| Interface | Description |
|---|---|
| StructureIOFile |
StructureIOFile extends StructureProvider with methods specific to
parsing files from the filesystem.
|
| StructureProvider |
A class that can provide a protein structure object from somewhere.
|
| Class | Description |
|---|---|
| BcifFileReader |
Parse binary Cif files and provide capabilities to store them locally.
|
| BondMaker |
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.
|
| CAConverter |
Converts full atom representations to Calpha only ones.
|
| ChargeAdder |
A class to add appropriate charge information to a structure.
|
| CifFileReader |
Parse text Cif files and provide capabilities to store them locally.
|
| EntityFinder |
Heuristical finding of Entities (called Compounds in legacy PDB format)
in a given Structure.
|
| FastaAFPChainConverter |
A collection of static utilities to convert between
AFPChains and FastaSequences. |
| FastaStructureParser |
Reads a protein sequence from a fasta file and attempts to match it to a
3D structure.
|
| FileConvert |
Methods to convert a structure object into different file formats.
|
| FileParsingParameters |
A 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 |
Superclass for classes which download and interact with the PDB's FTP server,
specifically
PDBFileReader and MMCIFFileReader. |
| MMCIFFileReader |
How to parse an mmCif file:
public static void main(String[] args) throws Exception {
String filename = "/path/to/something.cif.gz" ;
StructureIOFile reader = new MMCIFFileReader();
Structure struc = reader.getStructure(filename);
System.out.println(struc);
}
|
| MMTFFileReader |
A class to read MMTF files and cache them locally.
|
| PDBBioAssemblyParser |
Parses REMARK 350 records in a PDB file and creates transformations to
construct the quaternary structure of a protein from an asymmetric unit
|
| PDBFileParser |
This class implements the actual PDB file parsing.
|
| PDBFileReader |
The wrapper class for parsing a PDB file.
|
| SandboxStyleStructureProvider |
The "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
a1/2a1v/2a1v.cif.gz
a1/2a1v/2a1v.dssp.gz
a1/2a1v/2a1v.pdb-250.jpg.gz
a1/2a1v/2a1v.pdb-500.jpg.gz
a1/2a1v/2a1v.pdb-65.jpg.gz
a1/2a1v/2a1v.pdb-80.jpg.gz
a1/2a1v/2a1v.pdb1-250.jpg.gz
a1/2a1v/2a1v.pdb1-500.jpg.gz
a1/2a1v/2a1v.pdb1-65.jpg.gz
a1/2a1v/2a1v.pdb1-80.jpg.gz
a1/2a1v/2a1v.pdb1.gz
a1/2a1v/2a1v.stride.gz
a1/2a1v/2a1v.xml.gz
a1/2a1v/pdb2a1v.ent.gz
a1/2a1v/r2a1vsf.ent.gz
a1/2a1w/2a1w-deriv.cif.gz
a1/2a1w/2a1w-extatom.xml.gz
a1/2a1w/2a1w-noatom.xml.gz
a1/2a1w/2a1w.cif.gz
a1/2a1w/2a1w.dssp.gz
a1/2a1w/2a1w.pdb-250.jpg.gz
a1/2a1w/2a1w.pdb-500.jpg.gz
a1/2a1w/2a1w.pdb-65.jpg.gz
a1/2a1w/2a1w.pdb-80.jpg.gz
a1/2a1w/2a1w.pdb1-250.jpg.gz
a1/2a1w/2a1w.pdb1-500.jpg.gz
a1/2a1w/2a1w.pdb1-65.jpg.gz
a1/2a1w/2a1w.pdb1-80.jpg.gz
a1/2a1w/2a1w.pdb1.gz
a1/2a1w/2a1w.pdb2-250.jpg.gz
a1/2a1w/2a1w.pdb2-500.jpg.gz
a1/2a1w/2a1w.pdb2-65.jpg.gz
a1/2a1w/2a1w.pdb2-80.jpg.gz
a1/2a1w/2a1w.pdb2.gz
a1/2a1w/2a1w.pdb3-250.jpg.gz
a1/2a1w/2a1w.pdb3-500.jpg.gz
a1/2a1w/2a1w.pdb3-65.jpg.gz
a1/2a1w/2a1w.pdb3-80.jpg.gz
a1/2a1w/2a1w.pdb3.gz
a1/2a1w/2a1w.pdb4-250.jpg.gz
a1/2a1w/2a1w.pdb4-500.jpg.gz
a1/2a1w/2a1w.pdb4-65.jpg.gz
a1/2a1w/2a1w.pdb4-80.jpg.gz
a1/2a1w/2a1w.pdb4.gz
a1/2a1w/2a1w.pdb5-250.jpg.gz
a1/2a1w/2a1w.pdb5-500.jpg.gz
a1/2a1w/2a1w.pdb5-65.jpg.gz
a1/2a1w/2a1w.pdb5-80.jpg.gz
a1/2a1w/2a1w.pdb5.gz
a1/2a1w/2a1w.pdb6-250.jpg.gz
a1/2a1w/2a1w.pdb6-500.jpg.gz
a1/2a1w/2a1w.pdb6-65.jpg.gz
a1/2a1w/2a1w.pdb6-80.jpg.gz
a1/2a1w/2a1w.pdb6.gz
a1/2a1w/2a1w.stride.gz
a1/2a1w/2a1w.xml.gz
a1/2a1w/pdb2a1w.ent.gz
a1/2a1w/r2a1wsf.ent.gz
a1/2a1x/2a1x-deriv.cif.gz
a1/2a1x/2a1x-extatom.xml.gz
a1/2a1x/2a1x-noatom.xml.gz
|
| SeqRes2AtomAligner |
Aligns the SEQRES residues to the ATOM residues.
|
| SSBondImpl |
A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
|
| StructureSequenceMatcher |
A utility class with methods for matching ProteinSequences with
Structures.
|
| Enum | Description |
|---|---|
| LocalPDBDirectory.FetchBehavior |
Controls when the class should fetch files from the ftp server
|
| LocalPDBDirectory.ObsoleteBehavior |
Behaviors for when an obsolete structure is requested.
|
| Exception | Description |
|---|---|
| PDBParseException |
An exception during the parsing of a PDB file.
|
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