com.chemaxon.calculations.stereoanal

Class StereoAnalysis

java.lang.Object

com.chemaxon.calculations.stereoanal.StereoAnalysis

@Beta
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

Author:

Laszlo Antal

Constructor Summary

Constructors

Constructor and Description
StereoAnalysis(Molecule mol) Creates an analysis.

Method Summary

Methods

Modifier and Type	Method and 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).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

StereoAnalysis

public StereoAnalysis(Molecule mol)

Creates an analysis.

Parameters:

mol - input molecule

Method Detail

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:

getEnhancedStereoFlags()