de.bioforscher.singa.structure.model.oak

Class LeafSubstructureFactory

java.lang.Object

de.bioforscher.singa.structure.model.oak.LeafSubstructureFactory

public class LeafSubstructureFactory
extends Object

The residue factory is used to create residues from a set of AtomFilter with their AtomNames. This also connects the atoms in the residues, where possible. No distance criterion is used but the knowledge of the residues and the usually connected atoms. Different options can be set.

Method Summary

Modifier and Type	Method and Description
static OakAminoAcid	createAminoAcidFromAtoms(LeafIdentifier leafIdentifier, AminoAcidFamily aminoAcidFamily, Map<String,OakAtom> atoms, StructureParserOptions options)
static OakLeafSubstructure<?>	createLeafSubstructure(LeafIdentifier leafIdentifier, StructuralFamily family)
static OakNucleotide	createNucleotideFromAtoms(LeafIdentifier leafIdentifier, NucleotideFamily nucleotideFamily, Map<String,OakAtom> atoms, StructureParserOptions options)

Methods inherited from class java.lang.Object

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

Method Detail

createLeafSubstructure

public static OakLeafSubstructure<?> createLeafSubstructure(LeafIdentifier leafIdentifier,
                                                            StructuralFamily family)

createNucleotideFromAtoms

public static OakNucleotide createNucleotideFromAtoms(LeafIdentifier leafIdentifier,
                                                      NucleotideFamily nucleotideFamily,
                                                      Map<String,OakAtom> atoms,
                                                      StructureParserOptions options)

createAminoAcidFromAtoms

public static OakAminoAcid createAminoAcidFromAtoms(LeafIdentifier leafIdentifier,
                                                    AminoAcidFamily aminoAcidFamily,
                                                    Map<String,OakAtom> atoms,
                                                    StructureParserOptions options)