public interface IStereoElement<F extends IChemObject,C extends IChemObject> extends ICDKObject
LEFT
and RIGHT
are provided but are synonymous
with the values 1
(odd) and 2
(even).TH
: TetrahedralCT
: CisTrans a double-bondAL
: Extended Tetrahedral (Allenal)AT
: AtropisomericSP
: Square PlanarSPY
: Square PyramidalTBPY
: Trigonal BipyramidalPBPY
: Pentagonal BipyramidalOC
: OctahedralHBPY8
: Hexagonal BipyramidalHBPY9
: Heptagonal BipyramidalGRP_RAC1
.
This information can also be encoded in CXSMILES. By default all stereocentres are GRP_ABS
.
The stereo group information is stored in the high bytes of the stereo configuration. You can access the basic
information as follows:
int grpconfig = stereo.getGroupInfo();
if (grpconfig & IStereoElement.GRP_RAC1) {
// group is RAC1
} else if (config & IStereoElement.GRP_REL1) {
// group is OR1
}
You can also unpack the various parts of the information manually.
int grpconfig = stereo.getGroupInfo();
switch (grpconfig & IStereoElement.GRP_TYPE_MASK) {
case IStereoElement.GRP_ABS:
break;
case IStereoElement.GRP_AND:
break;
case IStereoElement.GRP_OR:
break;
}
// the group number 1, 2, 3, 4 is a little more tricky, you can mask off the value as
// follows but it's shifted up into position
int num = grpconfig & IStereoElement.GRP_NUM_MASK;
// to get the number 1, 2, 3, etc you can simply shift it down as follows
int num_act = grpconfig >>> IStereoElement.GRP_NUM_SHIFT;
Modifier and Type | Field and Description |
---|---|
static int |
AL
ExtendedTetrahedral a.k.a.
|
static int |
Allenal
ExtendedTetrahedral (e.g.
|
static int |
AT
Atropisomeric (e.g.
|
static int |
Atropisomeric
Atropisomeric (e.g.
|
static int |
CFG_MASK |
static int |
CisTrans
Geometric CisTrans (e.g.
|
static int |
CLS_MASK |
static int |
CT
Geometric CisTrans (e.g.
|
static int |
CU
ExtendedCisTrans a.k.a.
|
static int |
Cumulene
Cumulene
|
static int |
GRP_ABS
Absolute stereo group, the exact stereo configuration of this atom is known.
|
static int |
GRP_MASK
Mask for the stereo group information
|
static int |
GRP_NUM_MASK
Mask for the stereo group number information, 0x0 ..
|
static int |
GRP_NUM_SHIFT |
static int |
GRP_RAC
Racemic stereo group type, the stereo configuration of this atom is a mixture of R/S.
|
static int |
GRP_RAC1
Convenience field for testing if the stereo is group RAC1 (&1).
|
static int |
GRP_RAC2
Convenience field for testing if the stereo is group RAC2 (&2).
|
static int |
GRP_RAC3
Convenience field for testing if the stereo is group RAC3 (&3).
|
static int |
GRP_RAC4
Convenience field for testing if the stereo is group RAC4 (&4).
|
static int |
GRP_RAC5
Convenience field for testing if the stereo is group RAC5 (&5).
|
static int |
GRP_REL
Relative stereo group type, the stereo configuration of this atom is unknown but is relative to another
atom in the same group.
|
static int |
GRP_REL1
Convenience field for testing if the stereo is group OR1 (&1).
|
static int |
GRP_REL2
Convenience field for testing if the stereo is group OR2 (&2).
|
static int |
GRP_REL3
Convenience field for testing if the stereo is group OR3 (&3).
|
static int |
GRP_REL4
Convenience field for testing if the stereo is group OR4 (&4).
|
static int |
GRP_REL5
Convenience field for testing if the stereo is group OR5 (&5).
|
static int |
GRP_TYPE_MASK
Mask for the stereo group type information, GRP_ABS, GRP_AND, GRP_OR
|
static int |
HBPY8
Hexagonal Bipyramidal (HBPY-8)
|
static int |
HBPY9
Heptagonal Bipyramidal (HBPY-9)
|
static int |
HeptagonalBipyramidal
Heptagonal Bipyramidal (HBPY-9)
|
static int |
HexagonalBipyramidal
Hexagonal Bipyramidal (HBPY-8)
|
static int |
LEFT |
static int |
OC
Octahedral (OC-6)
|
static int |
Octahedral
Octahedral (OC-6)
|
static int |
OPPOSITE |
static int |
PBPY
Pentagonal Bipyramidal (PBPY-7)
|
static int |
PentagonalBipyramidal
Pentagonal Bipyramidal (PBPY-7)
|
static int |
RIGHT |
static int |
SP
Square Planar (SP-4) (e.g.
|
static int |
SP4
Square Planar Configutation in 4 Shape
|
static int |
SPU
Square Planar Configutation in U Shape
|
static int |
SPY
Square Pyramidal (SPY-5)
|
static int |
SPZ
Square Planar Configutation in Z Shape
|
static int |
SquarePlanar
Square Planar (SP-4) (e.g.
|
static int |
SquarePyramidal
Square Pyramidal (SPY-5)
|
static int |
TBPY
Trigonal Bipyramidal (TBPY-5)
|
static int |
Tetrahedral
Tetrahedral (T-4) (e.g.
|
static int |
TH
Tetrahedral (T-4) (e.g.
|
static int |
TOGETHER |
static int |
TrigonalBipyramidal
Trigonal Bipyramidal (TBPY-5)
|
Modifier and Type | Method and Description |
---|---|
boolean |
contains(IAtom atom)
Does the stereo element contain the provided atom.
|
List<C> |
getCarriers()
The carriers of the stereochemistry
|
int |
getConfig()
Access the configuration order and class of the stereochemistry.
|
int |
getConfigClass()
The configuration class of the stereochemistry.
|
int |
getConfigOrder()
The configuration order of the stereochemistry.
|
F |
getFocus()
The focus atom or bond at the 'centre' of the stereo-configuration.
|
int |
getGroupInfo()
Access the stereo group information - see class doc.
|
IStereoElement |
map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
IStereoElement<F,C> |
map(Map<IChemObject,IChemObject> chemobjs) |
void |
setConfigOrder(int cfg)
Set the configuration order of the stereochemistry.
|
void |
setGroupInfo(int grp)
Set the stereo group information - see class doc.
|
getBuilder
static final int CLS_MASK
static final int CFG_MASK
static final int LEFT
static final int RIGHT
static final int OPPOSITE
static final int TOGETHER
static final int CT
static final int TH
static final int AL
static final int CU
static final int AT
static final int SP
static final int SPY
static final int TBPY
static final int OC
static final int PBPY
static final int HBPY8
static final int HBPY9
static final int CisTrans
static final int Tetrahedral
static final int Allenal
static final int Cumulene
static final int Atropisomeric
static final int SquarePlanar
static final int SquarePyramidal
static final int TrigonalBipyramidal
static final int Octahedral
static final int PentagonalBipyramidal
static final int HexagonalBipyramidal
static final int HeptagonalBipyramidal
static final int SPU
static final int SP4
static final int SPZ
static final int GRP_MASK
static final int GRP_TYPE_MASK
static final int GRP_NUM_MASK
static final int GRP_NUM_SHIFT
static final int GRP_ABS
static final int GRP_RAC
static final int GRP_REL
static final int GRP_RAC1
static final int GRP_RAC2
static final int GRP_RAC3
static final int GRP_RAC4
static final int GRP_RAC5
static final int GRP_REL1
static final int GRP_REL2
static final int GRP_REL3
static final int GRP_REL4
static final int GRP_REL5
F getFocus()
int getConfigClass()
int getConfigOrder()
void setConfigOrder(int cfg)
cfg
- the new configurationint getConfig()
int getGroupInfo()
void setGroupInfo(int grp)
grp
- the group infoboolean contains(IAtom atom)
atom
- an atom to test membershipIStereoElement<F,C> map(Map<IChemObject,IChemObject> chemobjs)
IStereoElement map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
atoms
- nullable atom mapping, used to convert the original atoms to their mapped
counterpartsbonds
- nullable bond mapping, used to convert the original bonds to their mapped
counterpartsCopyright © 2021. All rights reserved.