Merge pull request #832 from MDAnalysis/issue-777-remove-BioPDB

remove Bio.PDBParser (Issue #777)

package/CHANGELOG

@@ -36,6 +36,7 @@ Enhancements
   * Added read-only property giving Universe init kwargs (Issue #292)
 
 Fixes
+
   * rmsd now returns proper value when given array of weights (Issue #814)
   * change_release now finds number and dev (Issue #776)
   * test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
@@ -45,11 +46,17 @@ Fixes
   * GRO files with an incomplete set of velocities can now be read (Issue #820)
 
 Changes
-
   * Generalized contact analysis class `Contacts` added. (Issue #702)
+  * Removed Bio.PDBParser and sloppy structure builder and all of
+    MDAnalysis.coordinates.pdb (Issue #777)
+  * PDB parsers/readers/writers replaced by "permissive"/"primitive"
+    counterparts (formerly known as PrimitivePDBReader); the
+    'permissive' keyword for Universe is now ignored and only the
+    native MDAnalysis PDBReader is being used (Issue #777)
 
 Deprecations (Issue #599)
-
+  * Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/
+    Writer/Parser (Issue #777)
   * Deprecated all `get_*` and `set_*` methods of Groups.
   * Deprecation warnings for accessing atom attributes from Residue,
     ResidueGroup, Segment, SegmentGroup. Will not be present or will

package/MDAnalysis/analysis/density.py

@@ -80,6 +80,10 @@
    :members:
    :inherited-members:
 
+.. deprecated:: 0.15.0
+    The "permissive" flag is not used anymore (and effectively
+    defaults to True); it will be completely removed in 0.16.0.
+
 """
 from __future__ import print_function
 from six.moves import range
@@ -501,7 +505,7 @@ def current_coordinates():
     pm = ProgressMeter(u.trajectory.n_frames, interval=interval, quiet=quiet,
                        format="Histogramming %(n_atoms)6d atoms in frame "
                        "%(step)5d/%(numsteps)d  [%(percentage)5.1f%%]\r")
-    start, stop, step = u.trajectory.check_slice_indices(start, stop, step)                    
+    start, stop, step = u.trajectory.check_slice_indices(start, stop, step)
     for ts in u.trajectory[start:stop:step]:
         if update_selection:
            group = u.select_atoms(atomselection)
@@ -515,8 +519,8 @@ def current_coordinates():
 
         h[:], edges[:] = np.histogramdd(coord, bins=bins, range=arange, normed=False)
         grid += h  # accumulate average histogram
-   
-    
+
+
     n_frames = len(range(start, stop, step))
     grid /= float(n_frames)
 
@@ -727,11 +731,7 @@ def __init__(self, pdb, delta=1.0, atomselection='resname HOH and name O',
         :Arguments:
 
           pdb
-            PDB file or :class:`MDAnalysis.Universe`; a PDB is read with the
-            simpl PDB reader. If the Bio.PDB reader is required, either set
-            the *permissive_pdb_reader* flag to ``False`` in
-            :data:`MDAnalysis.core.flags` or supply a Universe
-            that was created with the `permissive` = ``False`` keyword.
+            PDB file or :class:`MDAnalysis.Universe`;
           atomselection
             selection string (MDAnalysis syntax) for the species to be analyzed
           delta

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -208,7 +208,7 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 
   import MDAnalysis.analysis.hbonds
 
-  u = MDAnalysis.Universe(PSF, PDB, permissive=True)
+  u = MDAnalysis.Universe(PSF, PDB)
   h = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u, 'protein', 'resname TIP3', distance=3.0, angle=120.0)
   h.run()
 

package/MDAnalysis/analysis/helanal.py

@@ -466,7 +466,7 @@ def stats(some_list):
     return [list_mean, list_sd, list_abdev]
 
 
-def helanal_main(pdbfile, selection="name CA", start=None, end=None, ref_axis=None, permissive=False):
+def helanal_main(pdbfile, selection="name CA", start=None, end=None, ref_axis=None):
     """Simple HELANAL run on a single frame PDB/GRO.
 
     Computed data are returned as a dict and also logged at level INFO to the
@@ -503,7 +503,7 @@ def helanal_main(pdbfile, selection="name CA", start=None, end=None, ref_axis=No
        *MDAnalysis.analysis.helanal* instead of being printed to stdout.
     """
 
-    universe = MDAnalysis.Universe(pdbfile, permissive=permissive)
+    universe = MDAnalysis.Universe(pdbfile)
     if not (start is None and end is None):
         if start is None:
             start = universe.atoms[0].resid