Merge pull request #700 from kain88-de/pdb-charge-alignment

PDB charges are not written anymore.
MDAnalysis · Feb 8, 2016 · 41c86ed · 41c86ed
2 parents 8bd70bf + b9d2e14
commit 41c86ed
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Showing 3 changed files with 11 additions and 21 deletions.
diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -40,6 +40,7 @@ Changes
   * Short TRZ titles are striped from trailing spaces. A friendlier error
     message is raised when the TRZ writer is asked to write a title longer
     than 80 characters. (Issue #689)
+  * PDB doesn't save charge information anymore
 
 Fixes
 

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
@@ -672,33 +672,23 @@ class PrimitivePDBWriter(base.Writer):
        Initial support for multi-frame PDB files.
 
     .. versionchanged:: 0.7.6
-       The *multiframe* keyword was added to select the writing mode. The writing
-       of bond information (CONECT_ records) is now disabled by default but can be
-       enabled with the *bonds* keyword.
+       The *multiframe* keyword was added to select the writing mode. The
+       writing of bond information (CONECT_ records) is now disabled by default
+       but can be enabled with the *bonds* keyword.
 
     .. versionchanged:: 0.11.0
        Frames now 0-based instead of 1-based
+
+    .. versionchanged:: 0.14.0
+       PDB doesn't save charge information
+
     """
-    #          1         2         3         4         5         6         7         8
-    # 123456789.123456789.123456789.123456789.123456789.123456789.123456789.123456789.
-    # ATOM__seria nameAres CressI   xxxxxxxxyyyyyyyyzzzzzzzzOCCUPAtempft          elCH
-    # ATOM  %5d   %-4s %-3s %4d %1s %8.3f   %8.3f   %8.3f   %6.2f %6.2f           %2s
-    #                 %1s  %1s                                                      %2d
-    #            =        =      ===                                    ==========
-    # ATOM  %5d %-4s%1s%-3s %1s%4d%1s   %8.3f%8.3f%8.3f%6.2f%6.2f          %2s%2d
-    # ATOM  %(serial)5d %(name)-4s%(altLoc)1s%(resName)-3s %(chainID)1s%(resSeq)4d%(iCode)1s   %(x)8.3f%(y)8.3f%(
-    # z)8.3f%(occupancy)6.2f%(tempFactor)6.2f          %(element)2s%(charge)2d
-
-    # Strict PDB format:
-    #fmt = {'ATOM':   "ATOM  %(serial)5d %(name)-4s%(altLoc)1s%(resName)-3s %(chainID)1s%(resSeq)4d%(iCode)1s   %(
-    # x)8.3f%(y)8.3f%(z)8.3f%(occupancy)6.2f%(tempFactor)6.2f          %(element)2s%(charge)2d\n",
-    # PDB format as used by NAMD/CHARMM: 4-letter resnames and segID, altLoc ignored
     fmt = {
         'ATOM': (
             "ATOM  {serial:5d} {name:<4s}{altLoc:<1s}{resName:<4s}"
             "{chainID:1s}{resSeq:4d}{iCode:1s}"
             "   {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
-            "{tempFactor:6.2f}      {segID:<4s}{element:>2s}{charge:.2f}\n"),
+            "{tempFactor:6.2f}      {segID:<4s}{element:>2s}\n"),
         'REMARK': "REMARK     {0}\n",
         'COMPND': "COMPND    {0}\n",
         'HEADER': "HEADER    {0}\n",
@@ -1130,7 +1120,6 @@ def _write_timestep(self, ts, multiframe=False):
             vals['tempFactor'] = temp if temp is not None else 0.0
             vals['segID'] = segid[:4]
             vals['element'] = guess_atom_element(atom.name.strip())[:2]
-            vals['charge'] = 0
 
             # .. _ATOM: http://www.wwpdb.org/documentation/format32/sect9.html
             self.pdbfile.write(self.fmt['ATOM'].format(**vals))

diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -739,5 +739,5 @@ def test_atomname_alignment(self):
 
     def test_atomtype_alignment(self):
         result_line = ("ATOM      1  H5T GUA R   1       7.974   6.430   9.561"
-                       "  1.00  0.00      RNAA H0.00\n")
-        assert_equal(result_line, self.writtenstuff[4])
+                       "  1.00  0.00      RNAA H\n")
+        assert_equal(self.writtenstuff[4], result_line)