ambit2.core.data

Class MoleculeTools

java.lang.Object

ambit2.core.data.MoleculeTools

public class MoleculeTools
extends Object

Various structure processing. TODO refactor.

Author:

Nina Jeliazkova
Modified 2005-4-7

Field Summary

Fields

Modifier and Type	Field and Description
static int	_FPLength
protected static org.openscience.cdk.tools.CDKHydrogenAdder	adder
protected static String	bracketLeft
protected static String	bracketRight
protected static String	delim
protected static org.openscience.cdk.fingerprint.Fingerprinter	fingerprinter
protected static Logger	logger
protected static StructureTypeProcessor	sp
static String[]	substanceType
static int	substTypeInorganic
static int	substTypeMetallic
static int	substTypeMixture
static int	substTypeOrganic

Constructor Summary

Constructors

Constructor and Description
MoleculeTools()

Method Summary

Modifier and Type	Method and Description
static void	add1ImplicitHAtom(org.openscience.cdk.interfaces.IAtom atom)
static boolean	analyzeSubstance(org.openscience.cdk.interfaces.IAtomContainer molecule)
static void	bitset2bigint16(BitSet bs, int size, BigInteger[] h16)
static long	bitset2Long(BitSet bs)
static void	clearProperties(org.openscience.cdk.interfaces.IChemObject chemObject)
static void	convertExplicitHAtomsToImplicit(org.openscience.cdk.interfaces.IAtomContainer mol)
static void	convertImplicitToExplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer) Adds explicit hydrogens (without coordinates) to the IAtomContainer, equaling the number of set implicit hydrogens.
static org.openscience.cdk.interfaces.IAtomContainer	copyChangeBuilders(org.openscience.cdk.interfaces.IAtomContainer molecule, org.openscience.cdk.interfaces.IChemObjectBuilder newBuilder) Just copy atoms and bonds, discard all the flags, they will be recalculated later
static BitSet	getFingerPrint(String smiles)
static BitSet	getFingerPrint(String smiles, int fpLength)
static org.openscience.cdk.interfaces.IAtomContainer	getMolecule(String smiles)
protected static int	getSubstanceType(String formula)
protected static boolean	hasBondOrderUnsetAromatic(org.openscience.cdk.interfaces.IAtomContainer mol)
static org.openscience.cdk.interfaces.IAtom	newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IAtom	newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtom atom)
static org.openscience.cdk.interfaces.IAtom	newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IElement element)
static org.openscience.cdk.interfaces.IAtom	newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder, String atom)
static org.openscience.cdk.interfaces.IAtomContainer	newAtomContainer(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IAtomContainer	newAtomContainer(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtomContainer molecule)
static org.openscience.cdk.interfaces.IAtomContainerSet	newAtomContainerSet(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IBond	newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IBond	newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtom a1, org.openscience.cdk.interfaces.IAtom a2)
static org.openscience.cdk.interfaces.IBond	newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtom a1, org.openscience.cdk.interfaces.IAtom a2, org.openscience.cdk.interfaces.IBond.Order order)
static org.openscience.cdk.interfaces.IBond	newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtom a1, org.openscience.cdk.interfaces.IAtom a2, org.openscience.cdk.interfaces.IBond.Order order, org.openscience.cdk.interfaces.IBond.Stereo stereo)
static org.openscience.cdk.interfaces.IChemFile	newChemFile(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IChemModel	newChemModel(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IChemSequence	newChemSequence(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IElement	newElement(org.openscience.cdk.interfaces.IChemObjectBuilder builder, String element)
static org.openscience.cdk.interfaces.ILonePair	newLonePair(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtom atom)
static org.openscience.cdk.interfaces.IAtomContainer	newMolecule(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IAtomContainerSet	newMoleculeSet(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.IPseudoAtom	newPseudoAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder, String element)
static org.openscience.cdk.interfaces.IRing	newRing(org.openscience.cdk.interfaces.IChemObjectBuilder builder, int i)
static org.openscience.cdk.interfaces.IRingSet	newRingSet(org.openscience.cdk.interfaces.IChemObjectBuilder builder)
static org.openscience.cdk.interfaces.ISingleElectron	newSingleElectron(org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.interfaces.IAtom atom)
static org.openscience.cdk.interfaces.IAtomContainer	readCMLMolecule(InputStream in)
static org.openscience.cdk.interfaces.IAtomContainer	readCMLMolecule(String cml)
static org.openscience.cdk.interfaces.IAtomContainer	readMolfile(Reader reader)
static org.openscience.cdk.interfaces.IAtomContainer	readMolfile(String molfile)
static org.openscience.cdk.interfaces.IAtomContainer	readPDBfile(String molfile)
static boolean	repairBondOrder4(org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static Logger logger

_FPLength

public static final int _FPLength

See Also:

Constant Field Values

adder

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

fingerprinter

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

substanceType

public static final 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 String delim

bracketLeft

protected static String bracketLeft

bracketRight

protected static String bracketRight

Constructor Detail

MoleculeTools

public MoleculeTools()

Method Detail

getMolecule

public static org.openscience.cdk.interfaces.IAtomContainer getMolecule(String smiles)
                                                                 throws org.openscience.cdk.exception.InvalidSmilesException

Throws:

org.openscience.cdk.exception.InvalidSmilesException

getFingerPrint

public static BitSet getFingerPrint(String smiles,
                                    int fpLength)
                             throws Exception

Throws:

Exception

getFingerPrint

public static BitSet getFingerPrint(String smiles)
                             throws Exception

Throws:

Exception

bitset2Long

public static long bitset2Long(BitSet bs)

bitset2bigint16

public static void bitset2bigint16(BitSet bs,
                                   int size,
                                   BigInteger[] h16)

analyzeSubstance

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

Throws:

IOException

getSubstanceType

protected static int getSubstanceType(String formula)

hasBondOrderUnsetAromatic

protected static boolean hasBondOrderUnsetAromatic(org.openscience.cdk.interfaces.IAtomContainer mol)

repairBondOrder4

public static boolean repairBondOrder4(org.openscience.cdk.interfaces.IAtomContainer mol)
                                throws Exception

Throws:

Exception

readMolfile

public static org.openscience.cdk.interfaces.IAtomContainer readMolfile(Reader reader)
                                                                 throws Exception

Throws:

Exception

readMolfile

public static org.openscience.cdk.interfaces.IAtomContainer readMolfile(String molfile)
                                                                 throws Exception

Throws:

Exception

readPDBfile

public static org.openscience.cdk.interfaces.IAtomContainer readPDBfile(String molfile)
                                                                 throws Exception

Throws:

Exception

readCMLMolecule

public static org.openscience.cdk.interfaces.IAtomContainer readCMLMolecule(String cml)
                                                                     throws Exception

Throws:

Exception

readCMLMolecule

public static org.openscience.cdk.interfaces.IAtomContainer readCMLMolecule(InputStream in)
                                                                     throws Exception

Throws:

Exception

newAtom

public static org.openscience.cdk.interfaces.IAtom newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           org.openscience.cdk.interfaces.IElement element)

newAtom

public static org.openscience.cdk.interfaces.IAtom newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           org.openscience.cdk.interfaces.IAtom atom)

newAtom

public static org.openscience.cdk.interfaces.IAtom newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           String atom)

newAtom

public static org.openscience.cdk.interfaces.IAtom newAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newPseudoAtom

public static org.openscience.cdk.interfaces.IPseudoAtom newPseudoAtom(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                       String element)

newLonePair

public static org.openscience.cdk.interfaces.ILonePair newLonePair(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                   org.openscience.cdk.interfaces.IAtom atom)

newBond

public static org.openscience.cdk.interfaces.IBond newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           org.openscience.cdk.interfaces.IAtom a1,
                                                           org.openscience.cdk.interfaces.IAtom a2,
                                                           org.openscience.cdk.interfaces.IBond.Order order,
                                                           org.openscience.cdk.interfaces.IBond.Stereo stereo)

newBond

public static org.openscience.cdk.interfaces.IBond newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           org.openscience.cdk.interfaces.IAtom a1,
                                                           org.openscience.cdk.interfaces.IAtom a2,
                                                           org.openscience.cdk.interfaces.IBond.Order order)

newBond

public static org.openscience.cdk.interfaces.IBond newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           org.openscience.cdk.interfaces.IAtom a1,
                                                           org.openscience.cdk.interfaces.IAtom a2)

newBond

public static org.openscience.cdk.interfaces.IBond newBond(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer newAtomContainer(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newMolecule

public static org.openscience.cdk.interfaces.IAtomContainer newMolecule(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newAtomContainer

public static org.openscience.cdk.interfaces.IAtomContainer newAtomContainer(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                             org.openscience.cdk.interfaces.IAtomContainer molecule)

newSingleElectron

public static org.openscience.cdk.interfaces.ISingleElectron newSingleElectron(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                               org.openscience.cdk.interfaces.IAtom atom)

newMoleculeSet

public static org.openscience.cdk.interfaces.IAtomContainerSet newMoleculeSet(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newAtomContainerSet

public static org.openscience.cdk.interfaces.IAtomContainerSet newAtomContainerSet(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newChemModel

public static org.openscience.cdk.interfaces.IChemModel newChemModel(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newChemSequence

public static org.openscience.cdk.interfaces.IChemSequence newChemSequence(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newChemFile

public static org.openscience.cdk.interfaces.IChemFile newChemFile(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newRingSet

public static org.openscience.cdk.interfaces.IRingSet newRingSet(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

newRing

public static org.openscience.cdk.interfaces.IRing newRing(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                           int i)

newElement

public static org.openscience.cdk.interfaces.IElement newElement(org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                                                                 String element)

copyChangeBuilders

public static org.openscience.cdk.interfaces.IAtomContainer copyChangeBuilders(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                               org.openscience.cdk.interfaces.IChemObjectBuilder newBuilder)

Just copy atoms and bonds, discard all the flags, they will be recalculated later

clearProperties

public static void clearProperties(org.openscience.cdk.interfaces.IChemObject chemObject)

convertImplicitToExplicitHydrogens

public static void convertImplicitToExplicitHydrogens(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Adds explicit hydrogens (without coordinates) to the IAtomContainer, equaling the number of set implicit hydrogens. Tetrahedrals with an implicit H now are set correctly.

Parameters:

atomContainer - the atom container to consider

convertExplicitHAtomsToImplicit

public static void convertExplicitHAtomsToImplicit(org.openscience.cdk.interfaces.IAtomContainer mol)
                                            throws Exception

Throws:

Exception

add1ImplicitHAtom

public static void add1ImplicitHAtom(org.openscience.cdk.interfaces.IAtom atom)