Module MMTK.PDB

This module provides classes that represent molecules in PDB file. They permit various manipulations and the creation of MMTK objects. Note that the classes defined in this module are specializations of classed defined in Scientific.IO.PDB; the methods defined in that module are also available.


Class PDBPeptideChain: Peptide chain in a PDB file

A subclass of Scientific.IO.PDB.PeptideChain. See the description of that class for the constructor and additional methods. In MMTK, PDBPeptideChain objects are usually obtained from a PDBConfiguration object via its attribute peptide_chains (see the documentation of Scientific.IO.PDB.Structure).

Methods:

Class PDBNucleotideChain: Nucleotide chain in a PDB file

A subclass of Scientific.IO.PDB.NucleotideChain. See the description of that class for the constructor and additional methods. In MMTK, PDBNucleotideChain objects are usually obtained from a PDBConfiguration object via its attribute nucleotide_chains (see the documentation of Scientific.IO.PDB.Structure).

Methods:

Class PDBMolecule: Molecule in a PDB file

A subclass of Scientific.IO.PDB.Molecule. See the description of that class for the constructor and additional methods. In MMTK, PDBMolecule objects are usually obtained from a PDBConfiguration object via its attribute molecules (see the documentation of Scientific.IO.PDB.Structure). A molecule is by definition any residue in a PDB file that is not an amino acid or nucleotide residue.

Methods:

Class PDBConfiguration: Everything in a PDB file

A PDBConfiguration object represents the full contents of a PDB file. It can be used to create MMTK objects for all or part of the molecules, or to change the configuration of an existing system.

Constructor: PDBConfiguration(filename)

filename

the name of a PDB file

Methods:

Class PDBOutputFile: PDB file for output

Constructor: PDBOutputFile(filename, subformat=None)

filename

the name of the PDB file that is created

subformat

a variant of the PDB format; these subformats are defined in module Scientific.IO.PDB. The default is the standard PDB format.

Methods: