de.bioforscher.singa.structure.parser.pfam

Class PfamParser

java.lang.Object

de.bioforscher.singa.structure.parser.pfam.PfamParser

public class PfamParser
extends Object

A parser for the The Pfam protein families database. This can be used to parse protein structures directly from Pfam. One can either parse all chains of a given Pfam-ID or only the domain ranges annotated with that Pfam-ID. According to:

 R.Y. Eberhardt, S.R. Eddy, J. Mistry, A.L. Mitchell, S.C. Potter, M. Punta, M. Qureshi, A. Sangrador-Vegas, G.A.
 Salazar, J. Tate, A. Bateman
 Nucleic Acids Research (2016)  Database Issue 44:D279-D285
 

Author:

fk

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PfamParser.Builder
static interface	PfamParser.ChainStep
static interface	PfamParser.DomainStep
static interface	PfamParser.FamilyStep
static class	PfamParser.PfamVersion
static interface	PfamParser.VersionStep

Constructor Summary

Constructors

Constructor and Description
PfamParser(PfamParser.Builder builder)

Method Summary

Modifier and Type	Method and Description
static PfamParser.VersionStep	create()
List<Chain>	getChains()
List<List<LeafSubstructure<?>>>	getDomains()

Methods inherited from class java.lang.Object

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

Constructor Detail

PfamParser

public PfamParser(PfamParser.Builder builder)

Method Detail

create

public static PfamParser.VersionStep create()

getDomains

public List<List<LeafSubstructure<?>>> getDomains()

getChains

public List<Chain> getChains()