Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> [ molecule overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

joelib.molecule
Class JOEMol  

java.lang.Object
  joelib.molecule.JOEMol

All Implemented Interfaces:

java.lang.Cloneable, java.io.Serializable

---

public class JOEMol

extends java.lang.Object

implements java.lang.Cloneable, java.io.Serializable

Molecule representation.

There are different possibilities to build a molecule.

1. 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());
    

2. 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();
    

2D coordinates can be generated using joelib.util.cdk.CDKTools which uses the structure layout module from the CDK.
3D coordinates can be generated using an external processing module (joelib.ext.External), if available, for 3D generation programs, like Corina.

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

---

Field Summary
protected  int	_access           Description of the Field
protected  java.util.Vector	_atom           Atoms of this molecule.
protected  boolean	_autoFormalCharge           Automatic formal charge calculation.
protected  boolean	_autoPartialCharge           Automatic partial charge calculation.
protected  java.util.Vector	_bond           Bonds of this molecule.
protected  double[]	_c           Coordinate array of the atom positions.
protected  int	_cur_pose_idx           Description of the Field
protected  double	_energy           Energy of this molecule.
protected  int	_flags           Molecule flags.
protected  joelib.io.IOType	_itype           Molecule input type.
protected  int	_mod           Modification counter.
protected  int	_natoms           Number of atoms in this molecule.
protected  int	_nbonds           Number of bonds in this molecule.
protected  joelib.io.IOType	_otype           Molecule output type.
protected  java.util.Vector	_pose           Description of the Field
protected  java.util.Vector	_residue           Residues for this molecule.
protected  java.lang.String	_title           Title for this molecule.
protected  java.util.Vector	_vconf           Of type double[].
protected  double[]	_xyz_pose           Description of the Field
private static joelib.io.IOType	DEFAULT_IO_TYPE
protected  GenericDataHolder	genericData           Holds additional molecule data, e.g.
private  int	hash
static int	JOE_AROM_CORRECTED_MOL           Molecule flag: aromaticity corrected molecule.
static int	JOE_AROMATIC_MOL           Molecule flag: aromaticity calculated.
private static int	JOE_ATOM_INCREMENT
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.
private static org.apache.log4j.Category	logger           Obtain a suitable logger.

 

Constructor Summary

JOEMol()           Constructor for the JOEMol.

JOEMol(joelib.io.IOType itype, joelib.io.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, java.lang.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(joelib.data.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(joelib.data.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, joelib.math.XYZVector p1, joelib.math.XYZVector p2)           Aligns atom a1 on p1 and atom a2 along p1->p2 vector.
joelib.util.iterator.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.
joelib.util.iterator.BondIterator	bondIterator()           Gets an iterator over all bonds.
void	center()           Centers molecule.
joelib.math.XYZVector	center(int nconf)           Centers conformer.
boolean	clear()           Clears molecule.
java.lang.Object	clone()           Clones molecule without additional data (e.g.
java.lang.Object	clone(boolean cloneDesc)           Clones this molecule.
java.lang.Object	clone(boolean cloneDesc, java.lang.String[] descriptors)           Clones this molecule.
joelib.util.iterator.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(java.util.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(joelib.data.JOEDataType dt)           Deletes all data elements os the given JOEDataType .
void	deleteData(joelib.data.JOEGenericData gd)           Delete all data elements which are equal to the given JOEGenericData element.
boolean	deleteData(java.lang.String s)           Description of the Method
void	deleteData(java.util.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(java.lang.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(java.util.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(java.util.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(joelib.util.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).
joelib.util.iterator.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
java.util.Vector	getConformers()           Returns a java.util.Vector of all conformer coordinates (double[] values).
double[]	getCoordinates()           Gets the coordinate array of this molecule.
joelib.data.JOEGenericData	getData(joelib.data.JOEDataType dt)           Returns the first data entry of the given data type.
joelib.data.JOEGenericData	getData(java.lang.String s)           Returns the data entry with the given name, if multiple data entries exists only the first one is taken.
joelib.data.JOEGenericData	getData(java.lang.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
joelib.io.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.
joelib.io.IOType	getOutputType()           Gets the outputType attribute of the JOEMol object
JOEResidue	getResidue(int idx)           Gets the residue attribute of the JOEMol object
joelib.util.iterator.RingIterator	getRingIterator()           Gets iterator for the Smallest Set of Smallest Rings (SSSR).
java.util.Vector	getSSSR()           Gets the Smallest Set of Smallest Rings (SSSR).
protected  joelib.util.iterator.RingIterator	getSSSRIterator(java.util.Vector rv)           Gets iterator for the Smallest Set of Smallest Rings (SSSR).
java.lang.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(joelib.data.JOEDataType dt)           Returns true if one ore more entries of the given JOEDataType exists.
boolean	hasData(java.lang.String s)           Description of the Method
protected  boolean	hasFlag(int flag)           Has this molecules set flags.
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.
joelib.util.iterator.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(java.util.Vector v)
void	reserveAtoms(int natoms)           Reserves a initial capacity of atoms.
joelib.util.iterator.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, java.lang.String[] descriptors)           Clones molecule.
JOEMol	set(JOEMol source, boolean cloneDesc, java.lang.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(java.util.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
protected  void	setFlag(int flag)           Sets a molecule flag for this 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(joelib.io.IOType type)           Sets the inputType attribute of the JOEMol object
void	setKekulePerceived()           Sets the kekulePerceived attribute of the JOEMol object
void	setOutputType(joelib.io.IOType type)           Sets the outputType attribute of the JOEMol object
void	setPartialChargesPerceived()           Sets the partialChargesPerceived attribute of the JOEMol object
void	setRingAtomsAndBondsPerceived()           Sets the ringAtomsAndBondsPerceived attribute of the JOEMol object
void	setSSSRPerceived()           Sets the sSSRPerceived attribute of the JOEMol object
void	setTitle(java.lang.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
private  boolean	sortAtomZ(joelib.util.types.AtomZPos a, joelib.util.types.AtomZPos b)           Description of the Method
void	sortBonds()           Description of the Method
private  boolean	sortVVInt(java.util.Vector a, java.util.Vector b)           Description of the Method Description of the Method Description of the Method Description of the Method 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
java.lang.String	toString()           Description of the Method
java.lang.String	toString(boolean writeDescriptors)           Description of the Method
java.lang.String	toString(joelib.io.IOType type)           Description of the Method
java.lang.String	toString(joelib.io.IOType type, boolean writeDescriptors)           Description of the Method
void	translate(joelib.math.XYZVector v)           Description of the Method
void	translate(joelib.math.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

logger

private static org.apache.log4j.Category logger

Obtain a suitable logger.

---

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

---

JOE_ATOM_INCREMENT

private static final int JOE_ATOM_INCREMENT

See Also:

Constant Field Values

---

DEFAULT_IO_TYPE

private static final joelib.io.IOType DEFAULT_IO_TYPE

---

genericData

protected GenericDataHolder genericData

Holds additional molecule data, e.g. atom, bond or moelcule properties.

---

_itype

protected joelib.io.IOType _itype

Molecule input type.

---

_otype

protected joelib.io.IOType _otype

Molecule output type.

---

_title

protected java.lang.String _title

Title for this molecule.

---

_atom

protected java.util.Vector _atom

Atoms of this molecule.

See Also:

JOEAtom

---

_bond

protected java.util.Vector _bond

Bonds of this molecule.

See Also:

JOEBond

---

_pose

protected java.util.Vector _pose

Description of the Field

---

_residue

protected java.util.Vector _residue

Residues for this molecule.

---

_vconf

protected java.util.Vector _vconf

Of type double[].

---

_c

protected double[] _c

Coordinate array of the atom positions.

---

_xyz_pose

protected double[] _xyz_pose

Description of the Field

---

_autoFormalCharge

protected boolean _autoFormalCharge

Automatic formal charge calculation.

---

_autoPartialCharge

protected boolean _autoPartialCharge

Automatic partial charge calculation.

---

_energy

protected double _energy

Energy of this molecule.

---

_access

protected int _access

Description of the Field

---

_cur_pose_idx

protected int _cur_pose_idx

Description of the Field

---

_flags

protected int _flags

Molecule flags.

See Also:

JOE_SSSR_MOL 55 , JOE_RINGFLAGS_MOL 55 , JOE_AROMATIC_MOL 55 , JOE_ATOMTYPES_MOL 55 , JOE_CHIRALITY_MOL 55 , JOE_PCHARGE_MOL 55 , JOE_HYBRID_MOL 55 , JOE_IMPVAL_MOL 55 , JOE_KEKULE_MOL 55 , JOE_CLOSURE_MOL 55 , JOE_H_ADDED_MOL 55 , JOE_PH_CORRECTED_MOL 55 , JOE_AROM_CORRECTED_MOL 55 , JOE_CHAINS_MOL 55 , JOE_CURRENT_CONFORMER 55

---

_mod

protected int _mod

Modification counter.

See Also:

getMod() 55

---

_natoms

protected int _natoms

Number of atoms in this molecule.

---

_nbonds

protected int _nbonds

Number of bonds in this molecule.

---

hash

private int hash

Constructor Detail

JOEMol

public JOEMol()

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

---

JOEMol

public JOEMol(joelib.io.IOType itype,
              joelib.io.IOType otype)

Constructor for the JOEMol.

---

JOEMol

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

Constructor for the JOEMol.

---

JOEMol

public JOEMol(JOEMol source,
              boolean cloneDesc)

Constructor for the JOEMol.

---

JOEMol

public JOEMol(JOEMol source)

Clones the molecule without data elements.

Method Detail

setAdd

public JOEMol setAdd(JOEMol source)

Sets the add attribute of the JOEMol object

---

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() .

---

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.

---

setAutomaticPartialCharge

public void setAutomaticPartialCharge(boolean val)

Sets the automaticPartialCharge attribute of the JOEMol object

---

getBond

public JOEBond getBond(int idx)

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

---

getBond

public JOEBond getBond(int bgn,
                       int end)

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

---

getBond

public JOEBond getBond(JOEAtom bgn,
                       JOEAtom end)

Gets the bond attribute of the JOEMol object

---

setChainsPerceived

public void setChainsPerceived()

Sets the chainsPerceived attribute of the JOEMol object

---

isChiral

public boolean isChiral()

Gets the chiral attribute of the JOEMol object

---

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

---

getConformer

public double[] getConformer(int i)

Gets the conformer attribute of the JOEMol object

---

setConformers

public void setConformers(java.util.Vector v)

Sets the conformers attribute of the JOEMol object

---

getConformers

public java.util.Vector getConformers()

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

---

getCoordinates

public double[] getCoordinates()

Gets the coordinate array of this molecule.

---

setCorrectedForPH

public void setCorrectedForPH()

Sets the correctedForPH attribute of the JOEMol object

---

isCorrectedForPH

public boolean isCorrectedForPH()

Gets the correctedForPH attribute of the JOEMol object

---

getData

public joelib.data.JOEGenericData getData(joelib.data.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 joelib.data.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 joelib.data.JOEPairData for storing descriptor values. Read the joelib.data.JOEDataType description for details.

---

getData

public joelib.data.JOEGenericData getData(java.lang.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 joelib.data.JOEPairData element with a unparsed String value, the descriptor value will be automatically parsed from a String value to the representing result (joelib.desc.DescResult) class. If no data element with this name exists in this molecule, null is returned.

There exist a lot of default data types which where defined in joelib.data.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 joelib.data.JOEPairData for storing descriptor values. Read the joelib.data.JOEDataType description for details.

Missing descriptor values can be calculated by using DescriptorHelper.descFromMol(JOEMol, String)>DescriptorHelper.descFromMol(JOEMol, String) 55 .
Example:

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

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

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

---

getData

public joelib.data.JOEGenericData getData(java.lang.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 joelib.data.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.

There exist a lot of default data types which where defined in joelib.data.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 joelib.data.JOEPairData for storing descriptor values. Read the joelib.data.JOEDataType description for details.

Missing descriptor values can be calculated by using DescriptorHelper.descFromMol(JOEMol, String)>DescriptorHelper.descFromMol(JOEMol, String) 55 .
Example:

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

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

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

---

setEnergy

public void setEnergy(double energy)

Sets the energy attribute of the JOEMol object

---

getEnergy

public double getEnergy()

Gets the energy attribute of the JOEMol object

---

getExactMass

public double getExactMass()

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

---

getFirstAtom

public JOEAtom getFirstAtom()

Gets the firstAtom attribute of the JOEMol object

---

getFlags

public int getFlags()

Gets the flags attribute of the JOEMol object

---

getGTDVector

public boolean getGTDVector(int[] gtd)

Gets the gTDVector attribute of the JOEMol object

---

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