Class PDBBioAssemblyParser

  • public class PDBBioAssemblyParser
    extends Object
    Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit
    Peter Rose, Andreas Prlic
    • Method Detail

      • pdb_REMARK_350_Handler

        public void pdb_REMARK_350_Handler​(String line)
        Parses REMARK 350 line. See format description:
        line -
      • setMacromolecularSizes

        public void setMacromolecularSizes()
        Set the macromolecularSize fields of the parsed bioassemblies. This can only be called after the full PDB file has been read so that all the info for all bioassemblies has been gathered. Note that an explicit method to set the field is necessary here because in PDB files the transformations contain only the author chain ids, corresponding to polymeric chains, whilst in mmCIF files the transformations contain all asym ids of both polymers and non-polymers.