public static Structure readStructure ( String pdbId , int bioAssemblyId ) { // pre-computed files use lower case PDB IDs pdbId = pdbId . toLowerCase ( ) ; // we just need this to track where to store PDB files // this checks the PDB_DIR property (and uses a tmp location if not set) AtomCache cache = new AtomCache ( ) ; cache . setUseMmCif ( true ) ; FileParsingParameters p = cache . getFileParsingParams ( ) ; // some bio assemblies are large, we want an all atom representation and avoid // switching to a Calpha-only representation for large molecules // note, this requires several GB of memory for some of the largest assemblies, such a 1MX4 p . setAtomCaThreshold ( Integer . MAX_VALUE ) ; // parse remark 350 p . setParseBioAssembly ( true ) ; // download missing files Structure structure = null ; try { structure = StructureIO . getBiologicalAssembly ( pdbId , bioAssemblyId ) ; } catch ( Exception e ) { e . printStackTrace ( ) ; return null ; } return structure ; }
Load a specific biological assembly for a PDB entry