chemaxon.calculations.stereo

Class Stereochemistry

java.lang.Object

chemaxon.calculations.stereo.Stereochemistry

public class Stereochemistry
extends Object

Central class for accessing functions analyzing the topology of a molecule.

Since:

Marvin 5.6

Version:

Marvin 5.12, 10/12/2012

Author:

Gyorgy Pirok, Andras Volford, Peter Cseh

Field Summary

Fields

Modifier and Type	Field and Description
static int	EVEN
static int	ODD

Constructor Summary

Constructors

Constructor and Description
Stereochemistry()

Method Summary

Methods

Modifier and Type	Method and Description
int	asymmetricAtomCount() Calculates the number of atoms having four different ligands.
int[]	asymmetricAtoms() Retrieves the indexes of atom having four different ligands.
int	chiralCenterCount() Calculates the number of chiral centers.
int[]	chiralCenters() Determines the chiral center atoms.
static <T extends MoleculeGraph> T	getEnantiomer(T m) Get the enantiomer pair of the given molecule
MoleculeGraph	getMolecule() Retrieves the input molecule
static int[]	getPossibleAtomCenteredStereoAtoms(MoleculeGraph m) Returns the indexes of atom-centered stereoactive atoms.
static int[]	getPossibleAtomCenteredStereoAtomsWithNoParity(MoleculeGraph m) Returns the indexes of atoms that have the possibility to have tetrahedral stereo and have no exact parity set on them.
int[]	graphInvariant()
boolean	isAsymmetricAtom(int a) Determines if an atom is asymmetric or not.
boolean	isChiral() Determines if the molecule contains an atom with R or S stereo configuration.
boolean	isChiralCenter(int a) Determines if an atom can be a tetrahedral stereogenic center.
void	setMolecule(MoleculeGraph mol) Specifies a molecule to calculate with.
String	stereo(int a) Calculates absolute stereo configuration of the given atom.
String	stereo(int a1, int a2) Calculates absolute stereo configuration of the given double bond.
int	stereoDoubleBondCount() Calculates the number of stereo double bonds.

Methods inherited from class java.lang.Object

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

Field Detail

ODD

public static final int ODD

See Also:

Constant Field Values

EVEN

public static final int EVEN

See Also:

Constant Field Values

Constructor Detail

Stereochemistry

public Stereochemistry()

Method Detail

getMolecule

public MoleculeGraph getMolecule()

Retrieves the input molecule

Returns:

the molecule to calculate with

setMolecule

public void setMolecule(MoleculeGraph mol)

Specifies a molecule to calculate with.

Parameters:

mol - the molecule to calculate with

asymmetricAtomCount

public int asymmetricAtomCount()

Calculates the number of atoms having four different ligands.

Returns:

number of asymmetric atoms

asymmetricAtoms

public int[] asymmetricAtoms()

Retrieves the indexes of atom having four different ligands.

Returns:

indexes of asymmetric atoms

Since:

Marvin 5.3

chiralCenterCount

public int chiralCenterCount()

Calculates the number of chiral centers.

Returns:

number of chiral center atoms

chiralCenters

public int[] chiralCenters()

Determines the chiral center atoms.

Returns:

indexes of chiral center atoms

Since:

Marvin 5.3

graphInvariant

public int[] graphInvariant()

isAsymmetricAtom

public boolean isAsymmetricAtom(int a)

Determines if an atom is asymmetric or not. Asymmetric atoms have four different ligands.

Parameters:

a - index of the atom

Returns:

true if the atom is asymmetric.

isChiral

public boolean isChiral()

Determines if the molecule contains an atom with R or S stereo configuration.

Returns:

true if the molecule is chiral.

isChiralCenter

public boolean isChiralCenter(int a)

Determines if an atom can be a tetrahedral stereogenic center.

Parameters:

a - index of the atom

Returns:

true if the atom is stereogenic.

stereo

public String stereo(int a)

Calculates absolute stereo configuration of the given atom. Returns "R" or "S" correspondingly, if the atom is stereo, otherwise it returns an empty string,

Parameters:

a - index of the atom

Returns:

the absolute stereo configuration of the atom

stereo

public String stereo(int a1,
            int a2)

Calculates absolute stereo configuration of the given double bond. Returns "E" or "Z" correspondingly, if the bond is a stereo double bond, otherwise it returns an empty string. Double bonds in small rings are not considered stereo bonds.

Parameters:

a1 - index of the atom at one end of the double bond

a2 - index of the atom at the other end of the double bond

Returns:

the absolute stereo configuration of the atom

stereoDoubleBondCount

public int stereoDoubleBondCount()

Calculates the number of stereo double bonds.

Returns:

number of stereo double bonds atoms

getEnantiomer

public static <T extends MoleculeGraph> T getEnantiomer(T m)

Get the enantiomer pair of the given molecule

Parameters:

m - molecule

Returns:

the enantiomer pair of the original structure

getPossibleAtomCenteredStereoAtoms

public static int[] getPossibleAtomCenteredStereoAtoms(MoleculeGraph m)

Returns the indexes of atom-centered stereoactive atoms. These stereo types are: tetrahedral stereo, axal stereo and cis-trans stereo in cases like CC1CCC(C)CC1.

Parameters:

m - the molecule

Returns:

the array of indexes or an empty array if no such atom found.

Since:

Marvin 5.12

getPossibleAtomCenteredStereoAtomsWithNoParity

public static int[] getPossibleAtomCenteredStereoAtomsWithNoParity(MoleculeGraph m)

Returns the indexes of atoms that have the possibility to have tetrahedral stereo and have no exact parity set on them.

Parameters:

m - the molecule

Returns:

the array of indexes or an empty array if no such atom found.

Since:

Marvin 5.12