org.helm.notation2.tools

Class BuilderMolecule

java.lang.Object

org.helm.notation2.tools.BuilderMolecule

public final class BuilderMolecule
extends Object

class to build molecules for the HELMNotation

Author:

hecht

Method Summary

Methods

Modifier and Type	Method and Description
static List<org.helm.chemtoolkit.AbstractMolecule>	buildMoleculefromPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers, List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections) method to build molecules for the whole HELMNotation
static RgroupStructure	buildMoleculefromSinglePolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymernotation) method to build a molecule for a single polymer
static org.helm.chemtoolkit.AbstractMolecule	getMolecule(String smiles)
static org.helm.chemtoolkit.AbstractMolecule	getMoleculeForMonomer(Monomer monomer) method to build a molecule for a given monomer
static org.helm.chemtoolkit.AbstractMolecule	mergeRgroups(org.helm.chemtoolkit.AbstractMolecule molecule) method to merge all unused rgroups into a molecule

Methods inherited from class java.lang.Object

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

Method Detail

buildMoleculefromSinglePolymer

public static RgroupStructure buildMoleculefromSinglePolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymernotation)
                                                      throws BuilderMoleculeException,
                                                             HELM2HandledException,
                                                             ChemistryException

method to build a molecule for a single polymer

Parameters:

polymernotation - a single polymer

Returns:

molecule for the given single polymer

Throws:

BuilderMoleculeException - if the polymer type is BLOB or unknown

HELM2HandledException - if the polymer contains HELM2 features

ChemistryException - if the Chemistry Engine can not be initialized

buildMoleculefromPolymers

public static List<org.helm.chemtoolkit.AbstractMolecule> buildMoleculefromPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers,
                                                                    List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections)
                                                                             throws BuilderMoleculeException,
                                                                                    ChemistryException

method to build molecules for the whole HELMNotation

Parameters:

polymers - all polymers of the HELMNotation

connections - all connections of the HELMNotation

Returns:

list of built molecules

Throws:

BuilderMoleculeException - if HELM2 features were contained

ChemistryException - if the Chemistry Engine can not be iniialized

mergeRgroups

public static org.helm.chemtoolkit.AbstractMolecule mergeRgroups(org.helm.chemtoolkit.AbstractMolecule molecule)
                                                          throws BuilderMoleculeException,
                                                                 ChemistryException

method to merge all unused rgroups into a molecule

Parameters:

molecule - input molecule

Returns:

molecule with all merged unused rgroups

Throws:

BuilderMoleculeException - if the molecule can't be built

ChemistryException - if the Chemistry Engine ca not be initialized

getMoleculeForMonomer

public static org.helm.chemtoolkit.AbstractMolecule getMoleculeForMonomer(Monomer monomer)
                                                                   throws BuilderMoleculeException,
                                                                          ChemistryException

method to build a molecule for a given monomer

Parameters:

monomer - input monomer

Returns:

generated molecule for the given monomer

Throws:

BuilderMoleculeException - if the monomer can't be built

ChemistryException - if the Chemistry Engine can not be initialized

getMolecule

public static org.helm.chemtoolkit.AbstractMolecule getMolecule(String smiles)
                                                         throws IOException,
                                                                org.helm.chemtoolkit.CTKException,
                                                                ChemistryException

Parameters:

smiles - given input smiles

Returns:

converted smiles into molecule

Throws:

ChemistryException - if chemistry could not be initialized

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

IOException - if smiles can not be read