Package org.biojava.nbio.structure.io
package org.biojava.nbio.structure.io
Input and Output of Structures
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ClassDescriptionParse binary Cif files and provide capabilities to store them locally.Adds 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.Converts full atom representations to Calpha only ones.A class to add appropriate charge information to a structure.Parse text Cif files and provide capabilities to store them locally.Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure.A collection of static utilities to convert between
AFPChainsand FastaSequences.Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.Methods to convert a structure object into different file formats.A class that configures parameters that can be sent to the PDB file parsersFileParsingParameters.setParseCAOnly(boolean)- parse only the Atom records for C-alpha atomsFileParsingParameters.setParseSecStruc(boolean)- a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.Superclass for classes which download and interact with the PDB's FTP server, specificallyPDBFileReaderandCifFileReader.Controls when the class should fetch files from the ftp serverBehaviors for when an obsolete structure is requested.A class to read MMTF files and cache them locally.Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unitThis class implements the actual PDB file parsing.The wrapper class for parsing a PDB file.An exception during the parsing of a PDB file.Aligns the SEQRES residues to the ATOM residues.A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.An enum of supported file formats.StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.A class that can provide a protein structure object from somewhere.A utility class with methods for matching ProteinSequences with Structures.