Source code for MDAnalysis.topology.ExtendedPDBParser

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"""
Extended PDB topology parser
============================

.. versionadded:: 0.8

This topology parser uses a PDB file to build a minimum internal structure
representation (list of atoms). The only difference from
:mod:`~MDAnalysis.topology.PDBParser` is that this parser reads a
non-standard PDB-like format in which residue numbers can be five digits
instead of four.

The topology reader reads a PDB file line by line and ignores atom numbers but
reads residue numbers up to 99,999 correctly. If you have systems containing at
least 100,000 residues then you need to use a different file format that can
handle such residue numbers.

See Also
--------
* :mod:`MDAnalysis.topology.PDBParser`
* :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader`
* :class:`MDAnalysis.core.universe.Universe`


Classes
-------

.. autoclass:: ExtendedPDBParser
   :members:
   :inherited-members:

"""

from . import PDBParser




[docs]
class ExtendedPDBParser(PDBParser.PDBParser):
    """Parser that handles non-standard "extended" PDB file.

    Extended PDB files (MDAnalysis format specifier *XPDB*) may contain residue
    sequence numbers up to 99,999 by utilizing the insertion character field of
    the PDB standard.

    Creates a Topology with the following Attributes (if present):
     - serials
     - names
     - altLocs
     - chainids
     - tempfactors
     - occupancies
     - resids
     - resnames
     - segids
     - elements
     - bonds
     - formalcharges

   .. note::

      By default, atomtypes and masses will be guessed on Universe creation.
      This may change in release 3.0.
      See :ref:`Guessers` for more information.


    See Also
    --------
    :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader`

    .. versionadded:: 0.8
    """
    format = 'XPDB'