org.pistoiaalliance.helm.HELMSimilarityLibrary.utils

Class MoleculeGraphUtils

java.lang.Object

org.pistoiaalliance.helm.HELMSimilarityLibrary.utils.MoleculeGraphUtils

public class MoleculeGraphUtils
extends Object

MoleculeGraphUtils class implements a moleculeGraph of type Graph with a list of vertices and edges between vertices that are represented by neighbors for each vertex.

Author:

bueltel

Constructor Summary

Constructors

Constructor and Description
MoleculeGraphUtils()

Method Summary

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.

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeGraphUtils

public MoleculeGraphUtils()

Method Detail

buildMoleculeGraph

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

* Method builds a moleculeGraph from a list of PolymerNotations and a * list of Connections. Each vertex is a monomer and vertices are * neighbors if there is a connection between them.

Parameters:

listPolymerNotations - list of polymer notations

listOfConnections - list of connections

Returns:

The moleculeGraph of a list of polymer notations and connections

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if anything goes wrong

buildRNAPart

public static Graph buildRNAPart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                 int polymerNumber)
                          throws org.helm.notation2.parser.exceptionparser.NotationException

Builds the RNA part of the molecule.

Parameters:

polymer - the polymer notation of type rna to be build as a graph part

polymerNumber - number of the polymer

Returns:

RNA part molecule graph

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if anything goes wrong

org.helm.notation2.parser.exceptionparser.NotationException - if anything goes wrong

buildPeptidePart

public static Graph buildPeptidePart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                     int polymerNumber)

Builds the PEPTIDE part of the molecule.

Parameters:

polymer - the polymer notation of type peptide to be build as a graph part

polymerNumber - number of the polymer

Returns:

RNA part molecule graph

buildChemPart

public static Graph buildChemPart(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer,
                                  int polymerNumber)

Builds the CHEM part of the molecule.

Parameters:

polymer - the polymer notation of type chem to be build as a graph part

polymerNumber - number of the polymer

Returns:

RNA part molecule graph

addConnections

public 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.

Parameters:

moleculeGraph - The moleculeGraph of a HELM notation without connections

polymerList - list of polymers

listOfConnections - list of connections

Returns:

The moleculeGraph of a HELM notation with connections