ambit2.tautomers

Class CACTVSRanking

java.lang.Object

ambit2.tautomers.CACTVSRanking

public class CACTVSRanking
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static double	score2eV

Constructor Summary

Constructors

Constructor and Description
CACTVSRanking()

Method Summary

Modifier and Type	Method and Description
static double	calcScoreRank(org.openscience.cdk.interfaces.IAtomContainer mol)
static boolean	checkMethylGroup(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol)
static int	checkOximAciNitro(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol)
static int	checkPSSeTeH(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol)
static double	getEnergyRank(org.openscience.cdk.interfaces.IAtomContainer mol)
static int	getHNeighbours(org.openscience.cdk.interfaces.IAtom atom, org.openscience.cdk.interfaces.IAtomContainer mol)
static String	scoreFragmentsToString(int nAromAt, int nOximGroup, int nC2O, int nN2O, int nP2O, int nC2X, int nCH3, int nYH, int nAciNitro)

Methods inherited from class java.lang.Object

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

Field Detail

score2eV

public static final double score2eV

See Also:

Constant Field Values

Constructor Detail

CACTVSRanking

public CACTVSRanking()

Method Detail

calcScoreRank

public static double calcScoreRank(org.openscience.cdk.interfaces.IAtomContainer mol)

Parameters:

mol -

Returns:

tautomer score as defined in J. Comput. Aided. Mol. Des. (2010) 24:521-551 (see table2 at page 530) additional simpler score table from J. Chem. Inf. Mod. Vol.46, No.6, 2006 (page 2349 table 2)

getEnergyRank

public static double getEnergyRank(org.openscience.cdk.interfaces.IAtomContainer mol)

checkMethylGroup

public static boolean checkMethylGroup(org.openscience.cdk.interfaces.IAtom atom,
                                       org.openscience.cdk.interfaces.IAtomContainer mol)

checkOximAciNitro

public static int checkOximAciNitro(org.openscience.cdk.interfaces.IAtom atom,
                                    org.openscience.cdk.interfaces.IAtomContainer mol)

Parameters:

atom - - target atom

mol - - target molecule

Returns:

1 if oxim group (C=N[OH]), 2 if aci-nitro group (C=N(=O)[OH]), otherwise return 0

checkPSSeTeH

public static int checkPSSeTeH(org.openscience.cdk.interfaces.IAtom atom,
                               org.openscience.cdk.interfaces.IAtomContainer mol)

getHNeighbours

public static int getHNeighbours(org.openscience.cdk.interfaces.IAtom atom,
                                 org.openscience.cdk.interfaces.IAtomContainer mol)

scoreFragmentsToString

public static String scoreFragmentsToString(int nAromAt,
                                            int nOximGroup,
                                            int nC2O,
                                            int nN2O,
                                            int nP2O,
                                            int nC2X,
                                            int nCH3,
                                            int nYH,
                                            int nAciNitro)