Uses of Interface
org.biojava.nbio.structure.io.StructureProvider

Packages that use StructureProvider

Package	Description
org.biojava.nbio.structure.io	Input and Output of Structures

Uses of StructureProvider in org.biojava.nbio.structure.io

Subinterfaces of StructureProvider in org.biojava.nbio.structure.io

Modifier and Type	Interface and Description
interface	StructureIOFile StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.

Classes in org.biojava.nbio.structure.io that implement StructureProvider

Modifier and Type	Class and Description
class	BcifFileReader Parse binary Cif files and provide capabilities to store them locally.
class	CifFileReader Parse text Cif files and provide capabilities to store them locally.
class	LocalPDBDirectory Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader.
class	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); }
class	MMTFFileReader A class to read MMTF files and cache them locally.
class	PDBFileReader The wrapper class for parsing a PDB file.
class	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