Package qsardes.molecule

Class Molecule

java.lang.Object

qsardes.molecule.Molecule

public final class Molecule
extends Object

Clones the internal molecular representation of a MoleculeBuilder object and adds manipulators and calculators.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final record	Molecule.IntrState	Stores the atomic intrinsic state, sigma and valence electrons count.

Constructor Summary

Constructors

Constructor	Description
Molecule(AbstractMoleculeBuilder mol_build)	Constructs a molecular representation.

Method Summary

Modifier and Type	Method	Description
final Molecule.IntrState	calc_intrinsic_state_kier_hall(org.openscience.cdk.interfaces.IAtom atom)	Gets atom Kier-Hall intrinsic state value and electrons valence counts.
final Molecule.IntrState	calc_intrinsic_state_kier_hall_elneg(org.openscience.cdk.interfaces.IAtom atom)	Gets atom intrinsic state based on Kier-Hall relative electronegativity value, as defined in Molconn-Z, and electrons valence counts.
final Molecule.IntrState	calc_intrinsic_state_molconn(org.openscience.cdk.interfaces.IAtom atom)	Gets atom intrinsic state value calculated according to the Molconn-Z valence electrons count definition, and gets electrons valence counts.
void	convert_impl_to_expl_hydrogens()	Converts the hydrogens of the internal CDK atom container representation from implicit to explicit.
org.openscience.cdk.interfaces.IAtomContainer	get_atom_container()	Gets the molecular CDK atom container.
org.jgrapht.graph.DefaultDirectedGraph<Integer,CustomEdge>	get_graph()	Gets the directed graph of the molecular representation.
void	remove_hydrogens()	Removes the hydrogens of the internal CDK atom container representation.

Methods inherited from class java.lang.Object

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

Constructor Details

Molecule

public Molecule(AbstractMoleculeBuilder mol_build)
         throws CloneNotSupportedException

Constructs a molecular representation.

Parameters:

mol_build - MolecularBuilder object.

Throws:

CloneNotSupportedException

Method Details

get_atom_container

public org.openscience.cdk.interfaces.IAtomContainer get_atom_container()

Gets the molecular CDK atom container.

Returns:

CDK atom container.

get_graph

public org.jgrapht.graph.DefaultDirectedGraph<Integer,CustomEdge> get_graph()

Gets the directed graph of the molecular representation.

Returns:

directed graph.

convert_impl_to_expl_hydrogens

public void convert_impl_to_expl_hydrogens()
                                    throws org.openscience.cdk.exception.CDKException

Converts the hydrogens of the internal CDK atom container representation from implicit to explicit.

Throws:

org.openscience.cdk.exception.CDKException

remove_hydrogens

public void remove_hydrogens()

Removes the hydrogens of the internal CDK atom container representation.

calc_intrinsic_state_kier_hall

public final Molecule.IntrState calc_intrinsic_state_kier_hall(org.openscience.cdk.interfaces.IAtom atom)

Gets atom Kier-Hall intrinsic state value and electrons valence counts.

Parameters:

atom - CDK atom

Returns:

calc_intrinsic_state_kier_hall_elneg

public final Molecule.IntrState calc_intrinsic_state_kier_hall_elneg(org.openscience.cdk.interfaces.IAtom atom)

Gets atom intrinsic state based on Kier-Hall relative electronegativity value, as defined in Molconn-Z, and electrons valence counts.

Parameters:

atom - CDK atom

Returns:

calc_intrinsic_state_molconn

public final Molecule.IntrState calc_intrinsic_state_molconn(org.openscience.cdk.interfaces.IAtom atom)

Gets atom intrinsic state value calculated according to the Molconn-Z valence electrons count definition, and gets electrons valence counts.

Parameters:

atom - CDK atom

Returns: