Package org.biojava.nbio.structure.io
package org.biojava.nbio.structure.io
Input and Output of Structures
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ClassDescriptionAdds 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.Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure.A collection of static utilities to convert between
AFPChainsandFastaSequences.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, specificallyPDBFileReaderandMMCIFFileReader.Controls when the class should fetch files from the ftp serverBehaviors for when an obsolete structure is requested.How to parse an mmCif file: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.The "Sandbox" style of organizing files is to have a directory structure like below, i.e.Aligns the SEQRES residues to the ATOM residues.A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.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.