ambit2.core.data
Class MoleculeTools

java.lang.Object
  ambit2.core.data.MoleculeTools

public class MoleculeTools
extends java.lang.Object

Various structure processing. TODO refactor.

Field Summary

static int	_FPLength
protected static org.openscience.cdk.tools.HydrogenAdder	adder
protected static java.lang.String	bracketLeft
protected static java.lang.String	bracketRight
protected static java.lang.String	delim
protected static org.openscience.cdk.fingerprint.Fingerprinter	fingerprinter
protected static StructureTypeProcessor	sp
static java.lang.String[]	substanceType
static int	substTypeInorganic
static int	substTypeMetallic
static int	substTypeMixture
static int	substTypeOrganic

Constructor Summary

MoleculeTools()

Method Summary

static boolean	analyzeSubstance(org.openscience.cdk.interfaces.IAtomContainer molecule)
static void	bitset2bigint16(java.util.BitSet bs, int size, java.math.BigInteger[] h16)
static long	bitset2Long(java.util.BitSet bs)
static java.util.BitSet	getFingerPrint(java.lang.String smiles)
static java.util.BitSet	getFingerPrint(java.lang.String smiles, int fpLength)
static org.openscience.cdk.interfaces.IMolecule	getMolecule(java.lang.String smiles)
protected static int	getSubstanceType(java.lang.String formula)
static org.openscience.cdk.interfaces.IMolecule	readCMLMolecule(java.io.Reader cmlReader)
static org.openscience.cdk.interfaces.IMolecule	readCMLMolecule(java.lang.String cml)
static org.openscience.cdk.interfaces.IMolecule	readMolfile(java.io.Reader molfile)
static org.openscience.cdk.interfaces.IMolecule	readMolfile(java.lang.String molfile)

Methods inherited from class java.lang.Object

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

Field Detail

_FPLength

public static final int _FPLength

See Also:

Constant Field Values

adder

protected static org.openscience.cdk.tools.HydrogenAdder adder

fingerprinter

protected static org.openscience.cdk.fingerprint.Fingerprinter fingerprinter

substanceType

public static final java.lang.String[] substanceType

substTypeOrganic

public static final int substTypeOrganic

See Also:

Constant Field Values

substTypeInorganic

public static final int substTypeInorganic

See Also:

Constant Field Values

substTypeMixture

public static final int substTypeMixture

See Also:

Constant Field Values

substTypeMetallic

public static final int substTypeMetallic

See Also:

Constant Field Values

sp

protected static StructureTypeProcessor sp

delim

protected static java.lang.String delim

bracketLeft

protected static java.lang.String bracketLeft

bracketRight

protected static java.lang.String bracketRight

Constructor Detail

MoleculeTools

public MoleculeTools()

Method Detail

getMolecule

public static org.openscience.cdk.interfaces.IMolecule getMolecule(java.lang.String smiles)
                                                            throws org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.InvalidSmilesException

getFingerPrint

public static java.util.BitSet getFingerPrint(java.lang.String smiles,
                                              int fpLength)
                                       throws java.lang.Exception

Throws:

java.lang.Exception

getFingerPrint

public static java.util.BitSet getFingerPrint(java.lang.String smiles)
                                       throws java.lang.Exception

Throws:

java.lang.Exception

bitset2Long

public static long bitset2Long(java.util.BitSet bs)

bitset2bigint16

public static void bitset2bigint16(java.util.BitSet bs,
                                   int size,
                                   java.math.BigInteger[] h16)

analyzeSubstance

public static boolean analyzeSubstance(org.openscience.cdk.interfaces.IAtomContainer molecule)

getSubstanceType

protected static int getSubstanceType(java.lang.String formula)

readMolfile

public static org.openscience.cdk.interfaces.IMolecule readMolfile(java.io.Reader molfile)
                                                            throws java.lang.Exception

Throws:

java.lang.Exception

readMolfile

public static org.openscience.cdk.interfaces.IMolecule readMolfile(java.lang.String molfile)
                                                            throws java.lang.Exception

Throws:

java.lang.Exception

readCMLMolecule

public static org.openscience.cdk.interfaces.IMolecule readCMLMolecule(java.lang.String cml)
                                                                throws java.lang.Exception

Throws:

java.lang.Exception

readCMLMolecule

public static org.openscience.cdk.interfaces.IMolecule readCMLMolecule(java.io.Reader cmlReader)
                                                                throws java.lang.Exception

Throws:

java.lang.Exception