AbstractMoleculeBuilder

java.lang.Object

qsardes.molecule.AbstractMoleculeBuilder

Direct Known Subclasses:: MoleculeBuilderQsarME, MoleculeBuilderQsarWB

public abstract class AbstractMoleculeBuilder extends Object

Builds a molecular representation.

Constructor Summary

Constructors

Constructor

Description

AbstractMoleculeBuilder(String smiles)

Constructs a molecular representation.
Method Summary

Modifier and Type

Method

Description

protected void

build_graph()

protected void

configure_atoms()

protected org.openscience.cdk.interfaces.IAtomContainer

get_atom_container()

int

get_atom_count()

int

get_bond_count()

org.jgrapht.graph.DefaultDirectedGraph<Integer,CustomEdge>

get_graph()

Gets the directed graph of the molecular representation.

int

get_implicit_hydrogens_count()

protected org.openscience.cdk.interfaces.IAtomContainer

set_atom_container(org.openscience.cdk.interfaces.IAtomContainer iac)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- AbstractMoleculeBuilder
  
  public AbstractMoleculeBuilder(String smiles) throws Exception
  
  Constructs a molecular representation.
  
  Parameters:
  
  smiles - Molecular SMILES.
  
  Throws:
  
  org.openscience.cdk.exception.InvalidSmilesException
  
  Exception
Method Details
- get_graph
  
  public org.jgrapht.graph.DefaultDirectedGraph<Integer,CustomEdge> get_graph()
  
  Gets the directed graph of the molecular representation.
  
  Returns:
  
  directed graph.
- get_atom_count
  
  public int get_atom_count()
- get_bond_count
  
  public int get_bond_count()
- get_implicit_hydrogens_count
  
  public int get_implicit_hydrogens_count()
- get_atom_container
  
  protected org.openscience.cdk.interfaces.IAtomContainer get_atom_container()
- set_atom_container
  
  protected org.openscience.cdk.interfaces.IAtomContainer set_atom_container(org.openscience.cdk.interfaces.IAtomContainer iac)
- configure_atoms
  
  protected void configure_atoms() throws org.openscience.cdk.exception.CDKException
  
  Throws:
  
  org.openscience.cdk.exception.CDKException
- build_graph
  
  protected void build_graph()