Input and Output of Structures
Interface Summary Interface Description StructureIOFileStructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem. StructureProviderA class that can provide a protein structure object from somewhere.
Class Summary Class Description BondMakerAdds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object. CAConverterConverts full atom representations to Calpha only ones. ChargeAdderA class to add appropriate charge information to a structure. EntityFinderHeuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure. FastaAFPChainConverterA collection of static utilities to convert between
FastaStructureParserReads a protein sequence from a fasta file and attempts to match it to a 3D structure. FileConvertMethods to convert a structure object into different file formats. FileParsingParametersA class that configures parameters that can be sent to the PDB file parsers
FileParsingParameters.setParseCAOnly(boolean)- parse only the Atom records for C-alpha atoms
FileParsingParameters.setParseSecStruc(boolean)- a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
GroupToSDF LocalPDBDirectory MMCIFFileReaderHow to parse an mmCif file: MMTFFileReaderA class to read MMTF files and cache them locally. PDBBioAssemblyParserParses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit PDBFileParserThis class implements the actual PDB file parsing. PDBFileReaderThe wrapper class for parsing a PDB file. SandboxStyleStructureProviderThe "Sandbox" style of organizing files is to have a directory structure like below, i.e. the files are organized into directory with two characters, based on the two middle characters of a PDB ID directory of PDB ID several files that are available for this PDB ID SeqRes2AtomAlignerAligns the SEQRES residues to the ATOM residues. SSBondImplA simple bean to store disulfide bridge information, the SSBOND records in the PDB files. StructureSequenceMatcherA utility class with methods for matching ProteinSequences with Structures.
Enum Summary Enum Description LocalPDBDirectory.FetchBehaviorControls when the class should fetch files from the ftp server LocalPDBDirectory.ObsoleteBehaviorBehaviors for when an obsolete structure is requested.
Exception Summary Exception Description PDBParseExceptionAn exception during the parsing of a PDB file.