SmiFlavor (cdk 2.2 API)

java.lang.Object
- org.openscience.cdk.smiles.SmiFlavor

public final class SmiFlavor
extends Object

Flags for customising SMILES generation.

Field Summary

Fields
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`	`CxFragmentGroup` Output fragment grouping for reactions.
`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.

Method Summary
- Methods inherited from class java.lang.Object
  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - Canonical
```
public static final int Canonical
```
    Output SMILES in a canonical order. The order is not guaranteed to be equivalent between releases.
    
    See Also:
    
    Constant Field Values
  - InChILabelling
```
public static final int InChILabelling
```
    Output SMILES in a canonical order using the InChI labelling algorithm.
    
    See Also:
    
    UniversalSmiles, Constant Field Values
  - AtomAtomMap
```
public static final int AtomAtomMap
```
    Output atom-atom mapping for reactions and atom classes for molecules. The map index is set on an atom with property CDKConstants.ATOM_ATOM_MAPPING using IChemObject.setProperty(Object, Object).
    
    See Also:
    
    Constant Field Values
  - AtomicMass
```
public static final int AtomicMass
```
    Output atomic mass on atoms. For historical reasons the atomic mass is often set on all atoms in a CDK molecule. Therefore to avoid SMILES like [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).
    
    See Also:
    
    Constant Field Values
  - UseAromaticSymbols
```
public static final int UseAromaticSymbols
```
    Writes aromatic atoms as lower case letters. For portability this option is not recommended.
    
    See Also:
    
    Constant Field Values
  - StereoTetrahedral
```
public static final int StereoTetrahedral
```
    Output tetrahedral stereochemistry on atoms as @ and @@.
    
    See Also:
    
    Stereo, Constant Field Values
  - StereoCisTrans
```
public static final int StereoCisTrans
```
    Output cis-trans stereochemistry specified by directional \ of / bonds.
    
    See Also:
    
    Stereo, Constant Field Values
  - StereoExTetrahedral
```
public static final int StereoExTetrahedral
```
    Output extended tetrahedral stereochemistry on atoms as @ and @@. Extended tetrahedral captures rotations around a cumulated carbon: CC=[C@]=CC.
    
    See Also:
    
    Stereo, Constant Field Values
  - StereoExCisTrans
```
public static final int StereoExCisTrans
```
    See Also:
    
    Constant Field Values
  - AtomicMassStrict
```
@Deprecated
public static final int AtomicMassStrict
```
    Deprecated. no longer needed, default CDK behaviour is now to pass through mass numbers if non-null
    
    Generate SMILES with the major isotopes, only omit mass numbers when it is unset.
    
    See Also:
    
    Constant Field Values
  - Stereo
```
public static final int Stereo
```
    Output supported stereochemistry types.
    
    See Also:
    
    StereoTetrahedral, StereoCisTrans, StereoExTetrahedral, Constant Field Values
  - Cx2dCoordinates
```
public static final int Cx2dCoordinates
```
    Output 2D coordinates.
    
    See Also:
    
    Constant Field Values
  - Cx3dCoordinates
```
public static final int Cx3dCoordinates
```
    Output 3D coordinates.
    
    See Also:
    
    Constant Field Values
  - CxCoordinates
```
public static final int CxCoordinates
```
    Output either 2D/3D coordinates.
    
    See Also:
    
    Constant Field Values
  - CxAtomLabel
```
public static final int CxAtomLabel
```
    Output atom labels, atom labels are specified by IPseudoAtom.getLabel().
    
    See Also:
    
    Constant Field Values
  - CxAtomValue
```
public static final int CxAtomValue
```
    Output atom values, atom values are specified by the property CDKConstants.COMMENT using IChemObject.setProperty(Object, Object)
    
    See Also:
    
    Constant Field Values
  - CxRadical
```
public static final int CxRadical
```
    Output radicals, radicals are specified by IAtomContainer.getConnectedSingleElectronsCount(IAtom)
    
    See Also:
    
    Constant Field Values
  - CxMulticenter
```
public static final int CxMulticenter
```
    Output multicenter bonds, positional variation is specified with Sgroups of the type SgroupType.ExtMulticenter.
    
    See Also:
    
    Constant Field Values
  - CxPolymer
```
public static final int CxPolymer
```
    Output polymer repeat units is specified with Sgroups.
    
    See Also:
    
    Constant Field Values
  - CxFragmentGroup
```
public static final int CxFragmentGroup
```
    Output fragment grouping for reactions.
    
    See Also:
    
    Constant Field Values
  - AtomAtomMapRenumber
```
public static final int AtomAtomMapRenumber
```
    Renumber AtomAtomMaps during canonical generation
    
    See Also:
    
    Constant Field Values
  - CxSmiles
```
public static final int CxSmiles
```
    Output CXSMILES layers.
    
    See Also:
    
    Constant Field Values
  - CxSmilesWithCoords
```
public static final int CxSmilesWithCoords
```
    Output CXSMILES layers and coordinates.
    
    See Also:
    
    Constant Field Values
  - Generic
```
public static final int Generic
```
    Output non-canonical SMILES without stereochemistry, atomic masses.
    
    See Also:
    
    Constant Field Values
  - Unique
```
public static final int Unique
```
    Output canonical SMILES without stereochemistry, atomic masses.
    
    See Also:
    
    Constant Field Values
  - Isomeric
```
public static final int Isomeric
```
    Output non-canonical SMILES with stereochemistry, atomic masses.
    
    See Also:
    
    Constant Field Values
  - Absolute
```
public static final int Absolute
```
    Output canonical SMILES with stereochemistry, atomic masses.
    
    See Also:
    
    Constant Field Values
  - Default
```
public static final int Default
```
    Default SMILES output write Stereochemistry, Atomic Mass, and CXSMILES layers. The ordering is not canonical.
    
    See Also:
    
    Constant Field Values
  - UniversalSmiles
```
public static final 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).
    Unfortunately there are several issues and general use is not recommended:
    - MAJOR: Molecules with delocalised charges are generally non-canonical, e.g. C(\C=C\N1CCCC1)=C/c2[n+](c3c(n2CC)nc4ccccc4n3)CC will generate two different SMILES depending on input order
    - MINOR: Double bond '/' '\' assignment is different from the original paper (O'Boyle) and will not match universal SMILES generated by Open Babel
    - MINOR: SMILES with '*' atoms can not be canonicalised by default, to avoid this we use the 'Rf' atom as a substitute. Structures with an 'Rf' atom can still be generated providing there are no '*' atoms.
    - MINOR: The InChI library (v1.03) is not thread safe
    See Also:
    
    Constant Field Values

Class SmiFlavor

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

Canonical

InChILabelling

AtomAtomMap

AtomicMass

UseAromaticSymbols

StereoTetrahedral

StereoCisTrans

StereoExTetrahedral

StereoExCisTrans

AtomicMassStrict

Stereo

Cx2dCoordinates

Cx3dCoordinates

CxCoordinates

CxAtomLabel

CxAtomValue

CxRadical

CxMulticenter

CxPolymer

CxFragmentGroup

AtomAtomMapRenumber

CxSmiles

CxSmilesWithCoords

Generic

Unique

Isomeric

Absolute

Default

UniversalSmiles