Eliminated Biopython PDB Reader/Writer and Parser (#777)

- 'permissive'=False has no effect anymore
- Added deprecation warnings for Primitive Readers/Writers and Parsers.
- Changed doc strings to eliminate references to
  BioPython Reader/Writer.
- Updated CHANGELOG to reflect changes.

package/CHANGELOG

@@ -46,6 +46,7 @@ Fixes
 
 Changes
 
+  * PDB parsers/readers/writers replaced by permissive counterparts (Issue #777)
   * Generalized contact analysis class added. (Issue #702)
 
 Deprecations (Issue #599)

package/MDAnalysis/coordinates/__init__.py

@@ -179,10 +179,8 @@
    |               |           |       | optional `netcdf4-python`_ module (coordinates and   |
    |               |           |       | velocities). Module :mod:`MDAnalysis.coordinates.TRJ`|
    +---------------+-----------+-------+------------------------------------------------------+
-   | Brookhaven    | pdb       |  r/w  | a simplified PDB format (as used in MD simulations)  |
-   | [#a]_         |           |       | is read by default; the full format can be read by   |
-   |               |           |       | supplying the `permissive=False` flag to             |
-   |               |           |       | :class:`MDAnalysis.Universe`. Multiple frames (MODEL)|
+   | Brookhaven    | pdb       |  r/w  | a relaxed PDB format (as used in MD simulations)     |
+   | [#a]_         |           |       | is read by default; Multiple frames (MODEL)          |
    |               |           |       | are supported but require the *multiframe* keyword.  |
    |               |           |       | Module :mod:`MDAnalysis.coordinates.PDB`             |
    +---------------+-----------+-------+------------------------------------------------------+
@@ -265,7 +263,7 @@
 - 2015-01-15 Timestep._init_unitcell() method added
 - 2015-06-11 Reworked Timestep init.  Base Timestep now does Vels & Forces
 - 2015-07-21 Major changes to Timestep and Reader API (release 0.11.0)
-
+- 2016-04-03 Removed references to Strict Readers for PDBS [jdetle]
 .. _Issue 49: https://github.com/MDAnalysis/mdanalysis/issues/49
 .. _Context Manager: http://docs.python.org/2/reference/datamodel.html#context-managers
 

package/MDAnalysis/coordinates/core.py

@@ -51,7 +51,8 @@ def get_reader_for(filename, permissive=False, format=None):
         filename of the input trajectory or coordinate file
     permissive : bool
         If set to ``True``, a reader is selected that is more tolerant of the
-        input (currently only implemented for PDB). [``False``]
+        input (currently a deprecated feature only implemented for PDB).
+        [``False``]
     kwargs
         Keyword arguments for the selected Reader class.
 
@@ -67,7 +68,7 @@ def get_reader_for(filename, permissive=False, format=None):
     if format is None:
         format = util.guess_format(filename)
     format = format.upper()
-    if permissive and format == 'PDB':
+    if format == 'PDB' and permissive:
         return _READERS['Permissive_PDB']
     try:
         return _READERS[format]
@@ -101,6 +102,7 @@ def reader(filename, **kwargs):
     filename : str or tuple
         filename (or tuple of filenames) of the input coordinate file
     permissive : bool
+
         If set to ``True``, a reader is selected that is more tolerant of the
         input (currently only implemented for PDB). [``False``]
     kwargs
@@ -113,8 +115,8 @@ def reader(filename, **kwargs):
     .. SeeAlso:: For trajectory formats: :class:`~DCD.DCDReader`,
        :class:`~XTC.XTCReader`, :class:`~TRR.TRRReader`,
        :class:`~XYZ.XYZReader`.  For single frame formats:
-       :class:`~CRD.CRDReader`, :class:`~PDB.PDBReader` and
-       :class:`~PDB.PrimitivePDBReader`, :class:`~GRO.GROReader`,
+       :class:`~CRD.CRDReader`, and
+       :class:`~PDB.PDBReader`, :class:`~GRO.GROReader`,
     """
     if isinstance(filename, tuple):
         Reader = get_reader_for(filename[0],

package/MDAnalysis/core/AtomGroup.py

@@ -4195,10 +4195,10 @@ def __init__(self, *args, **kwargs):
              topology) is always required.
 
           *permissive*
-             currently only relevant for PDB files: Set to ``True`` in order to ignore most errors
-             and read typical MD simulation PDB files; set to ``False`` to read with the Bio.PDB reader,
-             which can be useful for real Protein Databank PDB files. ``None``  selects the
-             MDAnalysis default (which is set in :class:`MDAnalysis.core.flags`) [``None``]
+             currently only relevant to PDBs, Readers and Writers and Parsers
+             returned by setting ::permisive = False are depecrated in favor
+             of their ::permissive = True counterparts
+
           *topology_format*
              provide the file format of the topology file; ``None`` guesses it from the file
              extension [``None``]
@@ -4260,6 +4260,9 @@ def __init__(self, *args, **kwargs):
         .. versionchanged:: 0.11.0
            Added the *is_anchor* and *anchor_name* keywords for finer behavior
            control when unpickling instances of :class:`MDAnalysis.core.AtomGroup.AtomGroup`.
+        .. versionchanged:: 0.14.1
+           *permissive* set to ``True`` and set to ``False`` both yield permissive
+           PDB readers, writers and parsers
         """
 
         from ..topology.core import get_parser_for

package/MDAnalysis/core/__init__.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- http://www.MDAnalysis.org
 # Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
@@ -390,22 +390,21 @@ def __doc__(self):
 
            >>> flags['%(name)s'] = value
 
-           The Bio.PDB reader (value=``False``) can deal with 'proper' PDB
-           files from the Protein Databank that contain special PDB features
-           such as insertion codes and it can auto-correct some common
-           mistakes; see :mod:`Bio.PDB` for details. However, Bio.PDB has been
-           known to read some simulation system PDB files **incompletely**; a
-           sure sign of problems is a warning that an atom has appeared twice
-           in a residue.
-
-           Therefore, the default for the PDB reader is ``True``, which
-           selects the "primitive" (or "permissive") reader
-           :class:`MDAnalysis.coordinates.PDB.PrimitivePDBReader`, which
+           The default for the PDB reader is ``True``, which
+           selects the (or "permissive") reader
+           :class:`MDAnalysis.coordinates.PDB.PDBReader`, which
            essentially just reads ATOM and HETATM lines and puts atoms in a
            list.
 
+           ``False`` selects the :class:
+           `MDAnalysis.coordinates.PDB.PrimitivePDBReader` which is a copy of
+           the :class:`MDAnalysis.coordinates.PDB.PDBReader` deprecated in favor
+           of its counterpart
+
            One can manually switch between the two by providing the *permissive*
            keyword to :class:`MDAnalysis.Universe`.
+
+
         """
     ),
     _Flag(

package/MDAnalysis/topology/ExtendedPDBParser.py

@@ -21,7 +21,7 @@
 
 This topology parser uses a PDB file to build a minimum internal structure
 representation (list of atoms). The only difference from
-:mod:`~MDAnalysis.topology.PrimitivePDBParser` is that this parser reads a
+: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.
 
@@ -37,7 +37,7 @@
 
 .. SeeAlso::
 
-   * :mod:`MDAnalysis.topology.PrimitivePDBParser`
+   * :mod:`MDAnalysis.topology.PDBParser`
    * :class:`MDAnalysis.coordinates.PDB.ExtendedPDBReader`
    * :class:`MDAnalysis.core.AtomGroup.Universe`
 
@@ -51,10 +51,10 @@
 """
 from __future__ import absolute_import
 
-from . import PrimitivePDBParser
+from . import PDBParser
 
 
-class ExtendedPDBParser(PrimitivePDBParser.PrimitivePDBParser):
+class ExtendedPDBParser(PDBParser.PDBParser):
     """Parser that obtains a list of atoms from an non-standard "extended" PDB file.
 
     Extended PDB files (MDAnalysis format specifier *XPDB*) may contain residue