org.helm.notation2.tools

Class MethodsMonomerUtils

java.lang.Object

org.helm.notation2.tools.MethodsMonomerUtils

public final class MethodsMonomerUtils
extends Object

MethodsMonomerUtils

Author:

hecht

Method Summary

Methods

Modifier and Type	Method and Description
static Monomer	generateTemporaryMonomer(String id, String polymerType, String naturalAnalog)
static List<Monomer>	getListOfHandledMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed
static List<Monomer>	getListOfHandledMonomersOnlyBase(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed
static List<Monomer>	getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) method to get all monomers for all MonomerNotations
static List<org.helm.notation2.parser.notation.polymer.MonomerNotation>	getListOfMonomerNotation(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to get all MonomerNotations for all given polymers
static Monomer	getMonomer(String type, String id, String info) method to get the monomer from the database!

Methods inherited from class java.lang.Object

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

Method Detail

getListOfHandledMonomers

public static List<Monomer> getListOfHandledMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)
                                              throws HELM2HandledException,
                                                     ChemistryException

method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed

Parameters:

monomerNotations - List of MonomerNotation

Returns:

List of Monomer

Throws:

HELM2HandledException - if the HELM2 features were there

ChemistryException - if the Chemistry Engine can not be initialized

getListOfHandledMonomersOnlyBase

public static List<Monomer> getListOfHandledMonomersOnlyBase(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)
                                                      throws HELM2HandledException,
                                                             NotationException,
                                                             ChemistryException

method to get all HELM1 valid MonomerNotations Only on these monomers required HELM1 functions are performed

Parameters:

monomerNotations - List of MonomerNotation

Returns:

List of Monomer

Throws:

HELM2HandledException - if HELM2 features are there

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

getListOfMonomerNotation

public static List<org.helm.notation2.parser.notation.polymer.MonomerNotation> getListOfMonomerNotation(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)

method to get all MonomerNotations for all given polymers

Parameters:

polymers - List of PolymerNotation

Returns:

List of MonomerNotation

getListOfMonomer

public static List<Monomer> getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)
                                      throws MonomerException,
                                             HELM2HandledException,
                                             org.helm.chemtoolkit.CTKException,
                                             NotationException,
                                             ChemistryException,
                                             MonomerLoadingException

method to get all monomers for all MonomerNotations

Parameters:

monomerNotations - List of MonomerNotation

Returns:

List of Monomer

Throws:

MonomerException - if the Monomer is not valid

HELM2HandledException - if HELM2 features are there

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

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

MonomerLoadingException - if monomers can not be loaded

getMonomer

public static Monomer getMonomer(String type,
                 String id,
                 String info)
                          throws MonomerException,
                                 NotationException,
                                 ChemistryException

method to get the monomer from the database!

Parameters:

type - Type of the Monomer

id - Id of the Monomer

info - natural analog of the monomer

Returns:

Monomer

Throws:

MonomerException - if the desired monomer is not in the database

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

generateTemporaryMonomer

public static Monomer generateTemporaryMonomer(String id,
                               String polymerType,
                               String naturalAnalog)
                                        throws NotationException,
                                               MonomerLoadingException,
                                               ChemistryException

Throws:

NotationException

MonomerLoadingException

ChemistryException