Package com.chemaxon.calculations.stereoanal

Class StereoAnalysis

java.lang.Object
com.chemaxon.calculations.stereoanal.StereoAnalysis
@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

  • Constructor Details

    • StereoAnalysis

      public StereoAnalysis(Molecule mol, String licenseEnvironment)
      Creates an analysis.
      Parameters:
      mol - input molecule
      licenseEnvironment - license environment

    • StereoAnalysis

      public StereoAnalysis(Molecule mol)
      Creates an analysis.
      Parameters:
      mol - input molecule

  • Method Details

    • getInputMolecule

      public Molecule getInputMolecule()
      Gets the input molecule.
      Returns:
      copy of input molecule

    • isAbsStereo

      public boolean isAbsStereo()
      Gets the absolute stereoconfiguration flag. "Chiral flag" in MDL molfiles.
      Returns:
      true for absolute, false for relative configuration

    • allStereoCenters

      public List<StereoCenter> allStereoCenters()
      All stereo centers of molecule.
      Returns:
      an immutable list of stereocenters

    • allStereoCentersWithAttachedData

      public List<StereoCenter> allStereoCentersWithAttachedData()
      All stereo centers with attached data.
      Returns:
      an immutable list of stereocenters

    • tetrahedralStereoCenters

      public List<TetrahedralStereoCenter> tetrahedralStereoCenters()
      Calculates the tetrahedral stereogenic centers.
      Returns:
      the immutable list of stereocenters

    • tetrahedralStereoCentersWithAttachedData

      public List<TetrahedralStereoCenter> tetrahedralStereoCentersWithAttachedData()
      Calculates the tetrahedral stereogenic centers (with attached data).
      Returns:
      the immutable list of stereocenters

    • errors

      public List<ErrorReport> errors()
      Error reports.
      Returns:
      an immutable list of errors

    • knownResolvedStereoCenters

      public List<TetrahedralStereoCenter> knownResolvedStereoCenters()
      Calculates the known, resolved tetrahedral stereogenic centers.
      Returns:
      the immutable list of stereocenters

    • knownResolvedStereoCentersWithAttachedData

      public List<TetrahedralStereoCenter> knownResolvedStereoCentersWithAttachedData()
      Calculates the known, resolved tetrahedral stereogenic centers (with attached data).
      Returns:
      the immutable list of stereocenters

    • unknownResolvedStereoCenters

      public List<TetrahedralStereoCenter> unknownResolvedStereoCenters()
      Calculates the unknown, resolved tetrahedral stereogenic centers.
      Returns:
      the immutable list of stereocenters

    • unknownResolvedStereoCentersWithAttachedData

      public List<TetrahedralStereoCenter> unknownResolvedStereoCentersWithAttachedData()
      Calculates the unknown, resolved tetrahedral stereogenic centers (with attached data).
      Returns:
      the immutable list of stereocenters

    • racemicStereoCenters

      public List<TetrahedralStereoCenter> racemicStereoCenters()
      Calculates the racemic tetrahedral stereogenic centers.
      Returns:
      the immutable list of stereocenters

    • racemicStereoCentersWithAttachedData

      public List<TetrahedralStereoCenter> racemicStereoCentersWithAttachedData()
      Calculates the racemic tetrahedral stereogenic centers (with attached data).
      Returns:
      the immutable list of stereocenters

    • unresolvedStereoCenters

      public List<TetrahedralStereoCenter> unresolvedStereoCenters()
      Calculates the unresolved tetrahedral stereogenic centers.
      Returns:
      the immutable list of stereocenters

    • unresolvedStereoCentersWithAttachedData

      public List<TetrahedralStereoCenter> unresolvedStereoCentersWithAttachedData()
      Calculates the unresolved tetrahedral stereogenic centers (with attached data).
      Returns:
      the immutable list of stereocenters

    • cisDoubleBonds

      public List<CisTransStereoCenter> cisDoubleBonds()
      Calculates the CIS double bonds.
      Returns:
      the immutable list of stereocenters

    • transDoubleBonds

      public List<CisTransStereoCenter> transDoubleBonds()
      Calculates the TRANS double bonds.
      Returns:
      the immutable list of stereocenters

    • cisTransDoubleBonds

      public List<CisTransStereoCenter> cisTransDoubleBonds()
      Calculates the CIS-TRANS double bonds.
      Returns:
      the immutable list of stereocenters

    • cisTransDoubleBondsWithAttachedData

      public List<CisTransStereoCenter> cisTransDoubleBondsWithAttachedData()
      Calculates the CIS-TRANS double bonds with attached data.
      Returns:
      the immutable list of stereocenters

    • axialStereoCenters

      public List<AxialStereoCenter> axialStereoCenters()
      Calculates the axial stereocenters.
      Returns:
      the immutable list of stereocenters

    • axialStereoCentersWithAttachedData

      public List<AxialStereoCenter> axialStereoCentersWithAttachedData()
      Calculates the axial stereocenters with attached data.
      Returns:
      the immutable list of stereocenters

    • knownAxialStereoCenters

      public List<AxialStereoCenter> knownAxialStereoCenters()
      Calculates the KNOWN axial stereocenters.
      Returns:
      the immutable list of stereocenters

    • unknownAxialStereoCenters

      public List<AxialStereoCenter> unknownAxialStereoCenters()
      Calculates the UNKNOWN axial stereocenters.
      Returns:
      the immutable list of stereocenters.

    • atropStereoCenters

      public List<AtropStereoCenter> atropStereoCenters()
      Calculates the atrop stereocenters.
      Returns:
      the immutable list of stereocenters

    • atropStereoCentersWithAttachedData

      public List<AtropStereoCenter> atropStereoCentersWithAttachedData()
      Calculates the atrop stereocenters with attached data.
      Returns:
      the immutable list of stereocenters

    • knownAtropStereoCenters

      public List<AtropStereoCenter> knownAtropStereoCenters()
      Calculates the KNOWN atrop stereocenters.
      Returns:
      the immutable list of stereocenters

    • unknownAtropStereoCenters

      public List<AtropStereoCenter> unknownAtropStereoCenters()
      Calculates the UNKNOWN atrop stereocenters.
      Returns:
      the immutable list of stereocenters.

    • getEnhancedStereoFlags

      public Set<String> getEnhancedStereoFlags()
      Returns the enhanced stereo flags of the molecule.
      Returns:
      set of string

    • 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: