public class MoleculeGraphUtils extends Object
| Constructor and Description |
|---|
MoleculeGraphUtils() |
| Modifier and Type | Method and Description |
|---|---|
static Graph |
addConnections(Graph moleculeGraph,
List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymerList,
List<org.helm.notation2.parser.notation.connection.ConnectionNotation> listOfConnections)
Adds the connections between polymers of the molecule.
|
static Graph |
buildChemPart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
int polymerNumber)
Builds the CHEM part of the molecule.
|
static Graph |
buildMoleculeGraph(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> listPolymerNotations,
List<org.helm.notation2.parser.notation.connection.ConnectionNotation> listOfConnections)
* Method builds a moleculeGraph from a list of PolymerNotations and a
* list of Connections.
|
static Graph |
buildPeptidePart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
int polymerNumber)
Builds the PEPTIDE part of the molecule.
|
static Graph |
buildRNAPart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
int polymerNumber)
Builds the RNA part of the molecule.
|
public static Graph buildMoleculeGraph(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> listPolymerNotations, List<org.helm.notation2.parser.notation.connection.ConnectionNotation> listOfConnections) throws org.helm.notation2.parser.exceptionparser.NotationException
listPolymerNotations - list of polymer notationslistOfConnections - list of connectionsorg.helm.notation2.parser.exceptionparser.NotationException - if anything goes wrongpublic static Graph buildRNAPart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int polymerNumber) throws org.helm.notation2.parser.exceptionparser.NotationException
polymer - the polymer notation of type rna to be build as a graph partpolymerNumber - number of the polymerorg.helm.notation2.parser.exceptionparser.NotationException - if anything goes wrongorg.helm.notation2.parser.exceptionparser.NotationException - if anything goes wrongpublic static Graph buildPeptidePart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int polymerNumber)
polymer - the polymer notation of type peptide to be build as a graph partpolymerNumber - number of the polymerpublic static Graph buildChemPart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer, int polymerNumber)
polymer - the polymer notation of type chem to be build as a graph partpolymerNumber - number of the polymerpublic static Graph addConnections(Graph moleculeGraph, List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymerList, List<org.helm.notation2.parser.notation.connection.ConnectionNotation> listOfConnections)
moleculeGraph - The moleculeGraph of a HELM notation without connectionspolymerList - list of polymerslistOfConnections - list of connectionsCopyright © 2018. All rights reserved.