public final class SmiFlavor extends Object
Modifier and Type | Field and Description |
---|---|
static int |
Absolute
Output canonical SMILES with stereochemistry, atomic masses.
|
static int |
AtomAtomMap
Output atom-atom mapping for reactions and atom classes for molecules.
|
static int |
AtomAtomMapRenumber
Renumber AtomAtomMaps during canonical generation
|
static int |
AtomicMass
Output atomic mass on atoms.
|
static int |
AtomicMassStrict
Deprecated.
no longer needed, default CDK behaviour is now to pass
through mass numbers if non-null
|
static int |
Canonical
Output SMILES in a canonical order.
|
static int |
Cx2dCoordinates
Output 2D coordinates.
|
static int |
Cx3dCoordinates
Output 3D coordinates.
|
static int |
CxAtomLabel
Output atom labels, atom labels are specified by
IPseudoAtom.getLabel() . |
static int |
CxAtomValue
Output atom values, atom values are specified by the property
CDKConstants.COMMENT using
IChemObject.setProperty(Object, Object) |
static int |
CxCoordinates
Output either 2D/3D coordinates.
|
static int |
CxDataSgroups
Output data Sgroups.
|
static int |
CxEnhancedStereo
Output enhanced stereo.
|
static int |
CxFragmentGroup
Output fragment grouping for reactions.
|
static int |
CxLigandOrder
Output ligand order information.
|
static int |
CxMulticenter
Output multicenter bonds, positional variation is specified with
Sgroup s
of the type SgroupType.ExtMulticenter . |
static int |
CxPolymer
Output polymer repeat units is specified with
Sgroup s. |
static int |
CxRadical
Output radicals, radicals are specified by
IAtomContainer.getConnectedSingleElectronsCount(IAtom) |
static int |
CxSmiles
Output CXSMILES layers.
|
static int |
CxSmilesWithCoords
Output CXSMILES layers and coordinates.
|
static int |
Default
Default SMILES output write Stereochemistry, Atomic Mass, and CXSMILES layers.
|
static int |
Generic
Output non-canonical SMILES without stereochemistry, atomic masses.
|
static int |
InChILabelling
Output SMILES in a canonical order using the InChI labelling algorithm.
|
static int |
Isomeric
Output non-canonical SMILES with stereochemistry, atomic masses.
|
static int |
Stereo
Output supported stereochemistry types.
|
static int |
StereoCisTrans
Output cis-trans stereochemistry specified by directional
\
of / bonds. |
static int |
StereoExCisTrans |
static int |
StereoExTetrahedral
Output extended tetrahedral stereochemistry on atoms as
@ and
@@ . |
static int |
StereoTetrahedral
Output tetrahedral stereochemistry on atoms as
@ and @@ . |
static int |
Unique
Output canonical SMILES without stereochemistry, atomic masses.
|
static int |
UniversalSmiles
Output canonical SMILES with stereochemistry and atomic masses, This output uses the
InChI labelling algorithm to generate a 'Universal SMILES' (O'Boyle, Noel. Journal of Cheminformatics. 2012. 4).
|
static int |
UseAromaticSymbols
Writes aromatic atoms as lower case letters.
|
public static final int Canonical
public static final int InChILabelling
UniversalSmiles
,
Constant Field Valuespublic static final int AtomAtomMap
CDKConstants.ATOM_ATOM_MAPPING
using IChemObject.setProperty(Object, Object)
.public static final int AtomicMass
[12CH3][12CH2][16OH]
major isotopes are not generated. If you
wish to generate SMILES with the major isotopes please use the flag
AtomicMassStrict
this will output all mass numbers and only be
omitted when the mass is unset (null).public static final int UseAromaticSymbols
public static final int StereoTetrahedral
@
and @@
.Stereo
,
Constant Field Valuespublic static final int StereoCisTrans
\
of /
bonds.Stereo
,
Constant Field Valuespublic static final int StereoExTetrahedral
@
and
@@
. Extended tetrahedral captures rotations around a cumulated
carbon: CC=[C@]=CC
.Stereo
,
Constant Field Valuespublic static final int StereoExCisTrans
@Deprecated public static final int AtomicMassStrict
public static final int Stereo
public static final int Cx2dCoordinates
public static final int Cx3dCoordinates
public static final int CxCoordinates
public static final int CxAtomLabel
IPseudoAtom.getLabel()
.public static final int CxAtomValue
CDKConstants.COMMENT
using
IChemObject.setProperty(Object, Object)
public static final int CxRadical
IAtomContainer.getConnectedSingleElectronsCount(IAtom)
public static final int CxMulticenter
Sgroup
s
of the type SgroupType.ExtMulticenter
.public static final int CxPolymer
Sgroup
s.public static final int CxFragmentGroup
public static final int CxLigandOrder
public static final int AtomAtomMapRenumber
public static final int CxDataSgroups
public static final int CxEnhancedStereo
public static final int CxSmiles
public static final int CxSmilesWithCoords
public static final int Generic
public static final int Unique
public static final int Isomeric
public static final int Absolute
public static final int Default
public static final int UniversalSmiles
C(\C=C\N1CCCC1)=C/c2[n+](c3c(n2CC)nc4ccccc4n3)CC
will generate two different
SMILES depending on input orderCopyright © 2021. All rights reserved.