@PublicAPI public interface PairwiseComparison
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();
Modifier and Type | Method and 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(java.lang.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 bonds
|
void |
setTargetRigidForced(boolean forced)
Set this molecule to be rigid in the input conformation even if it
contains rotatable bonds
|
double |
similarity(AlignmentMolecule target) |
double |
similarity(Molecule target)
Calculates the 3D similarity between the previously set query and the
target.
|
void setQuery(Molecule query) throws chemaxon.marvin.alignment.AlignmentException
chemaxon.marvin.alignment.AlignmentException
double similarity(Molecule target) throws chemaxon.marvin.alignment.AlignmentException
target
- target to calculate similarityAlignmentException
void setQuery(AlignmentMolecule query) throws chemaxon.marvin.alignment.AlignmentException
chemaxon.marvin.alignment.AlignmentException
double similarity(AlignmentMolecule target) throws chemaxon.marvin.alignment.AlignmentException
chemaxon.marvin.alignment.AlignmentException
Molecule getAlignedMoleculesAsFragments()
Molecule getAlignedTarget()
Molecule getAlignedQuery()
void removeAllMolecules()
void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface c)
void setQueryRigidForced(boolean forced)
forced
- if true than rigid.void setTargetRigidForced(boolean forced)
forced
- if true than rigid.void addNodeColorWeight(int t1, int t2, double w)
double getShapeTanimoto() throws chemaxon.marvin.alignment.AlignmentException
chemaxon.marvin.alignment.AlignmentException
void setLicenseEnvironment(java.lang.String env)
void setCount(int count)