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