Package chemaxon.marvin.alignment
Interface PairwiseComparison
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- All Known Implementing Classes:
PairwiseAlignment
,PairwiseSimilarity3D
@PublicAPI public interface PairwiseComparison
This interface designed for comparing two molecules in 3D by various overlay methodologies. One of molecules is called the query and the other is the target. The comparison results in the best overlay: the orientation and the conformation. The shape Tanimoto and the overlay score may be retrieved. Example usage:PairwiseComparison pc = new PairwiseAlignment(); pc.setQueryRigidForced(true); pc.setTargetRigidForced(false); pc.setCount(4); pc.setQuery(Molecule query); double score = pc.similarity(Molecule target); double tanimoto = pc.getShapeTanimoto();
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addNodeColorWeight(int t1, int t2, double w)
Molecule
getAlignedMoleculesAsFragments()
After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.Molecule
getAlignedQuery()
Molecule
getAlignedTarget()
double
getShapeTanimoto()
void
removeAllMolecules()
void
setCount(int count)
void
setLicenseEnvironment(String env)
void
setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
void
setQuery(AlignmentMolecule query)
void
setQuery(Molecule query)
void
setQueryRigidForced(boolean forced)
Set this molecule to be rigid in the input conformation even if it contains rotatable bondsvoid
setTargetRigidForced(boolean forced)
Set this molecule to be rigid in the input conformation even if it contains rotatable bondsdouble
similarity(AlignmentMolecule target)
double
similarity(Molecule target)
Calculates the 3D similarity between the previously set query and the target.
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Method Detail
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setQuery
void setQuery(Molecule query) throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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similarity
double similarity(Molecule target) throws chemaxon.marvin.alignment.AlignmentException
Calculates the 3D similarity between the previously set query and the target.- Parameters:
target
- target to calculate similarity- Returns:
- the similarity value.
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setQuery
void setQuery(AlignmentMolecule query) throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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similarity
double similarity(AlignmentMolecule target) throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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getAlignedMoleculesAsFragments
Molecule getAlignedMoleculesAsFragments()
After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.- Returns:
- the aligned molecules.
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getAlignedTarget
Molecule getAlignedTarget()
- Returns:
- the target molecule in the final orientation and conformation.
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getAlignedQuery
Molecule getAlignedQuery()
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removeAllMolecules
void removeAllMolecules()
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setProgressBar
void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
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setQueryRigidForced
void setQueryRigidForced(boolean forced)
Set this molecule to be rigid in the input conformation even if it contains rotatable bonds- Parameters:
forced
- if true than rigid.
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setTargetRigidForced
void setTargetRigidForced(boolean forced)
Set this molecule to be rigid in the input conformation even if it contains rotatable bonds- Parameters:
forced
- if true than rigid.
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addNodeColorWeight
void addNodeColorWeight(int t1, int t2, double w)
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getShapeTanimoto
double getShapeTanimoto() throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setLicenseEnvironment
void setLicenseEnvironment(String env)
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setCount
void setCount(int count)
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