch() Deprecated. Returns true if mols have different stereo chemistry else false if no stereo mismatch.
boolean	isSubgraph() Deprecated. Checks if query is a subgraph of the target.
boolean	isTimeOut() Deprecated.
static Map<IBond,IBond>	makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2, Map<IAtom,IAtom> mapping) Deprecated. Returns bond map between source and target molecules based on the atoms
static List<Map<IBond,IBond>>	makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2, List<Map<IAtom,IAtom>> mappings) Deprecated. Returns bond maps between source and target molecules based on the atoms
void	resetTimeOut() Deprecated.
void	setBondInSensitiveTimeOut(double bondInSensitiveTimeOut) Deprecated. set timeout in mins (default 1.00 min) for bond insensitive searches
void	setBondSensitiveTimeOut(double bondSensitiveTimeOut) Deprecated. set timeout in mins (default 0.10 min) for bond sensitive searches
void	setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) Deprecated. initialize query and target molecules.
void	setMatchBonds(boolean matchBonds) Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

Isomorphism

public Isomorphism(Algorithm algorithmType,
           boolean bondTypeFlag)

Deprecated.

This is the algorithm factory and entry port for all the MCS algorithm in the Isomorphism supported algorithm Algorithm types:

1. 0: Default,
2. 1: MCSPlus,
3. 2: VFLibMCS,
4. 3: CDKMCS,
5. 4: SubStructure

Parameters:

algorithmType - Algorithm

bondTypeFlag -

Method Detail

makeBondMapsOfAtomMaps

public static List<Map<IBond,IBond>> makeBondMapsOfAtomMaps(IAtomContainer ac1,
                                            IAtomContainer ac2,
                                            List<Map<IAtom,IAtom>> mappings)

Deprecated.

Returns bond maps between source and target molecules based on the atoms

Parameters:

ac1 - source molecule

ac2 - target molecule

mappings - mappings between source and target molecule atoms

Returns:

bond maps between source and target molecules based on the atoms

makeBondMapOfAtomMap

public static Map<IBond,IBond> makeBondMapOfAtomMap(IAtomContainer ac1,
                                    IAtomContainer ac2,
                                    Map<IAtom,IAtom> mapping)

Deprecated.

Returns bond map between source and target molecules based on the atoms

Parameters:

ac1 - source molecule

ac2 - target molecule

mapping - mappings between source and target molecule atoms

Returns:

bond map between source and target molecules based on the atoms

isTimeOut

public boolean isTimeOut()

Deprecated.

resetTimeOut

public void resetTimeOut()

Deprecated.

init

public void init(IQueryAtomContainer reactant,
        IAtomContainer product)
          throws CDKException

Deprecated.

Description copied from class: AbstractMCS

initialize query and target molecules. Note: Here its assumed that hydrogens are implicit and user has called these two methods percieveAtomTypesAndConfigureAtoms and CDKAromicityDetector before initializing calling this method.

Specified by:

init in class AbstractMCS

Parameters:

reactant -

product -

Throws:

CDKException

init

public void init(IAtomContainer reactant,
        IAtomContainer product,
        boolean removeHydrogen,
        boolean cleanAndConfigureMolecule)
          throws CDKException

Deprecated.

initialize query and target molecules.

Specified by:

init in class AbstractMCS

Parameters:

reactant -

product -

removeHydrogen - true if remove H (implicit) before mapping

cleanAndConfigureMolecule - eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etc

Throws:

CDKException

init

public void init(String sourceMolFileName,
        String targetMolFileName,
        boolean removeHydrogen,
        boolean cleanAndConfigureMolecule)
          throws CDKException

Deprecated.

Initialize the query and targetAtomCount mol via mol files

Parameters:

sourceMolFileName - source mol file name

targetMolFileName - target mol file name

removeHydrogen - set true to make hydrogens implicit before search

cleanAndConfigureMolecule - eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etc

Throws:

CDKException

setChemFilters

public void setChemFilters(boolean stereoFilter,
                  boolean fragmentFilter,
                  boolean energyFilter)

Deprecated.

initialize query and target molecules.

Specified by:

setChemFilters in class AbstractMCS

Parameters:

stereoFilter - set true to rank the solutions as per stereo matches

fragmentFilter - set true to return matches with minimum fragments

energyFilter - set true to return matches with minimum bond changes based on the bond breaking energy

getFragmentSize

public Integer getFragmentSize(int key)

Deprecated.

Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph. Amongst the solutions, a solution with lowest fragment size is preferred.

Specified by:

getFragmentSize in class AbstractMCS

Parameters:

key - Index of the mapping solution

Returns:

Fragment count(s) generated after removing the mapped parts

getStereoScore

public Integer getStereoScore(int key)

Deprecated.

Returns a number which denotes the quality of the mcs. A solution with highest stereo score is preferred over other scores.

Specified by:

getStereoScore in class AbstractMCS

Parameters:

key - Index of the mapping solution

Returns:

true if no stereo mismatch occurs else false if stereo mismatch occurs

getEnergyScore

public Double getEnergyScore(int key)

Deprecated.

Returns summation energy score of the disorder if the MCS is removed from the target and query graph. Amongst the solutions, a solution with lowest energy score is preferred.

Specified by:

getEnergyScore in class AbstractMCS

Parameters:

key - Index of the mapping solution

Returns:

Total bond breaking energy required to remove the mapped part

getFirstMapping

public Map<Integer,Integer> getFirstMapping()

Deprecated.

Returns one of the best matches with atom indexes mapped.

Specified by:

getFirstMapping in class AbstractMCS

Returns:

Best Mapping Index

getAllMapping

public List<Map<Integer,Integer>> getAllMapping()

Deprecated.

Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule.

Specified by:

getAllMapping in class AbstractMCS

Returns:

All possible MCS Mapping Index

getFirstAtomMapping

public Map<IAtom,IAtom> getFirstAtomMapping()

Deprecated.

Returns one of the best matches with atoms mapped.

Specified by:

getFirstAtomMapping in class AbstractMCS

Returns:

Best Atom Mapping

getAllAtomMapping

public List<Map<IAtom,IAtom>> getAllAtomMapping()

Deprecated.

Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule.

Specified by:

getAllAtomMapping in class AbstractMCS

Returns:

All possible MCS atom Mappings

getReactantMolecule

public IAtomContainer getReactantMolecule()

Deprecated.

Returns modified query molecule on which mapping was performed.

Specified by:

getReactantMolecule in class AbstractMCS

Returns:

return modified reactant Molecule

getProductMolecule

public IAtomContainer getProductMolecule()

Deprecated.

Returns modified target molecule on which mapping was performed.

Specified by:

getProductMolecule in class AbstractMCS

Returns:

return modified product Molecule

getTanimotoSimilarity

public double getTanimotoSimilarity()
                             throws IOException

Deprecated.

Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).

Specified by:

getTanimotoSimilarity in class AbstractMCS

Returns:

Tanimoto Similarity between 0 and 1

Throws:

IOException

getTanimotoAtomSimilarity

public double getTanimotoAtomSimilarity()
                                 throws IOException

Deprecated.

Throws:

IOException

getTanimotoBondSimilarity

public double getTanimotoBondSimilarity()
                                 throws IOException

Deprecated.

Throws:

IOException

isStereoMisMatch

public boolean isStereoMisMatch()

Deprecated.

Returns true if mols have different stereo chemistry else false if no stereo mismatch.

Specified by:

isStereoMisMatch in class AbstractMCS

Returns:

true if mols have different stereo chemistry else false if no stereo mismatch. true if stereo mismatch occurs else true if stereo mismatch occurs.

isSubgraph

public boolean isSubgraph()

Deprecated.

Checks if query is a subgraph of the target. Returns true if query is a subgraph of target else false

Specified by:

isSubgraph in class AbstractMCS

Returns:

true if query molecule is a subgraph of the target molecule

getEuclideanDistance

public double getEuclideanDistance()
                            throws IOException

Deprecated.

Returns Euclidean Distance between query and target molecule.

Specified by:

getEuclideanDistance in class AbstractMCS

Returns:

Euclidean Distance (lower the score, better the match)

Throws:

IOException

getBondSensitiveTimeOut

public double getBondSensitiveTimeOut()

Deprecated.

get timeout in mins for bond sensitive searches

Specified by:

getBondSensitiveTimeOut in class AbstractMCS

Returns:

the bondSensitiveTimeOut

setBondSensitiveTimeOut

public void setBondSensitiveTimeOut(double bondSensitiveTimeOut)

Deprecated.

set timeout in mins (default 0.10 min) for bond sensitive searches

Specified by:

setBondSensitiveTimeOut in class AbstractMCS

Parameters:

bondSensitiveTimeOut - the bond Sensitive Timeout in mins (default 0.10 min)

getBondInSensitiveTimeOut

public double getBondInSensitiveTimeOut()

Deprecated.

get timeout in mins for bond insensitive searches

Specified by:

getBondInSensitiveTimeOut in class AbstractMCS

Returns:

the bondInSensitiveTimeOut

setBondInSensitiveTimeOut

public void setBondInSensitiveTimeOut(double bondInSensitiveTimeOut)

Deprecated.

set timeout in mins (default 1.00 min) for bond insensitive searches

Specified by:

setBondInSensitiveTimeOut in class AbstractMCS

Parameters:

bondInSensitiveTimeOut - the bond insensitive Timeout in mins (default 0.15 min)

isMatchBonds

public boolean isMatchBonds()

Deprecated.

Returns:

the matchBonds

setMatchBonds

public void setMatchBonds(boolean matchBonds)

Deprecated.

Parameters:

matchBonds - the matchBonds to set

getAllBondMaps

public List<Map<IBond,IBond>> getAllBondMaps()

Deprecated.

Returns:

the allBondMCS

getFirstBondMap

public Map<IBond,IBond> getFirstBondMap()

Deprecated.

Returns:

the firstBondMCS