Package Bio :: Package PDB

Package PDB

Classes that deal with macromolecular crystal structures.

Includes: PDB and mmCIF parsers, a Structure class, a module to keep a local copy of the PDB up-to-date, selective IO of PDB files, etc.

Author: Thomas Hamelryck. Additional code by Kristian Rother.

Submodules

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Bio.PDB.AbstractPropertyMap: Class that maps (chain_id, residue_id) to a residue property.
Bio.PDB.Atom: Atom class, used in Structure objects.
Bio.PDB.Chain: Chain class, used in Structure objects.
Bio.PDB.DSSP
Bio.PDB.DSSP': Use the DSSP program to calculate secondary structure and accessibility.
Bio.PDB.Dice
Bio.PDB.Entity
Bio.PDB.FragmentMapper
Bio.PDB.FragmentMapper': Classify protein backbone structure according to Kolodny et al's fragment libraries.
Bio.PDB.HSExposure: Half-sphere exposure and coordination number calculation.
Bio.PDB.MMCIF2Dict: Turn an mmCIF file into a dictionary.
Bio.PDB.MMCIFParser: mmCIF parser (partly implemented in C).
Bio.PDB.Model: Model class, used in Structure objects.
Bio.PDB.NACCESS
Bio.PDB.NeighborSearch: Fast atom neighbor lookup using a KD tree (implemented in C++).
Bio.PDB.PDBExceptions: Some Bio.PDB-specific exceptions.
Bio.PDB.PDBIO
Bio.PDB.PDBIO': Output of PDB files.
Bio.PDB.PDBList
Bio.PDB.PDBList': Access the PDB over the internet (for example to download structures).
Bio.PDB.PDBParser
Bio.PDB.PDBParser': Parser for PDB files.
Bio.PDB.PSEA: Wrappers for PSEA, a program for secondary structure assignment.
Bio.PDB.Polypeptide: Polypeptide-related classes (construction and representation).
Bio.PDB.Residue
Bio.PDB.ResidueDepth
Bio.PDB.ResidueDepth': Calculation of residue depth using command line tool MSMS.
Bio.PDB.Selection: Selection of atoms, residues, etc.
Bio.PDB.Structure: The structure class, representing a macromolecular structure.
Bio.PDB.StructureAlignment
Bio.PDB.StructureAlignment': Map the residues of two structures to each other based on a FASTA alignment file.
Bio.PDB.StructureBuilder: Consumer class that builds a Structure object.
Bio.PDB.Superimposer
Bio.PDB.Superimposer': Superimpose two structures.
Bio.PDB.Vector
Bio.PDB.Vector': Vector class, including rotation-related functions.
Bio.PDB.mmCIF
Bio.PDB.parse_pdb_header
Bio.PDB.parse_pdb_header': Parse the header of a PDB file.

Variables

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__package__ = 'Bio.PDB'