Package org.helm.notation2.tools
Class MethodsMonomerUtils
java.lang.Object
org.helm.notation2.tools.MethodsMonomerUtils
public final class MethodsMonomerUtils extends Object
MethodsMonomerUtils
- Author:
- hecht
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Method Summary
Modifier and Type Method Description static MonomergenerateTemporaryMonomer(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 performedstatic 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 performedstatic List<Monomer>getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations)method to get all monomers for all MonomerNotationsstatic 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 polymersstatic MonomergetMonomer(String type, String id, String info)method to get the monomer from the database!
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Method Details
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getListOfHandledMonomers
public static List<Monomer> getListOfHandledMonomers(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) throws HELM2HandledException, ChemistryExceptionmethod 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 thereChemistryException- if the Chemistry Engine can not be initialized
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getListOfHandledMonomersOnlyBase
public static List<Monomer> getListOfHandledMonomersOnlyBase(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) throws HELM2HandledException, NotationException, ChemistryExceptionmethod 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 thereNotationException- if notation is not validChemistryException- if the Chemistry Engine can not be initialized
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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
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getListOfMonomer
public static List<Monomer> getListOfMonomer(List<org.helm.notation2.parser.notation.polymer.MonomerNotation> monomerNotations) throws MonomerException, HELM2HandledException, org.helm.chemtoolkit.CTKException, NotationException, ChemistryException, MonomerLoadingExceptionmethod to get all monomers for all MonomerNotations- Parameters:
monomerNotations- List of MonomerNotation- Returns:
- List of Monomer
- Throws:
MonomerException- if the Monomer is not validHELM2HandledException- if HELM2 features are thereorg.helm.chemtoolkit.CTKException- general ChemToolKit exception passed to HELMToolKitNotationException- if notation is not validChemistryException- if the Chemistry Engine can not be initializedMonomerLoadingException- if monomers can not be loaded
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getMonomer
public static Monomer getMonomer(String type, String id, String info) throws MonomerException, NotationException, ChemistryExceptionmethod to get the monomer from the database!- Parameters:
type- Type of the Monomerid- Id of the Monomerinfo- natural analog of the monomer- Returns:
- Monomer
- Throws:
MonomerException- if the desired monomer is not in the databaseNotationException- if notation is not validChemistryException- if the Chemistry Engine can not be initialized
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generateTemporaryMonomer
public static Monomer generateTemporaryMonomer(String id, String polymerType, String naturalAnalog) throws NotationException, MonomerLoadingException, ChemistryException
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