Class AbstractMCS
java.lang.Object
org.openscience.cdk.smsd.interfaces.AbstractMCS
- Direct Known Subclasses:
Isomorphism
Deprecated.
SMSD has been deprecated from the CDK with a newer, more recent
version of SMSD is available at http://github.com/asad/smsd.
Interface for all MCS algorithms.
- Author:
- Syed Asad Rahman <asad@ebi.ac.uk>
- Source code:
- main
- Belongs to CDK module:
- smsd
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionDeprecated.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.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.abstract double
Deprecated.get timeout in mins for bond insensitive searchesabstract double
Deprecated.get timeout in mins for bond sensitive searchesabstract Double
getEnergyScore
(int key) Deprecated.Returns summation energy score of the disorder if the MCS is removed from the target and query graph.abstract double
Deprecated.Returns Euclidean Distance between query and target molecule.Deprecated.Returns one of the best matches with atoms mapped.Deprecated.Returns one of the best matches with atom indexes mapped.abstract 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.abstract IAtomContainer
Deprecated.Returns modified target molecule on which mapping was performed.abstract IAtomContainer
Deprecated.Returns modified query molecule on which mapping was performed.abstract Integer
getStereoScore
(int key) Deprecated.Returns a number which denotes the quality of the mcs.abstract double
Deprecated.Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).abstract void
init
(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule) Deprecated.initialize query and target molecules.abstract void
init
(IQueryAtomContainer source, IAtomContainer target) Deprecated.initialize query and target molecules.abstract boolean
Deprecated.Returns true if mols have different stereo chemistry else false if no stereo mismatch.abstract boolean
Deprecated.Checks if query is a subgraph of the target.abstract void
setBondInSensitiveTimeOut
(double bondInSensitiveTimeOut) Deprecated.set timeout in mins (default 1.00 min) for bond insensitive searchesabstract void
setBondSensitiveTimeOut
(double bondSensitiveTimeOut) Deprecated.set timeout in mins (default 0.10 min) for bond sensitive searchesabstract void
setChemFilters
(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) Deprecated.initialize query and target molecules.
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Constructor Details
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AbstractMCS
public AbstractMCS()Deprecated.
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Method Details
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init
public abstract void init(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule) throws CDKException Deprecated.initialize query and target molecules.- Parameters:
source
- query moltarget
- target molremoveHydrogen
- true if remove H (implicit) before mappingcleanAndConfigureMolecule
- eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etc- Throws:
CDKException
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init
Deprecated.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.- Parameters:
source
- query moltarget
- target mol- Throws:
CDKException
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setChemFilters
public abstract void setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) Deprecated.initialize query and target molecules.- Parameters:
stereoFilter
- set true to rank the solutions as per stereo matchesfragmentFilter
- set true to return matches with minimum fragmentsenergyFilter
- set true to return matches with minimum bond changes based on the bond breaking energy
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getEnergyScore
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.- Parameters:
key
- Index of the mapping solution- Returns:
- Total bond breaking energy required to remove the mapped part
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getFragmentSize
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.- Parameters:
key
- Index of the mapping solution- Returns:
- Fragment count(s) generated after removing the mapped parts
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getProductMolecule
Deprecated.Returns modified target molecule on which mapping was performed.- Returns:
- return modified product Molecule
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getReactantMolecule
Deprecated.Returns modified query molecule on which mapping was performed.- Returns:
- return modified reactant Molecule
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getStereoScore
Deprecated.Returns a number which denotes the quality of the mcs. A solution with highest stereo score is preferred over other scores.- Parameters:
key
- Index of the mapping solution- Returns:
- true if no stereo mismatch occurs else false if stereo mismatch occurs
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isStereoMisMatch
public abstract boolean isStereoMisMatch()Deprecated.Returns true if mols have different stereo chemistry else false if no stereo mismatch.- 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.
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isSubgraph
public abstract boolean isSubgraph()Deprecated.Checks if query is a subgraph of the target. Returns true if query is a subgraph of target else false- Returns:
- true if query molecule is a subgraph of the target molecule
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getTanimotoSimilarity
Deprecated.Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).- Returns:
- Tanimoto Similarity between 0 and 1
- Throws:
IOException
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getEuclideanDistance
Deprecated.Returns Euclidean Distance between query and target molecule.- Returns:
- Euclidean Distance (lower the score, better the match)
- Throws:
IOException
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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.- Returns:
- All possible MCS atom Mappings
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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.- Returns:
- All possible MCS Mapping Index
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getFirstAtomMapping
Deprecated.Returns one of the best matches with atoms mapped.- Returns:
- Best Atom Mapping
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getFirstMapping
Deprecated.Returns one of the best matches with atom indexes mapped.- Returns:
- Best Mapping Index
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getBondSensitiveTimeOut
public abstract double getBondSensitiveTimeOut()Deprecated.get timeout in mins for bond sensitive searches- Returns:
- the bondSensitive TimeOut
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setBondSensitiveTimeOut
public abstract void setBondSensitiveTimeOut(double bondSensitiveTimeOut) Deprecated.set timeout in mins (default 0.10 min) for bond sensitive searches- Parameters:
bondSensitiveTimeOut
- the bond Sensitive Timeout in mins (default 0.30 min)
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getBondInSensitiveTimeOut
public abstract double getBondInSensitiveTimeOut()Deprecated.get timeout in mins for bond insensitive searches- Returns:
- the bondInSensitive TimeOut
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setBondInSensitiveTimeOut
public abstract void setBondInSensitiveTimeOut(double bondInSensitiveTimeOut) Deprecated.set timeout in mins (default 1.00 min) for bond insensitive searches- Parameters:
bondInSensitiveTimeOut
- the bond insensitive
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