Class 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.

    Spencer Bliven