Package chemaxon.marvin.alignment
Class PairwiseAlignment
- java.lang.Object
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- chemaxon.marvin.alignment.PairwiseAlignment
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- All Implemented Interfaces:
PairwiseComparison
@PublicAPI public class PairwiseAlignment extends Object implements PairwiseComparison
Align pairs of molecules (query and the target) using the shapeAlignment
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Constructor Summary
Constructors Constructor Description PairwiseAlignment()
PairwiseAlignment(AlignmentProperties ap)
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Method Summary
All Methods Instance Methods Concrete 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
setFlexibleRingSize(int s)
void
setLicenseEnvironment(String env)
void
setMinimumCommonSize(int mcs)
void
setMode(AlignmentAccuracyMode mode)
void
setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
void
setProgressMonitor(MProgressMonitor mp)
void
setQuery(AlignmentMolecule m)
void
setQuery(Molecule m)
void
setQueryRigidForced(boolean forced)
Set this molecule to be rigid in the input conformation even if it contains rotatable bondsvoid
setTargetRigidForced(boolean targetRigid)
Set this molecule to be rigid in the input conformation even if it contains rotatable bondsdouble
similarity(AlignmentMolecule am)
double
similarity(Molecule m)
Calculates the 3D similarity between the previously set query and the target.
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Constructor Detail
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PairwiseAlignment
public PairwiseAlignment(AlignmentProperties ap)
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PairwiseAlignment
public PairwiseAlignment()
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Method Detail
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addNodeColorWeight
public void addNodeColorWeight(int t1, int t2, double w)
- Specified by:
addNodeColorWeight
in interfacePairwiseComparison
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removeAllMolecules
public void removeAllMolecules()
- Specified by:
removeAllMolecules
in interfacePairwiseComparison
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setQuery
public void setQuery(Molecule m) throws chemaxon.marvin.alignment.AlignmentException
- Specified by:
setQuery
in interfacePairwiseComparison
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setQuery
public void setQuery(AlignmentMolecule m) throws chemaxon.marvin.alignment.AlignmentException
- Specified by:
setQuery
in interfacePairwiseComparison
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setMode
public void setMode(AlignmentAccuracyMode mode)
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similarity
public double similarity(Molecule m) throws chemaxon.marvin.alignment.AlignmentException
Description copied from interface:PairwiseComparison
Calculates the 3D similarity between the previously set query and the target.- Specified by:
similarity
in interfacePairwiseComparison
- Parameters:
m
- target to calculate similarity- Returns:
- the similarity value.
- Throws:
chemaxon.marvin.alignment.AlignmentException
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similarity
public double similarity(AlignmentMolecule am) throws chemaxon.marvin.alignment.AlignmentException
- Specified by:
similarity
in interfacePairwiseComparison
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setCount
public void setCount(int count)
- Specified by:
setCount
in interfacePairwiseComparison
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getAlignedMoleculesAsFragments
public Molecule getAlignedMoleculesAsFragments()
Description copied from interface:PairwiseComparison
After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.- Specified by:
getAlignedMoleculesAsFragments
in interfacePairwiseComparison
- Returns:
- the aligned molecules.
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getShapeTanimoto
public double getShapeTanimoto() throws chemaxon.marvin.alignment.AlignmentException
- Specified by:
getShapeTanimoto
in interfacePairwiseComparison
- Throws:
chemaxon.marvin.alignment.AlignmentException
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setProgressBar
public void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
- Specified by:
setProgressBar
in interfacePairwiseComparison
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setProgressMonitor
public void setProgressMonitor(MProgressMonitor mp)
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getAlignedTarget
public Molecule getAlignedTarget()
- Specified by:
getAlignedTarget
in interfacePairwiseComparison
- Returns:
- the target molecule in the final orientation and conformation.
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getAlignedQuery
public Molecule getAlignedQuery()
- Specified by:
getAlignedQuery
in interfacePairwiseComparison
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setQueryRigidForced
public void setQueryRigidForced(boolean forced)
Description copied from interface:PairwiseComparison
Set this molecule to be rigid in the input conformation even if it contains rotatable bonds- Specified by:
setQueryRigidForced
in interfacePairwiseComparison
- Parameters:
forced
- if true than rigid.
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setTargetRigidForced
public void setTargetRigidForced(boolean targetRigid)
Description copied from interface:PairwiseComparison
Set this molecule to be rigid in the input conformation even if it contains rotatable bonds- Specified by:
setTargetRigidForced
in interfacePairwiseComparison
- Parameters:
targetRigid
- if true than rigid.
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setMinimumCommonSize
public void setMinimumCommonSize(int mcs)
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setFlexibleRingSize
public void setFlexibleRingSize(int s)
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setLicenseEnvironment
public void setLicenseEnvironment(String env)
- Specified by:
setLicenseEnvironment
in interfacePairwiseComparison
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