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
Constants for atom parity and double bond stereo.
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Field Summary
Modifier and TypeFieldDescriptionstatic final int
Non-CIP stereodescriptor, anti (relative configuration).static final int
Either stereo atom type.static final int
Stereo atom type mask.static final int
No stereo atom type specified.static final int
Specific stereo atom type.static final int
Axially chiral atom with M configuration.static final int
Chirality mask in flags.static final int
Axially chiral atom with P configuration.static final int
Pseudo-asymmetric chiral atom of r configuration.static final int
Chiral atom of R configuration.static final int
Pseudo-asymmetric chiral atom of s configuration.static final int
Chiral atom of S configuration.static final int
R/S shown always.static final int
R/S shown always and highlight possible chiral centers as well.static final int
R/S not shown for any molecule.static final int
R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.static final int
Cis double bond.static final int
Cis and trans double bond mask.static final int
Double bond stereo mask.static final int
Deprecated.static final int
Unspecified double bond.static final int
Double bond stereo checking for all double bonds.static final int
Double bond stereo checking for marked double bonds only.static final int
No double bond stereo checking.static final int
Non-CIP stereodescriptor, endo (relative configuration).static final int
Non-CIP stereodescriptor, exo (relative configuration).static final int
Atom with allene like parity.static final int
Odd or even parity.static final int
Chiral atom of even parity (counterclockwise arrangement).static final int
Parity mask in flags.static final int
Atom with no parity.static final int
Chiral atom of odd parity (clockwise arrangement).static final int
Atom with tetrahedral parity.static final int
Unspecified parity flag.static final int
Absolute stereo group type for enhanced stereo representation.static final int
AND stereo group type for enhanced stereo representation.static final int
Empty stereo group type setting meaning no enhanced stereo label.static final int
OR stereo group type for enhanced stereo representation.static final int
Non-CIP stereodescriptor, syn (relative configuration).static final int
Trans double bond.
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Field Details
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PARITY_NONE
static final int PARITY_NONEAtom with no parity.- Since:
- 15.9.28
- See Also:
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PARITY_TETRAHEDRAL
static final int PARITY_TETRAHEDRALAtom with tetrahedral parity.- Since:
- 5.3
- See Also:
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PARITY_ALLENE
static final int PARITY_ALLENEAtom with allene like parity.- Since:
- 5.3
- See Also:
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PARITY_ODD
static final int PARITY_ODDChiral atom of odd parity (clockwise arrangement).- See Also:
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PARITY_EVEN
static final int PARITY_EVENChiral atom of even parity (counterclockwise arrangement).- See Also:
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PARITY_UNSPEC
static final int PARITY_UNSPECUnspecified 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:
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PARITY_EITHER
static final int PARITY_EITHEROdd or even parity.- See Also:
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PARITY_MASK
static final int PARITY_MASKParity mask in flags. -
CHIRALITYSUPPORT_NONE
static final int CHIRALITYSUPPORT_NONER/S not shown for any molecule.- See Also:
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CHIRALITYSUPPORT_SELECTED
static final int CHIRALITYSUPPORT_SELECTEDR/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.- See Also:
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CHIRALITYSUPPORT_ALL
static final int CHIRALITYSUPPORT_ALLR/S shown always.- See Also:
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CHIRALITYSUPPORT_ALL_POSSIBLE
static final int CHIRALITYSUPPORT_ALL_POSSIBLER/S shown always and highlight possible chiral centers as well.- See Also:
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CHIRALITY_R
static final int CHIRALITY_RChiral atom of R configuration.- See Also:
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CHIRALITY_S
static final int CHIRALITY_SChiral atom of S configuration.- See Also:
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CHIRALITY_r
static final int CHIRALITY_rPseudo-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:
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CHIRALITY_s
static final int CHIRALITY_sPseudo-asymmetric chiral atom of s configuration.- See Also:
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CHIRALITY_P
static final int CHIRALITY_PAxially chiral atom with P configuration.- See Also:
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CHIRALITY_M
static final int CHIRALITY_MAxially chiral atom with M configuration.- See Also:
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SYN
static final int SYNNon-CIP stereodescriptor, syn (relative configuration).- See Also:
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ANTI
static final int ANTINon-CIP stereodescriptor, anti (relative configuration).- See Also:
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ENDO
static final int ENDONon-CIP stereodescriptor, endo (relative configuration).- See Also:
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EXO
static final int EXONon-CIP stereodescriptor, exo (relative configuration).- See Also:
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CHIRALITY_MASK
static final int CHIRALITY_MASKChirality mask in flags. -
ATOMSTEREO_MASK
static final int ATOMSTEREO_MASKStereo atom type mask.- See Also:
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ATOMSTEREO_NONE
static final int ATOMSTEREO_NONENo stereo atom type specified. The atom has no wedge bonds.- See Also:
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ATOMSTEREO_SPECIFIC
static final int ATOMSTEREO_SPECIFICSpecific stereo atom type. The atom has wedge bond but not wiggly.- See Also:
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ATOMSTEREO_EITHER
static final int ATOMSTEREO_EITHEREither stereo atom type. The atom has wiggly wedge bond.- See Also:
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TRANS
static final int TRANSTrans double bond.- See Also:
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CIS
static final int CISCis double bond.- See Also:
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CIS_TRANS
static final int CIS_TRANSCis and trans double bond mask.- See Also:
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CTUNSPEC
static final int CTUNSPECUnspecified 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:
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CTUMASK
static final int CTUMASKDouble bond stereo mask. It equals CIS | TRANS | CTUNSPEC.- See Also:
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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_ALLDouble bond stereo checking for all double bonds.- See Also:
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DBS_MARKED
static final int DBS_MARKEDDouble bond stereo checking for marked double bonds only.- See Also:
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DBS_NONE
static final int DBS_NONENo double bond stereo checking.- See Also:
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STGRP_NONE
static final int STGRP_NONEEmpty stereo group type setting meaning no enhanced stereo label.- Since:
- Marvin 3.1.4
- See Also:
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STGRP_ABS
static final int STGRP_ABSAbsolute stereo group type for enhanced stereo representation. This group represents a chiral centre as drawn.- Since:
- Marvin 3.1.4
- See Also:
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STGRP_OR
static final int STGRP_OROR 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:
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STGRP_AND
static final int STGRP_ANDAND 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:
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Usage: