Class StereoAnalysis
- java.lang.Object
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- com.chemaxon.calculations.stereoanal.StereoAnalysis
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@Beta @PublicAPI public class StereoAnalysis extends Object
The stereo analysis module is able to calculate stereochemical descriptors for a molecule, giving an analysis in terms of the stereochemical properties.
API usage example:// read molecule Molecule inputMolecule = ... // construct new analysis StereoAnalysis analysis = new StereoAnalysis(inputMolecule); // list of all stereocenters of molecule List<StereoCenter> stereoCenters = analysis.allStereoCenters(); // value of first tetrahedral stereocenter TetrahedralStereoCenter sc = analysis.tetrahedralStereoCenters().get(0); TetrahedralStereoIUPACValue value = sc.getCIPValue(); // error list List<ErrorReport> errors = analysis.errors();
Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.
- Since:
- Marvin 6.2
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Constructor Summary
Constructors Constructor Description StereoAnalysis(Molecule mol)
Creates an analysis.StereoAnalysis(Molecule mol, String licenseEnvironment)
Creates an analysis.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description List<StereoCenter>
allStereoCenters()
All stereo centers of molecule.List<StereoCenter>
allStereoCentersWithAttachedData()
All stereo centers with attached data.List<AtropStereoCenter>
atropStereoCenters()
Calculates the atrop stereocenters.List<AtropStereoCenter>
atropStereoCentersWithAttachedData()
Calculates the atrop stereocenters with attached data.List<AxialStereoCenter>
axialStereoCenters()
Calculates the axial stereocenters.List<AxialStereoCenter>
axialStereoCentersWithAttachedData()
Calculates the axial stereocenters with attached data.List<CisTransStereoCenter>
cisDoubleBonds()
Calculates the CIS double bonds.List<CisTransStereoCenter>
cisTransDoubleBonds()
Calculates the CIS-TRANS double bonds.List<CisTransStereoCenter>
cisTransDoubleBondsWithAttachedData()
Calculates the CIS-TRANS double bonds with attached data.List<ErrorReport>
errors()
Error reports.Set<String>
getEnhancedStereoFlags()
Returns the enhanced stereo flags of the molecule.EnhancedStereoGroup
getEnhancedStereoGroup(String enhancedStereoFlag)
Gets the EnhancedStereoGroup to which the specified flag is mapped.Molecule
getInputMolecule()
Gets the input molecule.boolean
isAbsStereo()
Gets the absolute stereoconfiguration flag.List<AtropStereoCenter>
knownAtropStereoCenters()
Calculates the KNOWN atrop stereocenters.List<AxialStereoCenter>
knownAxialStereoCenters()
Calculates the KNOWN axial stereocenters.List<TetrahedralStereoCenter>
knownResolvedStereoCenters()
Calculates the known, resolved tetrahedral stereogenic centers.List<TetrahedralStereoCenter>
knownResolvedStereoCentersWithAttachedData()
Calculates the known, resolved tetrahedral stereogenic centers (with attached data).List<TetrahedralStereoCenter>
racemicStereoCenters()
Calculates the racemic tetrahedral stereogenic centers.List<TetrahedralStereoCenter>
racemicStereoCentersWithAttachedData()
Calculates the racemic tetrahedral stereogenic centers (with attached data).List<TetrahedralStereoCenter>
tetrahedralStereoCenters()
Calculates the tetrahedral stereogenic centers.List<TetrahedralStereoCenter>
tetrahedralStereoCentersWithAttachedData()
Calculates the tetrahedral stereogenic centers (with attached data).List<CisTransStereoCenter>
transDoubleBonds()
Calculates the TRANS double bonds.List<AtropStereoCenter>
unknownAtropStereoCenters()
Calculates the UNKNOWN atrop stereocenters.List<AxialStereoCenter>
unknownAxialStereoCenters()
Calculates the UNKNOWN axial stereocenters.List<TetrahedralStereoCenter>
unknownResolvedStereoCenters()
Calculates the unknown, resolved tetrahedral stereogenic centers.List<TetrahedralStereoCenter>
unknownResolvedStereoCentersWithAttachedData()
Calculates the unknown, resolved tetrahedral stereogenic centers (with attached data).List<TetrahedralStereoCenter>
unresolvedStereoCenters()
Calculates the unresolved tetrahedral stereogenic centers.List<TetrahedralStereoCenter>
unresolvedStereoCentersWithAttachedData()
Calculates the unresolved tetrahedral stereogenic centers (with attached data).
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Method Detail
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getInputMolecule
public Molecule getInputMolecule()
Gets the input molecule.- Returns:
- copy of input molecule
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isAbsStereo
public boolean isAbsStereo()
Gets the absolute stereoconfiguration flag. "Chiral flag" in MDL molfiles.- Returns:
- true for absolute, false for relative configuration
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allStereoCenters
public List<StereoCenter> allStereoCenters()
All stereo centers of molecule.- Returns:
- an immutable list of stereocenters
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allStereoCentersWithAttachedData
public List<StereoCenter> allStereoCentersWithAttachedData()
All stereo centers with attached data.- Returns:
- an immutable list of stereocenters
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tetrahedralStereoCenters
public List<TetrahedralStereoCenter> tetrahedralStereoCenters()
Calculates the tetrahedral stereogenic centers.- Returns:
- the immutable list of stereocenters
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tetrahedralStereoCentersWithAttachedData
public List<TetrahedralStereoCenter> tetrahedralStereoCentersWithAttachedData()
Calculates the tetrahedral stereogenic centers (with attached data).- Returns:
- the immutable list of stereocenters
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errors
public List<ErrorReport> errors()
Error reports.- Returns:
- an immutable list of errors
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knownResolvedStereoCenters
public List<TetrahedralStereoCenter> knownResolvedStereoCenters()
Calculates the known, resolved tetrahedral stereogenic centers.- Returns:
- the immutable list of stereocenters
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knownResolvedStereoCentersWithAttachedData
public List<TetrahedralStereoCenter> knownResolvedStereoCentersWithAttachedData()
Calculates the known, resolved tetrahedral stereogenic centers (with attached data).- Returns:
- the immutable list of stereocenters
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unknownResolvedStereoCenters
public List<TetrahedralStereoCenter> unknownResolvedStereoCenters()
Calculates the unknown, resolved tetrahedral stereogenic centers.- Returns:
- the immutable list of stereocenters
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unknownResolvedStereoCentersWithAttachedData
public List<TetrahedralStereoCenter> unknownResolvedStereoCentersWithAttachedData()
Calculates the unknown, resolved tetrahedral stereogenic centers (with attached data).- Returns:
- the immutable list of stereocenters
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racemicStereoCenters
public List<TetrahedralStereoCenter> racemicStereoCenters()
Calculates the racemic tetrahedral stereogenic centers.- Returns:
- the immutable list of stereocenters
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racemicStereoCentersWithAttachedData
public List<TetrahedralStereoCenter> racemicStereoCentersWithAttachedData()
Calculates the racemic tetrahedral stereogenic centers (with attached data).- Returns:
- the immutable list of stereocenters
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unresolvedStereoCenters
public List<TetrahedralStereoCenter> unresolvedStereoCenters()
Calculates the unresolved tetrahedral stereogenic centers.- Returns:
- the immutable list of stereocenters
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unresolvedStereoCentersWithAttachedData
public List<TetrahedralStereoCenter> unresolvedStereoCentersWithAttachedData()
Calculates the unresolved tetrahedral stereogenic centers (with attached data).- Returns:
- the immutable list of stereocenters
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cisDoubleBonds
public List<CisTransStereoCenter> cisDoubleBonds()
Calculates the CIS double bonds.- Returns:
- the immutable list of stereocenters
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transDoubleBonds
public List<CisTransStereoCenter> transDoubleBonds()
Calculates the TRANS double bonds.- Returns:
- the immutable list of stereocenters
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cisTransDoubleBonds
public List<CisTransStereoCenter> cisTransDoubleBonds()
Calculates the CIS-TRANS double bonds.- Returns:
- the immutable list of stereocenters
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cisTransDoubleBondsWithAttachedData
public List<CisTransStereoCenter> cisTransDoubleBondsWithAttachedData()
Calculates the CIS-TRANS double bonds with attached data.- Returns:
- the immutable list of stereocenters
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axialStereoCenters
public List<AxialStereoCenter> axialStereoCenters()
Calculates the axial stereocenters.- Returns:
- the immutable list of stereocenters
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axialStereoCentersWithAttachedData
public List<AxialStereoCenter> axialStereoCentersWithAttachedData()
Calculates the axial stereocenters with attached data.- Returns:
- the immutable list of stereocenters
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knownAxialStereoCenters
public List<AxialStereoCenter> knownAxialStereoCenters()
Calculates the KNOWN axial stereocenters.- Returns:
- the immutable list of stereocenters
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unknownAxialStereoCenters
public List<AxialStereoCenter> unknownAxialStereoCenters()
Calculates the UNKNOWN axial stereocenters.- Returns:
- the immutable list of stereocenters.
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atropStereoCenters
public List<AtropStereoCenter> atropStereoCenters()
Calculates the atrop stereocenters.- Returns:
- the immutable list of stereocenters
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atropStereoCentersWithAttachedData
public List<AtropStereoCenter> atropStereoCentersWithAttachedData()
Calculates the atrop stereocenters with attached data.- Returns:
- the immutable list of stereocenters
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knownAtropStereoCenters
public List<AtropStereoCenter> knownAtropStereoCenters()
Calculates the KNOWN atrop stereocenters.- Returns:
- the immutable list of stereocenters
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unknownAtropStereoCenters
public List<AtropStereoCenter> unknownAtropStereoCenters()
Calculates the UNKNOWN atrop stereocenters.- Returns:
- the immutable list of stereocenters.
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getEnhancedStereoFlags
public Set<String> getEnhancedStereoFlags()
Returns the enhanced stereo flags of the molecule.- Returns:
- set of string
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getEnhancedStereoGroup
public EnhancedStereoGroup getEnhancedStereoGroup(String enhancedStereoFlag)
Gets the EnhancedStereoGroup to which the specified flag is mapped.- Parameters:
enhancedStereoFlag
- enhanced stereo flag- Returns:
- an EnhancedStereoGroup
- Throws:
IllegalArgumentException
- if molecule does not contains the specified flag- See Also:
getEnhancedStereoFlags()
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