JOEMol (JOELib API Documentation)

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joelib.molecule
Class JOEMol

java.lang.Object
  joelib.molecule.JOEMol

All Implemented Interfaces:: Cloneable, Serializable

public class JOEMol
extends Object
implements Cloneable, Serializable

Molecule representation.

There are different possibilities to build a molecule.

Using SMILES notation to build a molecule.

 JOEMol mol=new JOEMol();
 String smiles="c1cc(OH)cc1";
 if (!JOESmilesParser.smiToMol(mol, smiles, setTitle.toString()))
 {
   System.err.println("SMILES entry \"" + smiles + "\" could not be loaded.");
 }
 System.out.println(mol.toString());

Using plain atoms and bonds to build a molecule.

 JOEMol mol = new JOEMol();
 // start molecule modification
 mol.beginModify();
 mol.reserveAtoms(2);

 // build carbon atom
 JOEAtom C = new JOEAtom();
 atomC.setAtomicNum(6);

 // build molecule
 for (int i=0; i<2; i++) {
   mol.addAtom(atom);
 }

 // add double bond
 mol.addBond(1,2, 2);

 //end molecule modification and store all
 //coordinates in coordinate array
 mol.endModify();

For speed optimization of loading descriptor molecule files have a look at the ResultFactory.

Author:

Jörg Kurt Wegner (wegnerj at informatik.uni-tuebingen.de) at the Department of Computer Architecture

CVS Version:

Revision: 1.80Date: 2004/07/25 20:43:23source code (CVS head)

License:

Licensed under the terms of the GNU General Public License (GPL).

References:

Field Summary
`static int`	`JOE_AROM_CORRECTED_MOL` Molecule flag: aromaticity corrected molecule.
`static int`	`JOE_AROMATIC_MOL` Molecule flag: aromaticity calculated.
`static int`	`JOE_ATOMTYPES_MOL` Molecule flag: atom types perceived.
`static int`	`JOE_CHAINS_MOL` Molecule flag: chain molecule.
`static int`	`JOE_CHIRALITY_MOL` Molecule flag: atom chirality flags perceived.
`static int`	`JOE_CLOSURE_MOL` Molecule flag: closure bonds perceived.
`static int`	`JOE_CURRENT_CONFORMER` Molecule flag: current conformer.
`static int`	`JOE_H_ADDED_MOL` Molecule flag: H atoms added molecule.
`static int`	`JOE_HYBRID_MOL` Molecule flag: atom hybridisation perceived.
`static int`	`JOE_IMPVAL_MOL` Molecule flag: implicit valences perceived.
`static int`	`JOE_KEKULE_MOL` Molecule flag: kekulization perceived.
`static int`	`JOE_PCHARGE_MOL` Molecule flag: partitial charges perceived.
`static int`	`JOE_PH_CORRECTED_MOL` Molecule flag: PH value perceived.
`static int`	`JOE_RINGFLAGS_MOL` Molecule flag: rings perceived.
`static int`	`JOE_SSSR_MOL` Molecule flag: SSSR calculated.

Constructor Summary
`JOEMol()` Constructor for the `JOEMol`.
`JOEMol(IOType itype, IOType otype)` Constructor for the `JOEMol`.
`JOEMol(JOEMol source)` Clones the molecule without data elements.
`JOEMol(JOEMol source, boolean cloneDesc)` Constructor for the `JOEMol`.
`JOEMol(JOEMol source, boolean cloneDesc, String[] descriptors)` Constructor for the `JOEMol`.

Method Summary
`boolean`	`addAtom(JOEAtom atom)` Adds (cloned) atom to the `JOEMol`.
`boolean`	`addBond(int first, int second, int order)` Adds a bond to the `JOEMol`.
`boolean`	`addBond(int first, int second, int order, int flags)` Adds a bond to the `JOEMol`.
`boolean`	`addBond(int first, int second, int order, int stereo, int insertpos)` Adds a bond to the `JOEMol`.
`boolean`	`addBond(JOEBond bond)` Adds (cloned) bond to the `JOEMol`.
`void`	`addConformer(double[] f)` Adds conformer coordinates to this molecule.
`void`	`addData(JOEGenericData d)` Adds a `JOEGenericData` object to this molecule but don't overwrite existing data elements with the same name, if they exists already.
`void`	`addData(JOEGenericData d, boolean overwrite)` Adds a `JOEGenericData` object to this molecule.
`boolean`	`addHydrogens()` Adds hydrogens atoms to this molecule.
`boolean`	`addHydrogens(boolean polaronly)` Adds hydrogens atoms to this molecule.
`boolean`	`addHydrogens(boolean polaronly, boolean correctForPH)` Adds hydrogens atoms to this molecule.
`boolean`	`addHydrogens(boolean polaronly, boolean correctForPH, boolean useCoordV)` Adds hydrogens atoms to this molecule.
`boolean`	`addHydrogens(JOEAtom atom)` Adds hydrogens atoms to the given atom.
`boolean`	`addPolarHydrogens()` Add polar hydrogens to molecule.
`boolean`	`addResidue(JOEResidue residue)` Adds residue information to this molecule.
`void`	`align(JOEAtom a1, JOEAtom a2, XYZVector p1, XYZVector p2)` Aligns atom a1 on p1 and atom a2 along p1->p2 vector.
`AtomIterator`	`atomIterator()` Gets an iterator over all atoms in this molecule.
`boolean`	`automaticFormalCharge()` Gets the flag if the automatic calculation of the formal charge of the atoms is allowed.
`boolean`	`automaticPartialCharge()` Gets the flag if the automatic calculation of the partial charge of the atoms is allowed.
`void`	`beginModify()` Begins modification of atoms and increase modification counter.
`BondIterator`	`bondIterator()` Gets an iterator over all bonds.
`void`	`center()` Centers molecule.
`XYZVector`	`center(int nconf)` Centers conformer.
`boolean`	`clear()` Clears molecule.
`Object`	`clone()` Clones molecule without additional data (e.g.
`Object`	`clone(boolean cloneDesc)` Clones this molecule.
`Object`	`clone(boolean cloneDesc, String[] descriptors)` Clones this molecule.
`ConformerIterator`	`conformerIterator()` Gets an iterator over all conformers.
`int`	`conformerNum()` Returns the number of conformers.
`void`	`connectTheDots()` Use inter-atomic distances to identify bonds.
`void`	`contiguousFragments(Vector cfl)` Each Vector contains the atom numbers of a contiguous fragment.
`void`	`copyConformer(double[] src, int idx)` Copies given conformer to this molecule.
`void`	`copyConformer(float[] src, int idx)` Copies given conformer to this molecule.
`boolean`	`correctForPH()` Corrects pH value of the molecule.
`JOEAtom`	`createAtom()` Creates only a new atom.
`JOEBond`	`createBond()` Creates only a new bond.
`int`	`dataSize()` Returns the number of data elements in this molecule.
`void`	`decrementMod()` Decrease modification counter.
`boolean`	`deleteAtom(JOEAtom atom)` Delete atom from molecule.
`boolean`	`deleteBond(JOEBond bond)` Delete the given `JOEBond` from this molecule.
`void`	`deleteConformer(int idx)` Delete conformer from molecule.
`void`	`deleteData(JOEDataType dt)` Deletes all data elements os the given `JOEDataType` .
`void`	`deleteData(JOEGenericData gd)` Delete all data elements which are `equal` to the given `JOEGenericData` element.
`boolean`	`deleteData(String s)` Description of the Method
`void`	`deleteData(Vector vg)` Description of the Method
`boolean`	`deleteHydrogen(JOEAtom atom)` Deletes hydrogen atom.
`boolean`	`deleteHydrogens()` Delete all hydrogen atoms from molecule.
`boolean`	`deleteHydrogens(JOEAtom atom)` Delete all hydrogen atoms from given atom.
`boolean`	`deleteNonPolarHydrogens()` Delete all non polar hydrogens from molecule.
`boolean`	`deleteResidue(JOEResidue residue)` Description of the Method
`void`	`destroyAtom(JOEAtom atom)` Destroys atom.
`void`	`destroyBond(JOEBond bond)` Destroys all bond.
`boolean`	`empty()` Returns `true` if this molecule contains no atoms.
`void`	`endModify()` Ends modification of atoms and decrease modification counter.
`void`	`endModify(boolean nukePerceivedData)` Ends modification of atoms and decrease modification counter.
`boolean`	`equals(JOEMol type)` Checks if two molecules are equal, ignoring descriptor values.
`boolean`	`equals(Object obj)` Checks if two molecules are equal, ignoring descriptor values.
`boolean`	`existsBond(int bgn, int end)` Returns `true` if this bond exists.
`void`	`finalize()` Destructor for this molecule.
`void`	`findChildren(Vector children, int first, int second)` Locates all atoms for which there exists a path to `second` without going through `first` children does not include `second` .
`void`	`findChildren(Vector children, JOEAtom bgn, JOEAtom end)` locates all atoms for which there exists a path to 'second' without going through 'first' children does not include 'second'
`void`	`findChiralCenters()` Description of the Method
`void`	`findLargestFragment(JOEBitVec lf)` each vector contains the atom numbers of a contig fragment the vectors are sorted by size from largest to smallest
`void`	`findRingAtomsAndBonds()` Description of the Method
`void`	`findSSSR()` Finds the Smallest Set of Smallest Rings (SSSR).
`GenericDataIterator`	`genericDataIterator()` Gets an iterator over the generic data elements of this molecule.
`JOEAtom`	`getAtom(int idx)` Gets an atom of the `JOEMol` object Atom index must be between `1` to `numAtoms()` .
`JOEBond`	`getBond(int idx)` Gets a bond of the `JOEMol` object.
`JOEBond`	`getBond(int bgn, int end)` Gets the bond attribute of the `JOEMol` object Atom index must be between `1` to `numAtoms()` .
`JOEBond`	`getBond(JOEAtom bgn, JOEAtom end)` Gets the bond attribute of the `JOEMol` object
`double[]`	`getConformer(int i)` Gets the conformer attribute of the JOEMol object
`Vector`	`getConformers()` Returns a `Vector` of all conformer coordinates (`double[]` values).
`double[]`	`getCoordinates()` Gets the coordinate array of this molecule.
`JOEGenericData`	`getData(JOEDataType dt)` Returns the first data entry of the given data type.
`JOEGenericData`	`getData(String s)` Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
`JOEGenericData`	`getData(String s, boolean parse)` Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
`double`	`getEnergy()` Gets the energy attribute of the `JOEMol` object
`double`	`getExactMass()` Gets mass given by isotopes (or most abundant isotope as necessary).
`JOEAtom`	`getFirstAtom()` Gets the firstAtom attribute of the `JOEMol` object
`int`	`getFlags()` Gets the flags attribute of the `JOEMol` object
`boolean`	`getGTDVector(int[] gtd)` Gets the gTDVector attribute of the `JOEMol` object
`IOType`	`getInputType()` Gets the inputType attribute of the `JOEMol` object
`int`	`getMod()` Gets the mod attribute of the `JOEMol` object
`double`	`getMolWt()` Gets standard molar mass given by IUPAC atomic masses.
`IOType`	`getOutputType()` Gets the outputType attribute of the `JOEMol` object
`String`	`getPartialChargeVendor()`
`JOEResidue`	`getResidue(int idx)` Gets the residue attribute of the JOEMol object
`RingIterator`	`getRingIterator()` Gets iterator for the Smallest Set of Smallest Rings (SSSR).
`Vector`	`getSSSR()` Gets the Smallest Set of Smallest Rings (SSSR).
`String`	`getTitle()` Gets the title attribute of the `JOEMol` object.
`double`	`getTorsion(int a, int b, int c, int d)` Gets the torsion attribute of the `JOEMol` object
`double`	`getTorsion(JOEAtom a, JOEAtom b, JOEAtom c, JOEAtom d)` Gets the torsion attribute of the `JOEMol` object
`boolean`	`has2D()` Description of the Method
`boolean`	`has3D()` Description of the Method
`boolean`	`hasAromaticCorrected()` Description of the Method
`boolean`	`hasAromaticPerceived()` Description of the Method
`boolean`	`hasAtomTypesPerceived()` Description of the Method
`boolean`	`hasChainsPerceived()` Description of the Method
`boolean`	`hasChiralityPerceived()` Description of the Method
`boolean`	`hasClosureBondsPerceived()` Description of the Method
`boolean`	`hasData(JOEDataType dt)` Returns `true` if one ore more entries of the given `JOEDataType` exists.
`boolean`	`hasData(String s)` Description of the Method
`int`	`hashCode()` Calculates the hashcode of a molecule using the methods `AbstractDatabase.getHashcode` and `AbstractDatabase.getSMILESHashcode`.
`boolean`	`hasHybridizationPerceived()` Description of the Method
`boolean`	`hasHydrogensAdded()` Description of the Method
`boolean`	`hasImplicitValencePerceived()` Description of the Method
`boolean`	`hasKekulePerceived()` Description of the Method
`boolean`	`hasNonZeroCoords()` Description of the Method
`boolean`	`hasPartialChargesPerceived()` Description of the Method
`boolean`	`hasRingAtomsAndBondsPerceived()` Description of the Method
`boolean`	`hasSSSRPerceived()` Description of the Method
`void`	`incrementMod()` Increase modification counter.
`boolean`	`insertAtom(JOEAtom atom)` Description of the Method
`boolean`	`isChiral()` Gets the chiral attribute of the JOEMol object
`boolean`	`isCorrectedForPH()` Gets the correctedForPH attribute of the JOEMol object
`boolean`	`kekulize()` Kekulizes the molecule.
`NativeValueIterator`	`nativeValueIterator()` Gets an iterator over native descriptor values (`int` or `double`) of this molecule.
`JOEAtom`	`newAtom()` Creates a new atom and adds it to molecule.
`JOEResidue`	`newResidue()` Returns and adds new residue informations for this molecule.
`int`	`numAtoms()` Returns the number of atoms.
`int`	`numBonds()` Returns the number of bonds.
`int`	`numConformers()` Returns the number of conformers of this molecule.
`int`	`numHvyAtoms()` Returns the number of heavy atoms.
`int`	`numResidues()` Returns the number of residues.
`int`	`numRotors()` Returns the number of rotatable bonds.
`boolean`	`perceiveKekuleBonds()` Description of the Method
`int`	`reHash()`
`void`	`renumberAtoms(Vector v)`
`void`	`reserveAtoms(int natoms)` Reserves a initial capacity of atoms.
`ResidueIterator`	`residueIterator()` Description of the Method
`void`	`rotate(double[] m)`
`void`	`rotate(double[][] u)`
`void`	`rotate(double[] m, int nconf)`
`JOEMol`	`set(JOEMol source)` Clones molecule without additional data (e.g.
`JOEMol`	`set(JOEMol source, boolean cloneDesc, String[] descriptors)` Clones molecule.
`JOEMol`	`set(JOEMol source, boolean cloneDesc, String[] descriptors, boolean addDescIfNotExist)` Clones molecule.
`JOEMol`	`setAdd(JOEMol source)` Sets the add attribute of the `JOEMol` object
`void`	`setAromaticCorrected()` Sets the aromaticCorrected attribute of the `JOEMol` object
`void`	`setAromaticPerceived()` Sets the aromaticPerceived attribute of the `JOEMol` object
`void`	`setAtomTypesPerceived()` Sets the atomTypesPerceived attribute of the `JOEMol` object
`void`	`setAutomaticFormalCharge(boolean val)` Sets the flag if the automatic calculation of the formal charge of the atoms is allowed.
`void`	`setAutomaticPartialCharge(boolean val)` Sets the automaticPartialCharge attribute of the `JOEMol` object
`void`	`setChainsPerceived()` Sets the chainsPerceived attribute of the `JOEMol` object
`void`	`setChiralityPerceived()` Sets the chiralityPerceived attribute of the `JOEMol` object
`void`	`setClosureBondsPerceived()` Sets the closureBondsPerceived attribute of the `JOEMol` object
`void`	`setConformer(int i)` Sets the conformer attribute of the JOEMol object
`void`	`setConformers(Vector v)` Sets the conformers attribute of the JOEMol object
`void`	`setCorrectedForPH()` Sets the correctedForPH attribute of the `JOEMol` object
`void`	`setEnergy(double energy)` Sets the energy attribute of the `JOEMol` object
`void`	`setHybridizationPerceived()` Sets the hybridizationPerceived attribute of the `JOEMol` object
`void`	`setHydrogensAdded()` Sets the hydrogensAdded attribute of the `JOEMol` object
`void`	`setImplicitValencePerceived()` Sets the implicitValencePerceived attribute of the `JOEMol` object
`void`	`setInputType(IOType type)` Sets the inputType attribute of the `JOEMol` object
`void`	`setKekulePerceived()` Sets the kekulePerceived attribute of the `JOEMol` object
`void`	`setOutputType(IOType type)` Sets the outputType attribute of the `JOEMol` object
`void`	`setPartialChargesPerceived()` Sets the partialChargesPerceived attribute of the `JOEMol` object
`void`	`setPartialChargeVendor(String vendor)`
`void`	`setRingAtomsAndBondsPerceived()` Sets the ringAtomsAndBondsPerceived attribute of the `JOEMol` object
`void`	`setSSSRPerceived()` Sets the sSSRPerceived attribute of the `JOEMol` object
`void`	`setTitle(String title)` Sets the title attribute of the `JOEMol` object
`void`	`setTorsion(JOEAtom a, JOEAtom b, JOEAtom c, JOEAtom d, double ang)` Sets the torsion attribute of the `JOEMol` object
`void`	`sortBonds()` Description of the Method
`boolean`	`stripSalts()` Deletes all atoms except for the largest contiguous fragment.
`void`	`toInertialFrame()` Description of the Method
`void`	`toInertialFrame(int conf, double[] rmat)` Description of the Method
`String`	`toString()` Description of the Method
`String`	`toString(boolean writeDescriptors)` Description of the Method
`String`	`toString(IOType type)` Description of the Method
`String`	`toString(IOType type, boolean writeDescriptors)` Description of the Method
`void`	`translate(XYZVector v)` Description of the Method
`void`	`translate(XYZVector v, int nconf)` Description of the Method
`void`	`unsetAromaticPerceived()` Description of the Method
`void`	`unsetImplicitValencePerceived()` Description of the Method
`void`	`unsetPartialChargesPerceived()` Description of the Method

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

JOE_SSSR_MOL

public static final int JOE_SSSR_MOL

Molecule flag: SSSR calculated.

See Also:: Constant Field Values

JOE_RINGFLAGS_MOL

public static final int JOE_RINGFLAGS_MOL

Molecule flag: rings perceived.

See Also:: Constant Field Values

JOE_AROMATIC_MOL

public static final int JOE_AROMATIC_MOL

Molecule flag: aromaticity calculated.

See Also:: Constant Field Values

JOE_ATOMTYPES_MOL

public static final int JOE_ATOMTYPES_MOL

Molecule flag: atom types perceived.

See Also:: Constant Field Values

JOE_CHIRALITY_MOL

public static final int JOE_CHIRALITY_MOL

Molecule flag: atom chirality flags perceived.

See Also:: Constant Field Values

JOE_PCHARGE_MOL

public static final int JOE_PCHARGE_MOL

Molecule flag: partitial charges perceived.

See Also:: Constant Field Values

JOE_HYBRID_MOL

public static final int JOE_HYBRID_MOL

Molecule flag: atom hybridisation perceived.

See Also:: Constant Field Values

JOE_IMPVAL_MOL

public static final int JOE_IMPVAL_MOL

Molecule flag: implicit valences perceived.

See Also:: Constant Field Values

JOE_KEKULE_MOL

public static final int JOE_KEKULE_MOL

Molecule flag: kekulization perceived.

See Also:: Constant Field Values

JOE_CLOSURE_MOL

public static final int JOE_CLOSURE_MOL

Molecule flag: closure bonds perceived.

See Also:: Constant Field Values

JOE_H_ADDED_MOL

public static final int JOE_H_ADDED_MOL

Molecule flag: H atoms added molecule.

See Also:: Constant Field Values

JOE_PH_CORRECTED_MOL

public static final int JOE_PH_CORRECTED_MOL

Molecule flag: PH value perceived.

See Also:: Constant Field Values

JOE_AROM_CORRECTED_MOL

public static final int JOE_AROM_CORRECTED_MOL

Molecule flag: aromaticity corrected molecule.

See Also:: Constant Field Values

JOE_CHAINS_MOL

public static final int JOE_CHAINS_MOL

Molecule flag: chain molecule.

See Also:: Constant Field Values

JOE_CURRENT_CONFORMER

public static final int JOE_CURRENT_CONFORMER

Molecule flag: current conformer.

See Also:: Constant Field Values

Constructor Detail

JOEMol

public JOEMol()

Constructor for the JOEMol. The 'Structured Data File' (SDF) molecule data format is used for default.

References:

mdlMolFormat

JOEMol

public JOEMol(IOType itype,
              IOType otype)

Constructor for the JOEMol.
Parameters:: itype - input type for this molecule; otype - output type for this molecule
See Also:: JOEMol(), JOEMol(JOEMol), JOEMol(JOEMol, boolean), JOEMol(JOEMol, boolean, String[])

JOEMol

public JOEMol(JOEMol source,
              boolean cloneDesc,
              String[] descriptors)

Constructor for the JOEMol.
Parameters:: source - The source molecule; cloneDesc - clones the PairData descriptors if true; descriptors - the descriptors to clone. If null all descriptors are cloned
See Also:: JOEMol(), JOEMol(IOType, IOType), JOEMol(JOEMol), JOEMol(JOEMol, boolean)

JOEMol

public JOEMol(JOEMol source,
              boolean cloneDesc)

Constructor for the JOEMol.
Parameters:: source - The source molecule; cloneDesc - clones the PairData descriptors if true
See Also:: JOEMol(), JOEMol(IOType, IOType), JOEMol(JOEMol), JOEMol(JOEMol, boolean), JOEMol(JOEMol, boolean, String[])

JOEMol

public JOEMol(JOEMol source)

Clones the molecule without data elements.
Parameters:: source - The source molecule
See Also:: JOEMol(), JOEMol(IOType, IOType), JOEMol(JOEMol, boolean), JOEMol(JOEMol, boolean, String[])

Method Detail

setAdd

public JOEMol setAdd(JOEMol source)

Sets the add attribute of the JOEMol object

Parameters:: source - The new add value
Returns:: Description of the Return Value

setAromaticCorrected

public void setAromaticCorrected()

Sets the aromaticCorrected attribute of the JOEMol object

setAromaticPerceived

public void setAromaticPerceived()

Sets the aromaticPerceived attribute of the JOEMol object

getAtom

public JOEAtom getAtom(int idx)

Gets an atom of the JOEMol object Atom index must be between 1 to numAtoms() .

Parameters:: idx - Description of the Parameter
Returns:: The atom value

setAtomTypesPerceived

public void setAtomTypesPerceived()

Sets the atomTypesPerceived attribute of the JOEMol object

setAutomaticFormalCharge

public void setAutomaticFormalCharge(boolean val)

Sets the flag if the automatic calculation of the formal charge of the atoms is allowed. This is for example used in the PH value correction method.

Parameters:: val - true if the calculation of the formal charge is allowed.

setAutomaticPartialCharge

public void setAutomaticPartialCharge(boolean val)

Sets the automaticPartialCharge attribute of the JOEMol object

Parameters:: val - The new automaticPartialCharge value

getBond

public JOEBond getBond(int idx)

Gets a bond of the JOEMol object. Bond index must be between 0 to (numBonds()-1) .

Parameters:: idx - Description of the Parameter
Returns:: The bond value

getBond

public JOEBond getBond(int bgn,
                       int end)

Gets the bond attribute of the JOEMol object Atom index must be between 1 to numAtoms() .

Parameters:: bgn - atom index of the start atom; end - atom index of the end atom
Returns:: The bond value

getBond

public JOEBond getBond(JOEAtom bgn,
                       JOEAtom end)

Gets the bond attribute of the JOEMol object

Parameters:: bgn - Description of the Parameter; end - Description of the Parameter
Returns:: The bond value

setChainsPerceived

public void setChainsPerceived()

Sets the chainsPerceived attribute of the JOEMol object

isChiral

public boolean isChiral()

Gets the chiral attribute of the JOEMol object

Returns:: The chiral value

setChiralityPerceived

public void setChiralityPerceived()

Sets the chiralityPerceived attribute of the JOEMol object

setClosureBondsPerceived

public void setClosureBondsPerceived()

Sets the closureBondsPerceived attribute of the JOEMol object

setConformer

public void setConformer(int i)

Sets the conformer attribute of the JOEMol object

Parameters:: i - The new conformer value

getConformer

public double[] getConformer(int i)

Gets the conformer attribute of the JOEMol object

Parameters:: i - Description of the Parameter
Returns:: The conformer value

setConformers

public void setConformers(Vector v)

Sets the conformers attribute of the JOEMol object

Parameters:: v - The new conformers value (v is of type double[])

getConformers

public Vector getConformers()

Returns a Vector of all conformer coordinates (double[] values).

Returns:: The conformers coordinates

getCoordinates

public double[] getCoordinates()

Gets the coordinate array of this molecule.

Returns:: The coordinates array

setCorrectedForPH

public void setCorrectedForPH()

Sets the correctedForPH attribute of the JOEMol object

isCorrectedForPH

public boolean isCorrectedForPH()

Gets the correctedForPH attribute of the JOEMol object

Returns:: The correctedForPH value

getData

public JOEGenericData getData(JOEDataType dt)

Returns the first data entry of the given data type. If this data type don't exists in this molecule, null is returned.

There exist a lot of default data types which where defined in JOEDataType. These data types are used for caching ring searches and storing special data types like comments or virtual bonds. Furthermore there exist the most important data type JOEPairData for storing descriptor values. Read the JOEDataType description for details.

Parameters:: dt - data type
Returns:: null if no element of this data type exists
See Also:: getData(String), getData(String, boolean), genericDataIterator(), addData(JOEGenericData), addData(JOEGenericData, boolean)

getData

public JOEGenericData getData(String s)

Returns the data entry with the given name, if multiple data entries exists only the first one is taken. If the data element is a JOEPairData element with a unparsed String value, the descriptor value will be automatically parsed from a String value to the representing result (DescResult) class. If no data element with this name exists in this molecule, null is returned.

Missing descriptor values can be calculated by using DescriptorHelper.descFromMol(JOEMol, String).
Example:

 DescResult result=null;
 try
 {
         result=DescriptorHelper.instance().descFromMol(mol, descriptorName);
 }
 catch (DescriptorException ex)
 {
         // descriptor can not be calculated
 }

Notice the difference between JOEGenericData and DescResult. DescResult values can be added to molecules by using JOEPairData

 JOEPairData dp = new JOEPairData();
 dp.setAttribute(descriptorName);
 dp.setValue(result);
 mol.addData(dp);

Parameters:: s - The data element (descriptor) name
Returns:: null if no element with this name exists
See Also:: getData(JOEDataType), getData(String, boolean), genericDataIterator(), addData(JOEGenericData), addData(JOEGenericData, boolean), JOEDataType, JOEPairData, DescResult, GenericDataHolder.getData(String, boolean), DescriptorHelper.descFromMol(JOEMol, String), DescriptorHelper.descFromMol(JOEMol, String, DescResult), DescriptorHelper.descFromMol(JOEMol, String, DescResult, boolean)

getData

public JOEGenericData getData(String s,
                              boolean parse)

Returns the data entry with the given name, if multiple data entries exists only the first one is taken. If the data element is a JOEPairData the parse flag can be used to parse this data elements. If no data element with this name exists in this molecule, null is returned.

Missing descriptor values can be calculated by using DescriptorHelper.descFromMol(JOEMol, String).
Example:

 DescResult result=null;
 try
 {
         result=DescriptorHelper.instance().descFromMol(mol, descriptorName);
 }
 catch (DescriptorException ex)
 {
         // descriptor can not be calculated
 }

Notice the difference between JOEGenericData and DescResult. DescResult values can be added to molecules by using JOEPairData

 JOEPairData dp = new JOEPairData();
 dp.setAttribute(descriptorName);
 dp.setValue(result);
 mol.addData(dp);

Parameters:: s - The data element (descriptor) name; parse - Parse data element
Returns:: null if no element with this name exists
See Also:: getData(JOEDataType), getData(String), genericDataIterator(), addData(JOEGenericData), addData(JOEGenericData, boolean), JOEDataType, JOEPairData, DescResult, GenericDataHolder.getData(String, boolean), DescriptorHelper.descFromMol(JOEMol, String), DescriptorHelper.descFromMol(JOEMol, String, DescResult), DescriptorHelper.descFromMol(JOEMol, String, DescResult, boolean)

setEnergy

public void setEnergy(double energy)

Sets the energy attribute of the JOEMol object

Parameters:: energy - The new energy value

getEnergy

public double getEnergy()

Gets the energy attribute of the JOEMol object

Returns:: The energy value

getExactMass

public double getExactMass()

Gets mass given by isotopes (or most abundant isotope as necessary).

Returns:: The molWt value

getFirstAtom

public JOEAtom getFirstAtom()

Gets the firstAtom attribute of the JOEMol object

Returns:: The firstAtom value

getFlags

public int getFlags()

Gets the flags attribute of the JOEMol object

Returns:: The flags value
See Also:: JOE_SSSR_MOL, JOE_RINGFLAGS_MOL, JOE_AROMATIC_MOL, JOE_ATOMTYPES_MOL, JOE_CHIRALITY_MOL, JOE_PCHARGE_MOL, JOE_HYBRID_MOL, JOE_IMPVAL_MOL, JOE_KEKULE_MOL, JOE_CLOSURE_MOL, JOE_H_ADDED_MOL, JOE_PH_CORRECTED_MOL, JOE_AROM_CORRECTED_MOL, JOE_CHAINS_MOL, JOE_CURRENT_CONFORMER

getGTDVector

public boolean getGTDVector(int[] gtd)

Gets the gTDVector attribute of the JOEMol object

Parameters:: gtd - Description of the Parameter
Returns:: The gTDVector value

setHybridizationPerceived

public void setHybridizationPerceived()

Sets the hybridizationPerceived attribute of the JOEMol object

setHydrogensAdded

public void setHydrogensAdded()

Sets the hydrogensAdded attribute of the JOEMol object

setImplicitValencePerceived

public void setImplicitValencePerceived()

Sets the implicitValencePerceived attribute of the JOEMol object

setInputType

public void setInputType(IOType type)

Sets the inputType attribute of the JOEMol object

Parameters:: type - The new inputType value

setKekulePerceived

public void setKekulePerceived()

Sets the kekulePerceived attribute of the JOEMol object

getMod

public int getMod()

Gets the mod attribute of the JOEMol object

Returns:: The mod value

getTitle

public final String getTitle()

Gets the title attribute of the JOEMol object.

Returns:: The title value

getInputType

public IOType getInputType()

Gets the inputType attribute of the JOEMol object

Returns:: The inputType value

getMolWt

public double getMolWt()

Gets standard molar mass given by IUPAC atomic masses.

Returns:: The molWt value

setOutputType

public void setOutputType(IOType type)

Sets the outputType attribute of the JOEMol object

Parameters:: type - The new outputType value

getOutputType

public IOType getOutputType()

Gets the outputType attribute of the JOEMol object

Returns:: The outputType value

setPartialChargeVendor

public void setPartialChargeVendor(String vendor)

getPartialChargeVendor

public String getPartialChargeVendor()

setPartialChargesPerceived

public void setPartialChargesPerceived()

Sets the partialChargesPerceived attribute of the JOEMol object

getResidue

public JOEResidue getResidue(int idx)

Gets the residue attribute of the JOEMol object

Parameters:: idx - Description of the Parameter
Returns:: The residue value

setRingAtomsAndBondsPerceived

public void setRingAtomsAndBondsPerceived()

Sets the ringAtomsAndBondsPerceived attribute of the JOEMol object

getRingIterator

public RingIterator getRingIterator()

Gets iterator for the Smallest Set of Smallest Rings (SSSR).

 RingIterator rit = mol.getRingIterator();
 JOERing ring;
 while(rit.hasNext())
 {
   ring = rit.nextRing();

 }

Returns:

The ring iterator

References:

fig96

getSSSR

public Vector getSSSR()

Gets the Smallest Set of Smallest Rings (SSSR).

Returns:

Vector of JOERing

See Also:

getRingIterator(), findSSSR()

References:

fig96

setSSSRPerceived

public void setSSSRPerceived()

Sets the sSSRPerceived attribute of the JOEMol object

setTitle

public void setTitle(String title)

Sets the title attribute of the JOEMol object

Parameters:: title - The new title value

setTorsion

public void setTorsion(JOEAtom a,
                       JOEAtom b,
                       JOEAtom c,
                       JOEAtom d,
                       double ang)

Sets the torsion attribute of the JOEMol object

Parameters:: a - The new torsion value; b - The new torsion value; c - The new torsion value; d - The new torsion value; ang - The new torsion value

getTorsion

public double getTorsion(int a,
                         int b,
                         int c,
                         int d)

Gets the torsion attribute of the JOEMol object

Parameters:: a - Description of the Parameter; b - Description of the Parameter; c - Description of the Parameter; d - Description of the Parameter
Returns:: The torsion value

getTorsion

public double getTorsion(JOEAtom a,
                         JOEAtom b,
                         JOEAtom c,
                         JOEAtom d)

Gets the torsion attribute of the JOEMol object

Parameters:: a - Description of the Parameter; b - Description of the Parameter; c - Description of the Parameter; d - Description of the Parameter
Returns:: The torsion value

addAtom

public boolean addAtom(JOEAtom atom)

Adds (cloned) atom to the JOEMol. Also checks for any bonds that should be made to the new atom. Atoms starts with the index 1, which is a difference to bonds which starts with the bond index 0.

It's recommended calling the beginModify() method before the first atom will be added and calling the endModify() method after the last atom has been added. This causes, that the coordinates of the atoms will also be stored in a coordinate array in the molecule.

Parameters:: atom - The JOEAtom to add, which will be deep cloned.
Returns:: true if successfull
See Also:: addBond(int, int, int), addBond(int, int, int, int), addBond(int, int, int, int, int), addBond(JOEBond), beginModify(), endModify(), endModify(boolean)

addBond

public boolean addBond(int first,
                       int second,
                       int order)

Adds a bond to the JOEMol. Bonds starts with the index 0, which is a difference to atoms which starts with the atom index 1.

Parameters:: first - The start atom index (atoms begins with index 1); second - The end atom index (atoms begins with index 1); order - The bond order
Returns:: true if successfull
See Also:: addAtom(JOEAtom), addBond(int, int, int, int), addBond(int, int, int, int, int), addBond(JOEBond), connectTheDots()

addBond

public boolean addBond(int first,
                       int second,
                       int order,
                       int flags)

Adds a bond to the JOEMol. Bonds starts with the index 0, which is a difference to atoms which starts with the atom index 1.

Parameters:: first - The start atom index (atoms begins with index 1); second - The end atom index (atoms begins with index 1); order - The bond order; flags - The stereo flag
Returns:: true if successfull
See Also:: addBond(int, int, int), addBond(int, int, int, int, int), addBond(JOEBond), connectTheDots()

addBond

public boolean addBond(int first,
                       int second,
                       int order,
                       int stereo,
                       int insertpos)

Adds a bond to the JOEMol. Bonds starts with the index 0, which is a difference to atoms which starts with the atom index 1.

Parameters:: first - The start atom index (atoms begins with index 1); second - The end atom index (atoms begins with index 1); order - The bond order; stereo - The stereo flag; insertpos - The position at which the bond should be inserted
Returns:: true if successfull
See Also:: addAtom(JOEAtom), addBond(int, int, int), addBond(int, int, int, int), addBond(JOEBond), connectTheDots()

addBond

public boolean addBond(JOEBond bond)

Adds (cloned) bond to the JOEMol. Bonds starts with the index 0, which is a difference to atoms which starts with the atom index 1.

Parameters:: bond - The JOEBond to add, which will be deep cloned.
Returns:: Description of the Return Value
See Also:: addAtom(JOEAtom), addBond(int, int, int), addBond(int, int, int, int), addBond(int, int, int, int, int), connectTheDots()

addConformer

public void addConformer(double[] f)

Adds conformer coordinates to this molecule.

Parameters:: f - The conformer coordinates

addData

public void addData(JOEGenericData d)

Adds a JOEGenericData object to this molecule but don't overwrite existing data elements with the same name, if they exists already.

Missing descriptor values can be calculated by using DescriptorHelper.descFromMol(JOEMol, String).
Example:

 DescResult result=null;
 try
 {
         result=DescriptorHelper.instance().descFromMol(mol, descriptorName);
 }
 catch (DescriptorException ex)
 {
         // descriptor can not be calculated
 }

Notice the difference between JOEGenericData and DescResult. DescResult values can be added to molecules by using JOEPairData

 JOEPairData dp = new JOEPairData();
 dp.setAttribute(descriptorName);
 dp.setValue(result);
 mol.addData(dp);

Parameters:: d - The new data value
See Also:: addData(JOEGenericData, boolean), getData(JOEDataType), getData(String), getData(String, boolean), genericDataIterator(), JOEDataType, JOEPairData, DescriptorHelper.descFromMol(JOEMol, String), DescriptorHelper.descFromMol(JOEMol, String, DescResult), DescriptorHelper.descFromMol(JOEMol, String, DescResult, boolean)

addData

public void addData(JOEGenericData d,
                    boolean overwrite)

Adds a JOEGenericData object to this molecule.

Missing descriptor values can be calculated by using DescriptorHelper.descFromMol(JOEMol, String).
Example:

 DescResult result=null;
 try
 {
         result=DescriptorHelper.instance().descFromMol(mol, descriptorName);
 }
 catch (DescriptorException ex)
 {
         // descriptor can not be calculated
 }

Notice the difference between JOEGenericData and DescResult. DescResult values can be added to molecules by using JOEPairData

 JOEPairData dp = new JOEPairData();
 dp.setAttribute(descriptorName);
 dp.setValue(result);
 mol.addData(dp);

Parameters:: d - The new data value; overwrite - Overwrite already existing data element, if true
See Also:: addData(JOEGenericData), getData(JOEDataType), getData(String), getData(String, boolean), genericDataIterator(), JOEDataType, JOEPairData, DescriptorHelper.descFromMol(JOEMol, String), DescriptorHelper.descFromMol(JOEMol, String, DescResult), DescriptorHelper.descFromMol(JOEMol, String, DescResult, boolean)

addHydrogens

public boolean addHydrogens()

Adds hydrogens atoms to this molecule. The pH value will be corrected.

Returns:: true if successfull
See Also:: JOEPhModel

addHydrogens

public boolean addHydrogens(boolean polaronly)

Adds hydrogens atoms to this molecule. All hydrogens in neighbourhood to N,O,P or S are treated as polar. The pH value will be corrected.

Parameters:: polaronly - Add only polar hydrogens, if true
Returns:: true if successfull
See Also:: JOEPhModel

addHydrogens

public boolean addHydrogens(boolean polaronly,
                            boolean correctForPH)

Adds hydrogens atoms to this molecule. All hydrogens in neighbourhood to N,O,P or S are treated as polar. The pH value correction mode can be choosen. Dont't use (experimental) coordinate vector for added hydrogens.

Parameters:: polaronly - Add only polar hydrogens, if true; correctForPH - Corrects molecule for pH if true
Returns:: true if successfull
See Also:: JOEPhModel

addHydrogens

public boolean addHydrogens(boolean polaronly,
                            boolean correctForPH,
                            boolean useCoordV)

Adds hydrogens atoms to this molecule. All hydrogens in neighbourhood to N,O,P or S are treated as polar. The pH value correction mode can be choosen. The (experimental) coordinate vector for added hydrogens mode can be choosen.

If useCoordV is true the coordinate vector for added H atoms will be used. This will be slower, because endModify() will be called after every added hydrogen atom. If useCoordV is false the coordinate vector for added H atoms will be ignored, which will be faster.

Parameters:: polaronly - Add only polar hydrogens, if true; correctForPH - Corrects molecule for pH if true; useCoordV - The coordinate vector for added hydrogens will be used if true
Returns:: true if successfull
See Also:: JOEPhModel, endModify(), endModify(boolean)

addHydrogens

public boolean addHydrogens(JOEAtom atom)

Adds hydrogens atoms to the given atom. The pH value will not be corrected.

Parameters:: atom - The atom to which the hydogens should be added
Returns:: true if successfull

addPolarHydrogens

public boolean addPolarHydrogens()

Add polar hydrogens to molecule. All hydrogens in neighbourhood to N,O,P or S are treated as polar. The pH value will be corrected.

Returns:: Description of the Return Value
See Also:: JOEPhModel

addResidue

public boolean addResidue(JOEResidue residue)

Adds residue information to this molecule.

Parameters:: residue - The residue information
Returns:: true if successfull

align

public void align(JOEAtom a1,
                  JOEAtom a2,
                  XYZVector p1,
                  XYZVector p2)

Aligns atom a1 on p1 and atom a2 along p1->p2 vector.

Parameters:: a1 - first atom; a2 - second atom; p1 - start point; p2 - end point

atomIterator

public AtomIterator atomIterator()

Gets an iterator over all atoms in this molecule. Possibility one:

 AtomIterator ait = mol.atomIterator();
 JOEAtom atom;
 while (ait.hasNext())
 {
   atom = ait.nextAtom();

 }

Atoms starts with the index 1, which is a difference to bonds which starts with the bond index 0. Possibility two:

 int atoms = mol.numAtoms();
 JOEAtom atom;
 for (int i=1; i<=atoms; i++)
 {
   atom=mol.getAtom(i);

 }

Returns:: the atom iterator for this molecule
See Also:: bondIterator(), conformerIterator(), getRingIterator(), genericDataIterator(), nativeValueIterator()

automaticFormalCharge

public boolean automaticFormalCharge()

Gets the flag if the automatic calculation of the formal charge of the atoms is allowed. This is for example used in the PH value correction method.

Returns:: true if the calculation of the formal charge is allowed.

automaticPartialCharge

public boolean automaticPartialCharge()

Gets the flag if the automatic calculation of the partial charge of the atoms is allowed.

Returns:

true if the calculation of the partial charge is allowed.

See Also:

JOEGastChrg

References:

gm78

beginModify

public void beginModify()

Begins modification of atoms and increase modification counter. The modification will be only processed if getMod() is 0!!! If you have called beginModify/endModify twice you can not expect that these changes are already available correctly. This fits especially for deleted and added atoms, because endModify updates the atomId's, writes the atom coordinates to the rotamer arrays and checks the aromaticity.

See Also:: endModify(), endModify(boolean), decrementMod(), incrementMod(), getMod()

bondIterator

public BondIterator bondIterator()

Gets an iterator over all bonds. Possibility one:

 BondIterator bit = bondIterator();
 JOEBond bond;
 while (bit.hasNext())
 {
   bond = bit.nextBond();

 }

Bonds starts with the index 0, which is a difference to atoms which starts with the atom index 1. Possibility two:

 int bonds = mol.numBonds();
 JOEBond bond;
 for (int i=0; i<bonds; i++)
 {
   bond=mol.getBond(i);

 }

Returns:: the bond iterator
See Also:: atomIterator(), conformerIterator(), getRingIterator(), genericDataIterator(), nativeValueIterator()

center

public void center()

Centers molecule.

See Also:: center(int)

center

public XYZVector center(int nconf)

Centers conformer.

Parameters:: nconf - number of the conformer
Returns:: the center of the conformer
See Also:: center()

clear

public boolean clear()

Clears molecule.

Returns:: true if successfull

clone

public Object clone()

Clones molecule without additional data (e.g. descriptor data).

Returns:: the cloned molecule

clone

public Object clone(boolean cloneDesc)

Clones this molecule.

Parameters:: cloneDesc - clones the PairData descriptors if true
Returns:: the cloned molecule

clone

public Object clone(boolean cloneDesc,
                    String[] descriptors)

Clones this molecule.

Parameters:: cloneDesc - clones the PairData descriptors if true
Returns:: the cloned molecule

conformerIterator

public ConformerIterator conformerIterator()

Gets an iterator over all conformers.

 ConformerIterator cit = mol.conformerIterator();
 double conformer[];
 while (cit.hasNext())
 {
   conformer = cit.nextConformer();

 }

Returns:: the conformer iterator
See Also:: atomIterator(), bondIterator(), getRingIterator(), genericDataIterator(), nativeValueIterator()

conformerNum

public final int conformerNum()

Returns the number of conformers.

Returns:: number of conformers

connectTheDots

public void connectTheDots()

Use inter-atomic distances to identify bonds.

For assigning atom types using a geometry-based algorithm have a look at ml91 and the structure based expert rules in JOEAtomTyper.

References:

ml91

contiguousFragments

public void contiguousFragments(Vector cfl)

Each Vector contains the atom numbers of a contiguous fragment. The integer arrays are sorted by size from largest to smallest.
Example:

 Vector fragments=new Vector();
 mol.contiguousFragments(fragments);
 int fragmentAtomIdx[];
 System.out.println(""+fragments.size()+" contiguous fragments in molecule '"+
                    mol.getTitle()+"' (salt ?).");
 for (int i = 0; i < fragments.size(); i++)
 {
   fragmentAtomIdx=(int[])fragments.get(i);
   System.out.print("Atoms of fragment "+i+":");
          for (int j = 0; j < fragmentAtomIdx.length; j++)
   {
     System.out.print(fragmentAtomIdx[j]);
     System.out.print(' ');
   }
   System.out.println();
 }

Parameters:: cfl - a Vector that stores the integer arrays for the contiguous fragments atom numbers
See Also:: stripSalts()

copyConformer

public void copyConformer(double[] src,
                          int idx)

Copies given conformer to this molecule.

Parameters:: src - the conformer; idx - the index of the conformer

copyConformer

public void copyConformer(float[] src,
                          int idx)

Copies given conformer to this molecule.

Parameters:: src - the conformer; idx - the index of the conformer

correctForPH

public boolean correctForPH()

Corrects pH value of the molecule.

Returns:: true if successfull
See Also:: JOEPhModel

createAtom

public JOEAtom createAtom()

Creates only a new atom.

Returns:: the created atom
See Also:: createBond(), addAtom(JOEAtom), newAtom()

createBond

public JOEBond createBond()

Creates only a new bond.

Returns:: the created bond
See Also:: createAtom()

dataSize

public int dataSize()

Returns the number of data elements in this molecule.

Returns:: number of data elements in this molecule

decrementMod

public void decrementMod()

Decrease modification counter.

See Also:: incrementMod(), getMod(), beginModify(), endModify(), endModify(boolean)

deleteAtom

public boolean deleteAtom(JOEAtom atom)

Delete atom from molecule.

Parameters:: atom - The atom to delete
Returns:: true if successfull

deleteBond

public boolean deleteBond(JOEBond bond)

Delete the given JOEBond from this molecule.

Parameters:: bond - The bond to delete
Returns:: true if successfull

deleteConformer

public void deleteConformer(int idx)

Delete conformer from molecule.

Parameters:: idx - The conformer number

deleteData

public boolean deleteData(String s)

Description of the Method

Parameters:: s - Description of the Parameter
Returns:: Description of the Return Value

deleteData

public void deleteData(JOEDataType dt)

Deletes all data elements os the given JOEDataType .

Parameters:: dt - type of the elements to delete

deleteData

public void deleteData(JOEGenericData gd)

Delete all data elements which are equal to the given JOEGenericData element.

Parameters:: gd - the element to delete

deleteData

public void deleteData(Vector vg)

Description of the Method

Parameters:: vg - Description of the Parameter

deleteHydrogen

public boolean deleteHydrogen(JOEAtom atom)

Deletes hydrogen atom.

 mol.beginModify();
 deleteHydrogen(atom );
 mol.endModify();

Parameters:: atom - Hydrogen atom to delete
Returns:: true if successfull

deleteHydrogens

public boolean deleteHydrogens()

Delete all hydrogen atoms from molecule.

 mol.beginModify();
 deleteHydrogens();
 mol.endModify();

Returns:: true if successfull

deleteHydrogens

public boolean deleteHydrogens(JOEAtom atom)

Delete all hydrogen atoms from given atom.

 mol.beginModify();
 deleteHydrogens(atom);
 mol.endModify();

Parameters:: atom - Atom from which hydrogen atoms should be deleted
Returns:: true if successfull

deleteNonPolarHydrogens

public boolean deleteNonPolarHydrogens()

Delete all non polar hydrogens from molecule. All hydrogens in neighbourhood to N,O,P or S are treated as polar.

Returns:: true if successfull

deleteResidue

public boolean deleteResidue(JOEResidue residue)

Description of the Method

Parameters:: residue - Description of the Parameter
Returns:: Description of the Return Value

destroyAtom

public void destroyAtom(JOEAtom atom)

Destroys atom.

Parameters:: atom - the atom

destroyBond

public void destroyBond(JOEBond bond)

Destroys all bond.

Parameters:: bond - the bond

empty

public boolean empty()

Returns true if this molecule contains no atoms.

Returns:: true if this molecule contains no atoms

endModify

public void endModify()

Ends modification of atoms and decrease modification counter. All flags will be deleted. The modification will be only processed if getMod() is 0!!! If you have called beginModify/endModify twice you can not expect that these changes are already available correctly. This fits especially for deleted and added atoms, because endModify updates the atomId's, writes the atom coordinates to the rotamer arrays and checks the aromaticity.

See Also:: endModify(boolean), beginModify(), decrementMod(), incrementMod(), getMod()

endModify

public void endModify(boolean nukePerceivedData)

Ends modification of atoms and decrease modification counter. The modification will be only processed if getMod() is 0!!! If you have called beginModify/endModify twice you can not expect that these changes are already available correctly. This fits especially for deleted and added atoms, because endModify updates the atomId's, writes the atom coordinates to the rotamer arrays and checks the aromaticity.

Parameters:: nukePerceivedData - if true all flags will be deleted
See Also:: endModify(), beginModify(), decrementMod(), incrementMod(), getMod()

equals

public boolean equals(Object obj)

Checks if two molecules are equal, ignoring descriptor values. This method uses the full equality check if the atom and bonds.

equals

public boolean equals(JOEMol type)

Checks if two molecules are equal, ignoring descriptor values. This method uses the full equality check if the atom and bonds.

existsBond

public boolean existsBond(int bgn,
                          int end)

Returns true if this bond exists.

Parameters:: bgn - atom index of the start atom; end - atom index of the end atom
Returns:: true if this bond exists

finalize

public void finalize()

Destructor for this molecule.

findChildren

public void findChildren(Vector children,
                         int first,
                         int second)

Locates all atoms for which there exists a path to second without going through first children does not include second .

Parameters:: children - Description of the Parameter; first - Description of the Parameter; second - Description of the Parameter

findChildren

public void findChildren(Vector children,
                         JOEAtom bgn,
                         JOEAtom end)

locates all atoms for which there exists a path to 'second' without going through 'first' children does not include 'second'

Parameters:: children - Description of the Parameter; bgn - Description of the Parameter; end - Description of the Parameter

findChiralCenters

public void findChiralCenters()

Description of the Method

findLargestFragment

public void findLargestFragment(JOEBitVec lf)

each vector contains the atom numbers of a contig fragment the vectors are sorted by size from largest to smallest

Parameters:: lf - Description of the Parameter

findRingAtomsAndBonds

public void findRingAtomsAndBonds()

Description of the Method

findSSSR

public void findSSSR()

Finds the Smallest Set of Smallest Rings (SSSR).

See Also:

getSSSR(), #getSSSRIterator(Vector)

To Do:

Find correct reference: Frerejacque, Bull. Soc. Chim. Fr., 5, 1008 (1939)

References:

fig96

genericDataIterator

public GenericDataIterator genericDataIterator()

Gets an iterator over the generic data elements of this molecule. There exist a lot of default data types which where defined in JOEDataType. These data types are used for caching ring searches and storing special data types like comments or virtual bonds. Furthermore there exist the most important data type JOEPairData for storing descriptor values. Read the JOEDataType description for details.

For getting all data elements the simple data iterator can be used.

 GenericDataIterator gdit = mol.genericDataIterator();
 JOEGenericData genericData;
 while(gdit.hasNext())
 {
   genericData = gdit.nextGenericData();

 }

For getting all descriptor data elements a slightly modified iterator can be used.

 GenericDataIterator gdit = mol.genericDataIterator();
 JOEGenericData genericData;
 while(gdit.hasNext())
 {
   genericData = gdit.nextGenericData();
   if (genericData.getDataType() == JOEDataType.JOE_PAIR_DATA)
   {
           JOEPairData pairData = (JOEPairData)genericData;

   }
 }

For getting all native value descriptors the simple data iterator can be used, also. Because this is a little bit tricky, the nativeValueIterator() would be the recommended method for getting these values. Though the complex access will be presented, because it's really instructive for understanding the data access under JOELib.

 GenericDataIterator gdit = mol.genericDataIterator();
 JOEGenericData genericData;
 while(gdit.hasNext())
 {
   genericData = gdit.nextGenericData();
   if (genericData.getDataType() == JOEDataType.JOE_PAIR_DATA)
   {
           JOEPairData pairData = (JOEPairData)genericData;
           // data must be parsed to check data type
           genericData = mol.getData(pairData.getAttribute(), true);
           pairData = (JOEPairData)genericData;
             if(JOEHelper.hasInterface(pairData, "NativeValue"))
             {
        double tmpDbl=((NativeValue) pairData).getDoubleNV();

             }
   }
 }

Returns:: the generic data iterator
See Also:: atomIterator(), bondIterator(), conformerIterator(), getRingIterator(), nativeValueIterator(), getData(String), getData(String, boolean), addData(JOEGenericData), addData(JOEGenericData, boolean), DescriptorHelper.molDescriptors(JOEMol), JOEDataType, JOEGenericData

has2D

public boolean has2D()

Description of the Method

Returns:: Description of the Return Value

has3D

public boolean has3D()

Description of the Method

Returns:: Description of the Return Value

hasAromaticCorrected

public boolean hasAromaticCorrected()

Description of the Method

Returns:: Description of the Return Value

hasAromaticPerceived

public boolean hasAromaticPerceived()

Description of the Method

Returns:: Description of the Return Value

hasAtomTypesPerceived

public boolean hasAtomTypesPerceived()

Description of the Method

Returns:: Description of the Return Value

hasChainsPerceived

public boolean hasChainsPerceived()

Description of the Method

Returns:: Description of the Return Value

hasChiralityPerceived

public boolean hasChiralityPerceived()

Description of the Method

Returns:: Description of the Return Value

hasClosureBondsPerceived

public boolean hasClosureBondsPerceived()

Description of the Method

Returns:: Description of the Return Value

hasData

public boolean hasData(String s)

Description of the Method

Parameters:: s - Description of the Parameter
Returns:: true if the generic attribute/value pair exists

hasData

public boolean hasData(JOEDataType dt)

Returns true if one ore more entries of the given JOEDataType exists.

Parameters:: dt - Description of the Parameter
Returns:: true if the generic attribute/value pair exists

hasHybridizationPerceived

public boolean hasHybridizationPerceived()

Description of the Method

Returns:: Description of the Return Value

hasHydrogensAdded

public boolean hasHydrogensAdded()

Description of the Method

Returns:: Description of the Return Value

hasImplicitValencePerceived

public boolean hasImplicitValencePerceived()

Description of the Method

Returns:: Description of the Return Value

hasKekulePerceived

public boolean hasKekulePerceived()

Description of the Method

Returns:: Description of the Return Value

hasNonZeroCoords

public boolean hasNonZeroCoords()

Description of the Method

Returns:: Description of the Return Value

hasPartialChargesPerceived

public boolean hasPartialChargesPerceived()

Description of the Method

Returns:: Description of the Return Value

hasRingAtomsAndBondsPerceived

public boolean hasRingAtomsAndBondsPerceived()

Description of the Method

Returns:: Description of the Return Value

hasSSSRPerceived

public boolean hasSSSRPerceived()

Description of the Method

Returns:: Description of the Return Value

hashCode

public int hashCode()

Calculates the hashcode of a molecule using the methods AbstractDatabase.getHashcode and AbstractDatabase.getSMILESHashcode.

incrementMod

public void incrementMod()

Increase modification counter.

See Also:: decrementMod(), getMod(), beginModify(), endModify(), endModify(boolean)

insertAtom

public boolean insertAtom(JOEAtom atom)

Description of the Method

Parameters:: atom - Description of the Parameter
Returns:: Description of the Return Value

kekulize

public boolean kekulize()

Kekulizes the molecule.

Returns:: true if successfull

nativeValueIterator

public NativeValueIterator nativeValueIterator()

Gets an iterator over native descriptor values (int or double) of this molecule.

 NativeValueIterator nativeIt = mol.nativeValueIterator();
 double value;
 String descName;
 while (nativeIt.hasNext())
 {
   value = nativeIt.nextDouble();
   descName = nativeIt.actualName();

 }

Returns:: The native value iterator
See Also:: atomIterator(), bondIterator(), conformerIterator(), getRingIterator(), genericDataIterator()

newAtom

public JOEAtom newAtom()

Creates a new atom and adds it to molecule.

Returns:: the new atom
See Also:: addAtom(JOEAtom), createAtom()

newResidue

public JOEResidue newResidue()

Returns and adds new residue informations for this molecule.

Returns:: The residue informations.

numAtoms

public int numAtoms()

Returns the number of atoms.

Returns:: The number of atoms

numBonds

public int numBonds()

Returns the number of bonds.

Returns:: The number of bonds

numConformers

public int numConformers()

Returns the number of conformers of this molecule.

Returns:: The number of conformers of this molecule

numHvyAtoms

public int numHvyAtoms()

Returns the number of heavy atoms. That is the number of all atoms except hydrogen atoms.

Returns:: The number of heavy atoms

numResidues

public int numResidues()

Returns the number of residues.

Returns:: The number of residues

numRotors

public int numRotors()

Returns the number of rotatable bonds.

Returns:: The number of rotatable bonds

perceiveKekuleBonds

public boolean perceiveKekuleBonds()

Description of the Method

Returns:: Description of the Return Value

reHash

public int reHash()

renumberAtoms

public void renumberAtoms(Vector v)

Parameters:: v - of type JOEAtom

reserveAtoms

public void reserveAtoms(int natoms)

Reserves a initial capacity of atoms.

Parameters:: natoms - The number of atoms to reserve

residueIterator

public ResidueIterator residueIterator()

Description of the Method

Returns:: Description of the Return Value

rotate

public void rotate(double[][] u)

Parameters:: u - Description of the Parameter

rotate

public void rotate(double[] m)

Parameters:: m - of size 9.

rotate

public void rotate(double[] m,
                   int nconf)

Parameters:: m - of size 9.; nconf - Description of the Parameter

set

public JOEMol set(JOEMol source)

Clones molecule without additional data (e.g. descriptor data).

Parameters:: source - Description of the Parameter
Returns:: Description of the Return Value

set

public JOEMol set(JOEMol source,
                  boolean cloneDesc,
                  String[] descriptors)

Clones molecule. Missing descriptor entries, defined in descriptors will be ignored.

Parameters:: source - Description of the Parameter; cloneDesc - clones the PairData descriptors if true; descriptors - descriptors to clone. If null all descriptors are cloned
Returns:: The new molecule

set

public JOEMol set(JOEMol source,
                  boolean cloneDesc,
                  String[] descriptors,
                  boolean addDescIfNotExist)

Clones molecule.

Parameters:: source - Description of the Parameter; cloneDesc - clones the PairData descriptors if true; descriptors - descriptors to clone. If null all descriptors are cloned; addDescIfNotExist - Missing descriptor entries, defined in descriptors will be automatically added to the molecule if true
Returns:: The new molecule

sortBonds

public void sortBonds()

Description of the Method

stripSalts

public boolean stripSalts()

Deletes all atoms except for the largest contiguous fragment.

Returns:: true if all smaller contiguous fragments were deleted
See Also:: contiguousFragments(Vector)

toInertialFrame

public void toInertialFrame(int conf,
                            double[] rmat)

Description of the Method

Parameters:: conf - Description of the Parameter; rmat - Description of the Parameter

toInertialFrame

public void toInertialFrame()

Description of the Method

toString

public String toString()

Description of the Method

Returns:: Description of the Return Value

toString

public String toString(IOType type)

Description of the Method

Parameters:: type - Description of the Parameter
Returns:: Description of the Return Value

toString

public String toString(boolean writeDescriptors)

Description of the Method

Parameters:: writeDescriptors - Description of the Parameter
Returns:: Description of the Return Value

toString

public String toString(IOType type,
                       boolean writeDescriptors)

Description of the Method

Parameters:: type - Description of the Parameter; writeDescriptors - Description of the Parameter
Returns:: Description of the Return Value

translate

public void translate(XYZVector v)

Description of the Method

Parameters:: v - Description of the Parameter

translate

public void translate(XYZVector v,
                      int nconf)

Description of the Method

Parameters:: v - Description of the Parameter; nconf - Description of the Parameter

unsetAromaticPerceived

public void unsetAromaticPerceived()

Description of the Method

unsetImplicitValencePerceived

public void unsetImplicitValencePerceived()

Description of the Method

unsetPartialChargesPerceived

public void unsetPartialChargesPerceived()

Description of the Method

Overview

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JOELib
Computational Chemistry Package
Comments and Questions? mail to J.K.Wegner

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joelib.molecule Class JOEMol

JOE_SSSR_MOL

JOE_RINGFLAGS_MOL

JOE_AROMATIC_MOL

JOE_ATOMTYPES_MOL

JOE_CHIRALITY_MOL

JOE_PCHARGE_MOL

JOE_HYBRID_MOL

JOE_IMPVAL_MOL

JOE_KEKULE_MOL

JOE_CLOSURE_MOL

JOE_H_ADDED_MOL

JOE_PH_CORRECTED_MOL

JOE_AROM_CORRECTED_MOL

JOE_CHAINS_MOL

JOE_CURRENT_CONFORMER

JOEMol

JOEMol

JOEMol

JOEMol

JOEMol

setAdd

setAromaticCorrected

setAromaticPerceived

getAtom

setAtomTypesPerceived

setAutomaticFormalCharge

setAutomaticPartialCharge

getBond

getBond

getBond

setChainsPerceived

isChiral

setChiralityPerceived

setClosureBondsPerceived

setConformer

getConformer

setConformers

getConformers

getCoordinates

setCorrectedForPH

isCorrectedForPH

getData

getData

getData

setEnergy

getEnergy

getExactMass

getFirstAtom

getFlags

getGTDVector

setHybridizationPerceived

setHydrogensAdded

setImplicitValencePerceived

setInputType

setKekulePerceived

getMod

getTitle

getInputType

getMolWt

setOutputType

getOutputType

setPartialChargeVendor

getPartialChargeVendor

setPartialChargesPerceived

getResidue

setRingAtomsAndBondsPerceived

getRingIterator

getSSSR

setSSSRPerceived

setTitle

setTorsion

getTorsion

getTorsion

addAtom

addBond

addBond

addBond

addBond

addConformer

joelib.molecule
Class JOEMol