ambit2.smarts

Class StereoChemUtils

java.lang.Object

ambit2.smarts.StereoChemUtils

public class StereoChemUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
StereoChemUtils()

Method Summary

Modifier and Type	Method and Description
static org.openscience.cdk.stereo.DoubleBondStereochemistry	bondChange(org.openscience.cdk.interfaces.IAtom at1, org.openscience.cdk.interfaces.IAtom at2, org.openscience.cdk.interfaces.IBond.Order initialBondOrder, org.openscience.cdk.interfaces.IBond.Order updatedBondOrder, org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc, StereoChange stChange)
static org.openscience.cdk.stereo.ExtendedTetrahedral	bondChange(org.openscience.cdk.interfaces.IAtom at1, org.openscience.cdk.interfaces.IAtom at2, org.openscience.cdk.interfaces.IBond.Order initialBondOrder, org.openscience.cdk.interfaces.IBond.Order updatedBondOrder, org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.stereo.ExtendedTetrahedral etc)
static org.openscience.cdk.stereo.TetrahedralChirality	bondChange(org.openscience.cdk.interfaces.IAtom at1, org.openscience.cdk.interfaces.IAtom at2, org.openscience.cdk.interfaces.IBond.Order initialBondOrder, org.openscience.cdk.interfaces.IBond.Order updatedBondOrder, org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.stereo.TetrahedralChirality thc)
static int	checkDoubleBondStereochemistry(org.openscience.cdk.stereo.DoubleBondStereochemistry dbs, org.openscience.cdk.interfaces.IAtomContainer mol)
static void	checkStereoElements(org.openscience.cdk.interfaces.IAtomContainer mol)
static int	checkTetrahedralChirality(org.openscience.cdk.stereo.TetrahedralChirality thc, org.openscience.cdk.interfaces.IAtomContainer mol)
static void	cloneAndCheckStereo(org.openscience.cdk.interfaces.IAtomContainer cloneMol, org.openscience.cdk.interfaces.IAtomContainer originalMol)
static org.openscience.cdk.stereo.DoubleBondStereochemistry	cloneDoubleBondStereochemistry(org.openscience.cdk.stereo.DoubleBondStereochemistry originalDBS, org.openscience.cdk.interfaces.IAtomContainer originalMol, org.openscience.cdk.interfaces.IAtomContainer cloneMol)
static org.openscience.cdk.stereo.DoubleBondStereochemistry	cloneDoubleBondStereochemistry(org.openscience.cdk.stereo.DoubleBondStereochemistry originalDBS, org.openscience.cdk.interfaces.IAtomContainer originalMol, org.openscience.cdk.interfaces.IAtomContainer cloneMol, org.openscience.cdk.interfaces.IAtom[] newAtoms, org.openscience.cdk.interfaces.IBond[] newBonds)
static org.openscience.cdk.stereo.TetrahedralChirality	cloneTetrahedralChirality(org.openscience.cdk.stereo.TetrahedralChirality originalTHC, org.openscience.cdk.interfaces.IAtomContainer originalMol, org.openscience.cdk.interfaces.IAtomContainer cloneMol)
static org.openscience.cdk.stereo.TetrahedralChirality	cloneTetrahedralChirality(org.openscience.cdk.stereo.TetrahedralChirality originalTHC, org.openscience.cdk.interfaces.IAtomContainer originalMol, org.openscience.cdk.interfaces.IAtomContainer cloneMol, org.openscience.cdk.interfaces.IAtom[] newAtoms)
static boolean	contains(org.openscience.cdk.interfaces.IStereoElement element, org.openscience.cdk.interfaces.IAtom at) Checks whether the stereo element contains the atom This function works with invalidated stereo elements.
static org.openscience.cdk.stereo.DoubleBondStereochemistry	deleteAtom(org.openscience.cdk.interfaces.IAtom at, org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc, StereoChange stChange)
static org.openscience.cdk.stereo.ExtendedTetrahedral	deleteAtom(org.openscience.cdk.interfaces.IAtom at, org.openscience.cdk.stereo.ExtendedTetrahedral etc)
static org.openscience.cdk.stereo.TetrahedralChirality	deleteAtom(org.openscience.cdk.interfaces.IAtom at, org.openscience.cdk.stereo.TetrahedralChirality thc)
static String	doubleBondStereochemistry2String(org.openscience.cdk.stereo.DoubleBondStereochemistry dbs, org.openscience.cdk.interfaces.IAtomContainer mol)
static String	extendedTetrahedral2String(org.openscience.cdk.stereo.ExtendedTetrahedral eth, org.openscience.cdk.interfaces.IAtomContainer mol)
static org.openscience.cdk.stereo.DoubleBondStereochemistry	findDBStereoElementByStereoBond(org.openscience.cdk.interfaces.IBond stereoBond, org.openscience.cdk.interfaces.IAtomContainer container)
static org.openscience.cdk.stereo.ExtendedTetrahedral	findExtendedTetrahedralByChiralCenter(org.openscience.cdk.interfaces.IAtom chirCenter, org.openscience.cdk.interfaces.IAtomContainer container)
static org.openscience.cdk.stereo.TetrahedralChirality	findTetrahedralChiralityByChiralCenter(org.openscience.cdk.interfaces.IAtom chirCenter, org.openscience.cdk.interfaces.IAtomContainer container)
static String	getAllStereoElementsStatus(org.openscience.cdk.interfaces.IAtomContainer mol, List<org.openscience.cdk.interfaces.IStereoElement> invElements)
static String	getStereoElementsStatus(org.openscience.cdk.interfaces.IAtomContainer mol)
static String	getTetrahedralChiralityStatusString(int status)
static boolean	isInvalidated(org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc)
static boolean	isInvalidated(org.openscience.cdk.stereo.ExtendedTetrahedral etc)
static boolean	isInvalidated(org.openscience.cdk.stereo.TetrahedralChirality thc)
static org.openscience.cdk.stereo.DoubleBondStereochemistry	restoreDBStereo(org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc, StereoChange stChange)
static void	setSteroElementsAsProperties(org.openscience.cdk.interfaces.IAtomContainer container)
static String	stereoElement2String(org.openscience.cdk.interfaces.IStereoElement element, org.openscience.cdk.interfaces.IAtomContainer mol)
static String	tetrahedralChirality2String(org.openscience.cdk.stereo.TetrahedralChirality thc, org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class java.lang.Object

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

Constructor Detail

StereoChemUtils

public StereoChemUtils()

Method Detail

cloneDoubleBondStereochemistry

public static org.openscience.cdk.stereo.DoubleBondStereochemistry cloneDoubleBondStereochemistry(org.openscience.cdk.stereo.DoubleBondStereochemistry originalDBS,
                                                                                                  org.openscience.cdk.interfaces.IAtomContainer originalMol,
                                                                                                  org.openscience.cdk.interfaces.IAtomContainer cloneMol,
                                                                                                  org.openscience.cdk.interfaces.IAtom[] newAtoms,
                                                                                                  org.openscience.cdk.interfaces.IBond[] newBonds)

Parameters:

originalDBS - - the stereo element from the original molecule that will be cloned

originalMol - - the original molecule

cloneMol - - the clone molecule. Its atoms and bond must have already be cloned

newAtoms - - the cloned/new atoms

newBonds - - the cloned/new bonds

Returns:

cloneDoubleBondStereochemistry

public static org.openscience.cdk.stereo.DoubleBondStereochemistry cloneDoubleBondStereochemistry(org.openscience.cdk.stereo.DoubleBondStereochemistry originalDBS,
                                                                                                  org.openscience.cdk.interfaces.IAtomContainer originalMol,
                                                                                                  org.openscience.cdk.interfaces.IAtomContainer cloneMol)

cloneTetrahedralChirality

public static org.openscience.cdk.stereo.TetrahedralChirality cloneTetrahedralChirality(org.openscience.cdk.stereo.TetrahedralChirality originalTHC,
                                                                                        org.openscience.cdk.interfaces.IAtomContainer originalMol,
                                                                                        org.openscience.cdk.interfaces.IAtomContainer cloneMol,
                                                                                        org.openscience.cdk.interfaces.IAtom[] newAtoms)

cloneTetrahedralChirality

public static org.openscience.cdk.stereo.TetrahedralChirality cloneTetrahedralChirality(org.openscience.cdk.stereo.TetrahedralChirality originalTHC,
                                                                                        org.openscience.cdk.interfaces.IAtomContainer originalMol,
                                                                                        org.openscience.cdk.interfaces.IAtomContainer cloneMol)

checkStereoElements

public static void checkStereoElements(org.openscience.cdk.interfaces.IAtomContainer mol)

checkDoubleBondStereochemistry

public static int checkDoubleBondStereochemistry(org.openscience.cdk.stereo.DoubleBondStereochemistry dbs,
                                                 org.openscience.cdk.interfaces.IAtomContainer mol)

Parameters:

dbs - - DoubleBondStereochemistry object to checked

mol - - target molecule (IAtomContainer)

Returns:

check result: 0 - OK 1 - stereo bond is null 2 - stereo bond is not present in the molecule 3 - stereo bond is not double bond 4 - stereo bond does not contain 2 atoms 5 - ligand bonds array is null 6 - one of the ligand bonds is not present in the molecule 7 - one of the ligand bonds is not adjacent to the stereo bond 8 - one of the ligand bonds is not single bond 9 - stereo Conformation is null

checkTetrahedralChirality

public static int checkTetrahedralChirality(org.openscience.cdk.stereo.TetrahedralChirality thc,
                                            org.openscience.cdk.interfaces.IAtomContainer mol)

Parameters:

thc - - TetrahedralChirality object to be checked

mol - - target molecule (IAtomContainer)

Returns:

check result: 0 - OK 1 - chiralAtom (chiral center) is null 2 - chiralAtom is not present in the molecule 3 - ligand atoms array is null 4 - ligand atoms array size is not 4 5 - one of the ligand atoms is null 6 - one of the ligand atoms is not present in the molecule 7 - one of the ligand atoms is not connected to the chiralAtom 8 - one of the ligand atoms is connected with non-single bond 9 - stereo is null 10 - chiralAtom with missing implicit H atom

getTetrahedralChiralityStatusString

public static String getTetrahedralChiralityStatusString(int status)

doubleBondStereochemistry2String

public static String doubleBondStereochemistry2String(org.openscience.cdk.stereo.DoubleBondStereochemistry dbs,
                                                      org.openscience.cdk.interfaces.IAtomContainer mol)

tetrahedralChirality2String

public static String tetrahedralChirality2String(org.openscience.cdk.stereo.TetrahedralChirality thc,
                                                 org.openscience.cdk.interfaces.IAtomContainer mol)

extendedTetrahedral2String

public static String extendedTetrahedral2String(org.openscience.cdk.stereo.ExtendedTetrahedral eth,
                                                org.openscience.cdk.interfaces.IAtomContainer mol)

stereoElement2String

public static String stereoElement2String(org.openscience.cdk.interfaces.IStereoElement element,
                                          org.openscience.cdk.interfaces.IAtomContainer mol)

cloneAndCheckStereo

public static void cloneAndCheckStereo(org.openscience.cdk.interfaces.IAtomContainer cloneMol,
                                       org.openscience.cdk.interfaces.IAtomContainer originalMol)

getStereoElementsStatus

public static String getStereoElementsStatus(org.openscience.cdk.interfaces.IAtomContainer mol)

getAllStereoElementsStatus

public static String getAllStereoElementsStatus(org.openscience.cdk.interfaces.IAtomContainer mol,
                                                List<org.openscience.cdk.interfaces.IStereoElement> invElements)

setSteroElementsAsProperties

public static void setSteroElementsAsProperties(org.openscience.cdk.interfaces.IAtomContainer container)

deleteAtom

public static org.openscience.cdk.stereo.TetrahedralChirality deleteAtom(org.openscience.cdk.interfaces.IAtom at,
                                                                         org.openscience.cdk.stereo.TetrahedralChirality thc)

deleteAtom

public static org.openscience.cdk.stereo.ExtendedTetrahedral deleteAtom(org.openscience.cdk.interfaces.IAtom at,
                                                                        org.openscience.cdk.stereo.ExtendedTetrahedral etc)

bondChange

public static org.openscience.cdk.stereo.TetrahedralChirality bondChange(org.openscience.cdk.interfaces.IAtom at1,
                                                                         org.openscience.cdk.interfaces.IAtom at2,
                                                                         org.openscience.cdk.interfaces.IBond.Order initialBondOrder,
                                                                         org.openscience.cdk.interfaces.IBond.Order updatedBondOrder,
                                                                         org.openscience.cdk.interfaces.IAtomContainer target,
                                                                         org.openscience.cdk.stereo.TetrahedralChirality thc)

bondChange

public static org.openscience.cdk.stereo.ExtendedTetrahedral bondChange(org.openscience.cdk.interfaces.IAtom at1,
                                                                        org.openscience.cdk.interfaces.IAtom at2,
                                                                        org.openscience.cdk.interfaces.IBond.Order initialBondOrder,
                                                                        org.openscience.cdk.interfaces.IBond.Order updatedBondOrder,
                                                                        org.openscience.cdk.interfaces.IAtomContainer target,
                                                                        org.openscience.cdk.stereo.ExtendedTetrahedral etc)

deleteAtom

public static org.openscience.cdk.stereo.DoubleBondStereochemistry deleteAtom(org.openscience.cdk.interfaces.IAtom at,
                                                                              org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc,
                                                                              StereoChange stChange)

bondChange

public static org.openscience.cdk.stereo.DoubleBondStereochemistry bondChange(org.openscience.cdk.interfaces.IAtom at1,
                                                                              org.openscience.cdk.interfaces.IAtom at2,
                                                                              org.openscience.cdk.interfaces.IBond.Order initialBondOrder,
                                                                              org.openscience.cdk.interfaces.IBond.Order updatedBondOrder,
                                                                              org.openscience.cdk.interfaces.IAtomContainer target,
                                                                              org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc,
                                                                              StereoChange stChange)

isInvalidated

public static boolean isInvalidated(org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc)

isInvalidated

public static boolean isInvalidated(org.openscience.cdk.stereo.TetrahedralChirality thc)

isInvalidated

public static boolean isInvalidated(org.openscience.cdk.stereo.ExtendedTetrahedral etc)

contains

public static boolean contains(org.openscience.cdk.interfaces.IStereoElement element,
                               org.openscience.cdk.interfaces.IAtom at)

Checks whether the stereo element contains the atom This function works with invalidated stereo elements. The standard IStereoElement.contains() method would throws Null pointer exception in some cases of invalidated elements

Parameters:

element -

at -

Returns:

findDBStereoElementByStereoBond

public static org.openscience.cdk.stereo.DoubleBondStereochemistry findDBStereoElementByStereoBond(org.openscience.cdk.interfaces.IBond stereoBond,
                                                                                                   org.openscience.cdk.interfaces.IAtomContainer container)

findTetrahedralChiralityByChiralCenter

public static org.openscience.cdk.stereo.TetrahedralChirality findTetrahedralChiralityByChiralCenter(org.openscience.cdk.interfaces.IAtom chirCenter,
                                                                                                     org.openscience.cdk.interfaces.IAtomContainer container)

findExtendedTetrahedralByChiralCenter

public static org.openscience.cdk.stereo.ExtendedTetrahedral findExtendedTetrahedralByChiralCenter(org.openscience.cdk.interfaces.IAtom chirCenter,
                                                                                                   org.openscience.cdk.interfaces.IAtomContainer container)

restoreDBStereo

public static org.openscience.cdk.stereo.DoubleBondStereochemistry restoreDBStereo(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                   org.openscience.cdk.stereo.DoubleBondStereochemistry dbsc,
                                                                                   StereoChange stChange)