@Deprecated public abstract class AbstractMCS extends Object
Constructor and Description |
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AbstractMCS()
Deprecated.
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Modifier and Type | Method and Description |
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abstract 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.
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abstract 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.
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abstract double |
getBondInSensitiveTimeOut()
Deprecated.
get timeout in mins for bond insensitive searches
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abstract double |
getBondSensitiveTimeOut()
Deprecated.
get timeout in mins for bond sensitive searches
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abstract Double |
getEnergyScore(int key)
Deprecated.
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
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abstract double |
getEuclideanDistance()
Deprecated.
Returns Euclidean Distance between query and target molecule.
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abstract Map<IAtom,IAtom> |
getFirstAtomMapping()
Deprecated.
Returns one of the best matches with atoms mapped.
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abstract Map<Integer,Integer> |
getFirstMapping()
Deprecated.
Returns one of the best matches with atom indexes mapped.
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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.
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abstract IAtomContainer |
getProductMolecule()
Deprecated.
Returns modified target molecule on which mapping was
performed.
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abstract IAtomContainer |
getReactantMolecule()
Deprecated.
Returns modified query molecule on which mapping was
performed.
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abstract Integer |
getStereoScore(int key)
Deprecated.
Returns a number which denotes the quality of the mcs.
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abstract double |
getTanimotoSimilarity()
Deprecated.
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
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abstract void |
init(IAtomContainer source,
IAtomContainer target,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
Deprecated.
initialize query and target molecules.
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abstract void |
init(IQueryAtomContainer source,
IAtomContainer target)
Deprecated.
initialize query and target molecules.
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abstract boolean |
isStereoMisMatch()
Deprecated.
Returns true if mols have different stereo
chemistry else false if no stereo mismatch.
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abstract boolean |
isSubgraph()
Deprecated.
Checks if query is a subgraph of the target.
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abstract void |
setBondInSensitiveTimeOut(double bondInSensitiveTimeOut)
Deprecated.
set timeout in mins (default 1.00 min) for bond insensitive searches
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abstract void |
setBondSensitiveTimeOut(double bondSensitiveTimeOut)
Deprecated.
set timeout in mins (default 0.10 min) for bond sensitive searches
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abstract void |
setChemFilters(boolean stereoFilter,
boolean fragmentFilter,
boolean energyFilter)
Deprecated.
initialize query and target molecules.
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public abstract void init(IAtomContainer source, IAtomContainer target, boolean removeHydrogen, boolean cleanAndConfigureMolecule) throws CDKException
source
- query moltarget
- target molremoveHydrogen
- true if remove H (implicit) before mappingcleanAndConfigureMolecule
- eg: percieveAtomTypesAndConfigureAtoms, detect aromaticity etcCDKException
public abstract void init(IQueryAtomContainer source, IAtomContainer target) throws CDKException
source
- query moltarget
- target molCDKException
public abstract void setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter)
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 energypublic abstract Double getEnergyScore(int key)
key
- Index of the mapping solutionpublic abstract Integer getFragmentSize(int key)
key
- Index of the mapping solutionpublic abstract IAtomContainer getProductMolecule()
public abstract IAtomContainer getReactantMolecule()
public abstract Integer getStereoScore(int key)
key
- Index of the mapping solutionpublic abstract boolean isStereoMisMatch()
public abstract boolean isSubgraph()
public abstract double getTanimotoSimilarity() throws IOException
IOException
public abstract double getEuclideanDistance() throws IOException
IOException
public abstract List<Map<IAtom,IAtom>> getAllAtomMapping()
public abstract List<Map<Integer,Integer>> getAllMapping()
public abstract Map<IAtom,IAtom> getFirstAtomMapping()
public abstract Map<Integer,Integer> getFirstMapping()
public abstract double getBondSensitiveTimeOut()
public abstract void setBondSensitiveTimeOut(double bondSensitiveTimeOut)
bondSensitiveTimeOut
- the bond Sensitive Timeout in mins (default 0.30 min)public abstract double getBondInSensitiveTimeOut()
public abstract void setBondInSensitiveTimeOut(double bondInSensitiveTimeOut)
bondInSensitiveTimeOut
- the bond insensitiveCopyright © 2021. All rights reserved.