Package com.actelion.research.chem
Class TautomerHelper
- java.lang.Object
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- com.actelion.research.chem.TautomerHelper
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public class TautomerHelper extends java.lang.Object
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Constructor Summary
Constructors Constructor Description TautomerHelper(StereoMolecule mol)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description StereoMolecule
createGenericTautomer()
If no tautomers can be formed then a copy of the original molecule is returned.int
getAtomRegionNumbers(int[] atomRegionNo)
Identifies connected tautomeric regions and assign region numbers to all atoms.StereoMolecule
getNextTautomer(StereoMolecule tautomer)
int
getTautomerCount()
static void
setMaxTautomers(int maxTautomers)
static void
setSuppressWarning(boolean suppressWarning)
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Constructor Detail
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TautomerHelper
public TautomerHelper(StereoMolecule mol)
- Parameters:
mol
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Method Detail
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setMaxTautomers
public static void setMaxTautomers(int maxTautomers)
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setSuppressWarning
public static void setSuppressWarning(boolean suppressWarning)
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getNextTautomer
public StereoMolecule getNextTautomer(StereoMolecule tautomer)
- Parameters:
tautomer
- null or another tautomer of same molecule, which receives the new bond orders- Returns:
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getTautomerCount
public int getTautomerCount()
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getAtomRegionNumbers
public int getAtomRegionNumbers(int[] atomRegionNo)
Identifies connected tautomeric regions and assign region numbers to all atoms. Atoms sharing the same region share the same number.
0: not member of a tautomer region; 1 and above: region number- Parameters:
atomRegionNo
- int[mol.getAtoms()] filled with 0- Returns:
- region count
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createGenericTautomer
public StereoMolecule createGenericTautomer()
If no tautomers can be formed then a copy of the original molecule is returned. Otherwise a copy of the original molecule is normalized to create a generic tautomer structure. The original molecule is not touched. Different tautomers of the same molecule should always result in the same generic tautomer structure. A generic tautomer contains one or more regions indicated by bond query features cBondQFSingle & cBondQFDouble. Bond types of all bonds of any tautomer region are cBondTypeSingle. The highest ranking atom in every region carries a label defining the number of double bonds and D and T atoms. The returned molecule has the fragment bit set. Canonicalizing the returned molecule with Canonizer mode ENCODE_ATOM_CUSTOM_LABELS produces the same idcode from any tautomer. If keepStereoCenters is true, then stereo centers with parity 1 or 2, if they are absolute or if they are part of an AND/OR group with more than one member, are considered stable (non racemising) and, thus, their proton is not considered being able to take part in a tautomeric transition.- Returns:
- generic tautomer with normalized tautomer regions and custom label to encode pi,D,T counts
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