Package org.biojava.nbio.structure.io

Class FastaStructureParser

java.lang.Object

org.biojava.nbio.structure.io.FastaStructureParser

public class FastaStructureParser
extends Object

Reads a protein sequence from a fasta file and attempts to match it to a 3D structure. Any gaps ('-') in the fasta file are preserved as null atoms in the output, allowing structural alignments to be read from fasta files.

Structures are loaded from an AtomCache. For this to work, the accession for each protein should be parsed from the fasta header line into a form understood by AtomCache.getStructure(String).

Lowercase letters are sometimes used to specify unaligned residues. This information can be preserved by using a CasePreservingSequenceCreator, which allows the case of residues to be accessed through the AbstractSequence.getUserCollection() method.

Author:

Spencer Bliven

Constructor Summary

Constructors

Constructor	Description
FastaStructureParser(File file, org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<org.biojava.nbio.core.sequence.ProteinSequence,org.biojava.nbio.core.sequence.compound.AminoAcidCompound> headerParser, org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(InputStream is, org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<org.biojava.nbio.core.sequence.ProteinSequence,org.biojava.nbio.core.sequence.compound.AminoAcidCompound> headerParser, org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> sequenceCreator, AtomCache cache)
FastaStructureParser(org.biojava.nbio.core.sequence.io.FastaReader<org.biojava.nbio.core.sequence.ProteinSequence,org.biojava.nbio.core.sequence.compound.AminoAcidCompound> reader, AtomCache cache)

Method Summary

Modifier and Type	Method	Description
String[]	getAccessions()	Gets the protein accessions mapped from the Fasta file.
ResidueNumber[][]	getResidues()	For each residue in the fasta file, return the ResidueNumber in the corresponding structure.
org.biojava.nbio.core.sequence.ProteinSequence[]	getSequences()	Gets the protein sequences read from the Fasta file.
Structure[]	getStructures()	Gets the protein structures mapped from the Fasta file.
void	process()	Parses the fasta file and loads it into memory.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaStructureParser

public FastaStructureParser(InputStream is,
                            org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<org.biojava.nbio.core.sequence.ProteinSequence,org.biojava.nbio.core.sequence.compound.AminoAcidCompound> headerParser,
                            org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> sequenceCreator,
                            AtomCache cache)

FastaStructureParser

public FastaStructureParser(File file,
                            org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface<org.biojava.nbio.core.sequence.ProteinSequence,org.biojava.nbio.core.sequence.compound.AminoAcidCompound> headerParser,
                            org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface<org.biojava.nbio.core.sequence.compound.AminoAcidCompound> sequenceCreator,
                            AtomCache cache)
                     throws FileNotFoundException

Throws:

FileNotFoundException

FastaStructureParser

public FastaStructureParser(org.biojava.nbio.core.sequence.io.FastaReader<org.biojava.nbio.core.sequence.ProteinSequence,org.biojava.nbio.core.sequence.compound.AminoAcidCompound> reader,
                            AtomCache cache)

Method Detail

process

public void process()
             throws IOException,
                    StructureException

Parses the fasta file and loads it into memory. Information can be subsequently accessed through getSequences(), getStructures(), getResidues(), and getAccessions().

Throws:

IOException

StructureException

getSequences

public org.biojava.nbio.core.sequence.ProteinSequence[] getSequences()

Gets the protein sequences read from the Fasta file. Returns null if process() has not been called.

Returns:

An array ProteinSequences from parsing the fasta file, or null if process() hasn't been called.

getStructures

public Structure[] getStructures()

Gets the protein structures mapped from the Fasta file. Returns null if process() has not been called.

Returns:

An array of Structures for each protein in the fasta file, or null if process() hasn't been called.

getResidues

public ResidueNumber[][] getResidues()

For each residue in the fasta file, return the ResidueNumber in the corresponding structure. If the residue cannot be found in the structure, that entry will be null. This can happen if that residue was not included in the PDB file (eg disordered residues), if the fasta sequence does not match the PDB sequence, or if errors occur during the matching process.

Returns:

A 2D array of ResidueNumbers, or null if process() hasn't been called.

See Also:

StructureSequenceMatcher.matchSequenceToStructure(ProteinSequence, Structure)

getAccessions

public String[] getAccessions()

Gets the protein accessions mapped from the Fasta file. Returns null if process() has not been called.

Returns:

An array of Structures for each protein in the fasta file, or null if process() hasn't been called.