Package chemaxon.struc

Interface StereoConstants

All Known Implementing Classes:

Hydrogenize, MolAtom, MolBond, Molecule, MoleculeGraph, MolExport, MolImport, MolSearch, QueryBond, RgMolecule, RGroupDecomposition, RxnMolecule, Search, SelectionMolecule, SgroupAtom, StandardizedMolSearch

@PublicApi
public interface StereoConstants

Constants for atom parity and double bond stereo.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	ANTI	Non-CIP stereodescriptor, anti (relative configuration).
static final int	ATOMSTEREO_EITHER	Either stereo atom type.
static final int	ATOMSTEREO_MASK	Stereo atom type mask.
static final int	ATOMSTEREO_NONE	No stereo atom type specified.
static final int	ATOMSTEREO_SPECIFIC	Specific stereo atom type.
static final int	CHIRALITY_M	Axially chiral atom with M configuration.
static final int	CHIRALITY_MASK	Chirality mask in flags.
static final int	CHIRALITY_P	Axially chiral atom with P configuration.
static final int	CHIRALITY_r	Pseudo-asymmetric chiral atom of r configuration.
static final int	CHIRALITY_R	Chiral atom of R configuration.
static final int	CHIRALITY_s	Pseudo-asymmetric chiral atom of s configuration.
static final int	CHIRALITY_S	Chiral atom of S configuration.
static final int	CHIRALITYSUPPORT_ALL	R/S shown always.
static final int	CHIRALITYSUPPORT_ALL_POSSIBLE	R/S shown always and highlight possible chiral centers as well.
static final int	CHIRALITYSUPPORT_NONE	R/S not shown for any molecule.
static final int	CHIRALITYSUPPORT_SELECTED	R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.
static final int	CIS	Cis double bond.
static final int	CIS_TRANS	Cis and trans double bond mask.
static final int	CTUMASK	Double bond stereo mask.
static final int	CTUNKNOWN	Deprecated. As of Marvin 6.1, Usage:
static final int	CTUNSPEC	Unspecified double bond.
static final int	DBS_ALL	Double bond stereo checking for all double bonds.
static final int	DBS_MARKED	Double bond stereo checking for marked double bonds only.
static final int	DBS_NONE	No double bond stereo checking.
static final int	ENDO	Non-CIP stereodescriptor, endo (relative configuration).
static final int	EXO	Non-CIP stereodescriptor, exo (relative configuration).
static final int	PARITY_ALLENE	Atom with allene like parity.
static final int	PARITY_EITHER	Odd or even parity.
static final int	PARITY_EVEN	Chiral atom of even parity (counterclockwise arrangement).
static final int	PARITY_MASK	Parity mask in flags.
static final int	PARITY_NONE	Atom with no parity.
static final int	PARITY_ODD	Chiral atom of odd parity (clockwise arrangement).
static final int	PARITY_TETRAHEDRAL	Atom with tetrahedral parity.
static final int	PARITY_UNSPEC	Unspecified parity flag.
static final int	STGRP_ABS	Absolute stereo group type for enhanced stereo representation.
static final int	STGRP_AND	AND stereo group type for enhanced stereo representation.
static final int	STGRP_NONE	Empty stereo group type setting meaning no enhanced stereo label.
static final int	STGRP_OR	OR stereo group type for enhanced stereo representation.
static final int	SYN	Non-CIP stereodescriptor, syn (relative configuration).
static final int	TRANS	Trans double bond.

Field Details

PARITY_NONE

static final int PARITY_NONE

Atom with no parity.

Since:

15.9.28

See Also:

• MoleculeGraph.getParityType(int)
• Constant Field Values

PARITY_TETRAHEDRAL

static final int PARITY_TETRAHEDRAL

Atom with tetrahedral parity.

Since:

5.3

See Also:

• MoleculeGraph.getParityType(int)
• Constant Field Values

PARITY_ALLENE

static final int PARITY_ALLENE

Atom with allene like parity.

Since:

5.3

See Also:

• MoleculeGraph.getParityType(int)
• Constant Field Values

PARITY_ODD

static final int PARITY_ODD

Chiral atom of odd parity (clockwise arrangement).

See Also:

• MolAtom.getFlags()
• Constant Field Values

PARITY_EVEN

static final int PARITY_EVEN

Chiral atom of even parity (counterclockwise arrangement).

See Also:

• MolAtom.getFlags()
• Constant Field Values

PARITY_UNSPEC

static final int PARITY_UNSPEC

Unspecified parity flag. Has meaning only in conjunction with specified parity information of an atom in case of query structures.
Used in the following sense: The parity of the atom is the specified one or unspecified.
For example, in the following SMARTS query the third atom has flag PARITY_UNSPEC | PARITY_ODD: [#6]C[C@@?H]([#6])Cl

See Also:

• MolAtom.getFlags()
• Constant Field Values

PARITY_EITHER

static final int PARITY_EITHER

Odd or even parity.

See Also:

• MolAtom.getFlags()
• Constant Field Values

PARITY_MASK

static final int PARITY_MASK

Parity mask in flags.

See Also:

• PARITY_ODD
• PARITY_EVEN
• PARITY_UNSPEC
• MolAtom.getFlags()
• Constant Field Values

CHIRALITYSUPPORT_NONE

static final int CHIRALITYSUPPORT_NONE

R/S not shown for any molecule.

See Also:

• Constant Field Values

CHIRALITYSUPPORT_SELECTED

static final int CHIRALITYSUPPORT_SELECTED

R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.

See Also:

• Constant Field Values

CHIRALITYSUPPORT_ALL

static final int CHIRALITYSUPPORT_ALL

R/S shown always.

See Also:

• Constant Field Values

CHIRALITYSUPPORT_ALL_POSSIBLE

static final int CHIRALITYSUPPORT_ALL_POSSIBLE

R/S shown always and highlight possible chiral centers as well.

See Also:

• Constant Field Values

CHIRALITY_R

static final int CHIRALITY_R

Chiral atom of R configuration.

See Also:

• MolAtom.getFlags()
• Constant Field Values

CHIRALITY_S

static final int CHIRALITY_S

Chiral atom of S configuration.

See Also:

• MolAtom.getFlags()
• Constant Field Values

CHIRALITY_r

static final int CHIRALITY_r

Pseudo-asymmetric chiral atom of r configuration. An atom that is a tetrahedrally substituted atom and bonded to four different entities, two and only two of which have opposite configurations, is stereogenic. The descriptors 'r' and 's' are used to denote such centers. The stereodescriptors 'r' and 's' are reflexion invariant.

See Also:

• Constant Field Values

CHIRALITY_s

static final int CHIRALITY_s

Pseudo-asymmetric chiral atom of s configuration.

See Also:

• Constant Field Values

CHIRALITY_P

static final int CHIRALITY_P

Axially chiral atom with P configuration.

See Also:

• Constant Field Values

CHIRALITY_M

static final int CHIRALITY_M

Axially chiral atom with M configuration.

See Also:

• Constant Field Values

SYN

static final int SYN

Non-CIP stereodescriptor, syn (relative configuration).

See Also:

• Constant Field Values

ANTI

static final int ANTI

Non-CIP stereodescriptor, anti (relative configuration).

See Also:

• Constant Field Values

ENDO

static final int ENDO

Non-CIP stereodescriptor, endo (relative configuration).

See Also:

• Constant Field Values

EXO

static final int EXO

Non-CIP stereodescriptor, exo (relative configuration).

See Also:

• Constant Field Values

CHIRALITY_MASK

static final int CHIRALITY_MASK

Chirality mask in flags.

See Also:

• CHIRALITY_R
• CHIRALITY_S
• MolAtom.getFlags()
• Constant Field Values

ATOMSTEREO_MASK

static final int ATOMSTEREO_MASK

Stereo atom type mask.

See Also:

• MolAtom.getFlags()
• Constant Field Values

ATOMSTEREO_NONE

static final int ATOMSTEREO_NONE

No stereo atom type specified. The atom has no wedge bonds.

See Also:

• MolAtom.getFlags()
• Constant Field Values

ATOMSTEREO_SPECIFIC

static final int ATOMSTEREO_SPECIFIC

Specific stereo atom type. The atom has wedge bond but not wiggly.

See Also:

• MolAtom.getFlags()
• Constant Field Values

ATOMSTEREO_EITHER

static final int ATOMSTEREO_EITHER

Either stereo atom type. The atom has wiggly wedge bond.

See Also:

• MolAtom.getFlags()
• Constant Field Values

TRANS

static final int TRANS

Trans double bond.

See Also:

• MolBond.getFlags()
• Constant Field Values

CIS

static final int CIS

Cis double bond.

See Also:

• MolBond.getFlags()
• Constant Field Values

CIS_TRANS

static final int CIS_TRANS

Cis and trans double bond mask.

See Also:

• MolBond.getFlags()
• Constant Field Values

CTUNSPEC

static final int CTUNSPEC

Unspecified double bond. Query flag. Only used in conjunction with CIS or TRANS. For example, in the following SMARTS query the second bond has flag CTUNSPEC | TRANS: F/?[#6]=C/Cl. This matches to molecules F/C=C/Cl and FC=CCl.

See Also:

• CIS
• TRANS
• MolBond.getFlags()
• Constant Field Values

CTUMASK

static final int CTUMASK

Double bond stereo mask. It equals CIS | TRANS | CTUNSPEC.

See Also:

• CIS
• TRANS
• CTUNSPEC
• MolBond.getFlags()
• Constant Field Values

CTUNKNOWN

@Deprecated
static final int CTUNKNOWN

Deprecated.

As of Marvin 6.1,
Usage:

 In the specified methods the CIS|TRANS or
 CIS|TRANS|CTUNSPEC values are used instead.
 

CIS/TRANS cannot be determined because bond angle is close to 180 degrees. This is not a flag in MolBond. This corresponds to CIS|TRANS (double bond) or CIS|TRANS|CTUNSPEC (C/T? double bond)

See Also:

• MolBond.calcStereo2(MolAtom, MolAtom)
• MoleculeGraph.getStereo2(int, int, int, int)
• Constant Field Values

DBS_ALL

static final int DBS_ALL

Double bond stereo checking for all double bonds.

See Also:

• Constant Field Values

DBS_MARKED

static final int DBS_MARKED

Double bond stereo checking for marked double bonds only.

See Also:

• Constant Field Values

DBS_NONE

static final int DBS_NONE

No double bond stereo checking.

See Also:

• Constant Field Values

STGRP_NONE

static final int STGRP_NONE

Empty stereo group type setting meaning no enhanced stereo label.

Since:

Marvin 3.1.4

See Also:

• MolAtom.getStereoGroupType()
• Enhanced Stereo section of the JChem Query Guide
• Constant Field Values

STGRP_ABS

static final int STGRP_ABS

Absolute stereo group type for enhanced stereo representation. This group represents a chiral centre as drawn.

Since:

Marvin 3.1.4

See Also:

• MolAtom.getStereoGroupType()
• Enhanced Stereo section of the JChem Query Guide
• Constant Field Values

STGRP_OR

static final int STGRP_OR

OR stereo group type for enhanced stereo representation. Must be used together with a number, eg. OR1, OR2, etc. This group type represents a pure sample of stereoisomers with the labelled chiral centre as drawn or in the opposite stereo configuration, however the relative stereo configuration of the same group must not change. (Ie. they are all as drawn or they are all flipped.)

Since:

Marvin 3.1.4

See Also:

• MolAtom.getStereoGroupType()
• Enhanced Stereo section of the JChem Query Guide
• Constant Field Values

STGRP_AND

static final int STGRP_AND

AND stereo group type for enhanced stereo representation. Must be used together with a number, eg. AND1, AND2, etc. This group type represents a mixture of stereoisomers with the labelled chiral centre as drawn and in the opposite stereo configuration, however the relative stereo configuration of the same group must not change. (Ie. they are all as drawn or they are all flipped.)

Since:

Marvin 3.1.4

See Also:

• MolAtom.getStereoGroupType()
• Enhanced Stereo section of the JChem Query Guide
• Constant Field Values