Package com.actelion.research.chem

Class CanonizerUtil

java.lang.Object

com.actelion.research.chem.CanonizerUtil

public class CanonizerUtil
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CanonizerUtil.IDCODE_TYPE
static class	CanonizerUtil.StrongHasher	64 bit hash, derived from numerical recipes Will move this class later to dd_core.

Constructor Summary

Constructors

Constructor	Description
CanonizerUtil()

Method Summary

Modifier and Type	Method	Description
static long	getBackboneHash(StereoMolecule m, boolean largestFragmentOnly)
static long	getHash(StereoMolecule m, CanonizerUtil.IDCODE_TYPE type, boolean largestFragmentOnly)
static java.lang.String	getIDCode(StereoMolecule mol, CanonizerUtil.IDCODE_TYPE type, boolean largestFragmentOnly)	Generates an IDCODE for a defined and simplified state of a given molecule.
static long	getNoStereoHash(StereoMolecule m, boolean largestFragmentOnly)
static long	getNoStereoTautomerHash(StereoMolecule m, boolean largestFragmentOnly)
static long	getTautomerHash(StereoMolecule m, boolean largestFragmentOnly)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CanonizerUtil

public CanonizerUtil()

Method Detail

getIDCode

public static java.lang.String getIDCode(StereoMolecule mol,
                                         CanonizerUtil.IDCODE_TYPE type,
                                         boolean largestFragmentOnly)

Generates an IDCODE for a defined and simplified state of a given molecule. Optionally the simplification and idcode generation are done for the largest unconnected fragment rather than considering all molecule fragments. Allowed simplification types are:
- NORMAL (with complete stereo information)
- NOSTEREO (without stereo information)
- TAUTOMER (generic tautomer: tautomer regions marked as [cBondQFSingle | cBondQFDouble] plus atom label encoding count of pi electrons, deuterium and tritium)
- NOSTEREO_TAUTOMER (combines NOSTEREO and TAUTOMER)
- BACKBONE (without stereo information; all bonds are changed to single bonds)

Parameters:

mol - source molecule to generate the IDCODE

type - type of IDCODE requested

largestFragmentOnly -

Returns:

getHash

public static long getHash(StereoMolecule m,
                           CanonizerUtil.IDCODE_TYPE type,
                           boolean largestFragmentOnly)

getNoStereoHash

public static long getNoStereoHash(StereoMolecule m,
                                   boolean largestFragmentOnly)

getTautomerHash

public static long getTautomerHash(StereoMolecule m,
                                   boolean largestFragmentOnly)

getNoStereoTautomerHash

public static long getNoStereoTautomerHash(StereoMolecule m,
                                           boolean largestFragmentOnly)

getBackboneHash

public static long getBackboneHash(StereoMolecule m,
                                   boolean largestFragmentOnly)