Merge pull request #178 from swails/master

Support gzip and bzip2 compression for StateDataReporter (based on filename extension) and other small fixes

wrappers/python/simtk/openmm/app/element.py

@@ -203,3 +203,8 @@ ununtrium =      Element(113, "ununtrium",      "Uut", 284*daltons)
 ununquadium =    Element(114, "ununquadium",    "Uuq", 289*daltons)
 ununpentium =    Element(115, "ununpentium",    "Uup", 288*daltons)
 ununhexium =     Element(116, "ununhexium",     "Uuh", 292*daltons)
+
+# Aliases to recognize common alternative spellings. Both the '==' and 'is'
+# relational operators will work with any chosen name
+sulphur = sulfur
+aluminium = aluminum

wrappers/python/simtk/openmm/app/internal/pdbstructure.py

@@ -436,7 +436,7 @@ class Chain(object):
         self._finalize()
 
     def get_residue(self, residue_number, insertion_code=' '):
-        return residues_by_num_icode[str(residue_number) + insertion_code]
+        return self.residues_by_num_icode[str(residue_number) + insertion_code]
 
     def __contains__(self, residue_number):
         return self.residues_by_number.__contains__(residue_number)
@@ -916,7 +916,6 @@ if __name__=='__main__':
     import doctest, sys
     doctest.testmod(sys.modules[__name__])
 
-    import sys
     import os
     import gzip
     import re

wrappers/python/simtk/openmm/app/statedatareporter.py

@@ -31,9 +31,10 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
+import bz2
+import gzip
 import simtk.openmm as mm
 import simtk.unit as unit
-from simtk.openmm.app import PDBFile
 import math
 
 class StateDataReporter(object):
@@ -67,6 +68,13 @@ class StateDataReporter(object):
         self._reportInterval = reportInterval
         self._openedFile = isinstance(file, str)
         if self._openedFile:
+            # Detect the desired compression scheme from the filename extension
+            # and open all files unbuffered
+            if file.endswith('.gz'):
+                self._out = gzip.GzipFile(fileobj=open(file, 'wb', 0))
+            elif file.endswith('.bz2'):
+                self._out = bz2.BZ2File(file, 'w', 0)
+            else:
                 self._out = open(file, 'w', 0)
         else:
             self._out = file
@@ -109,7 +117,10 @@ class StateDataReporter(object):
             self._initializeConstants(simulation)
             headers = self._constructHeaders()
             print >>self._out, '#"%s"' % ('"'+self._separator+'"').join(headers)
+            try:
                 self._out.flush()
+            except AttributeError:
+                pass
             self._hasInitialized = True
 
         # Check for errors.
@@ -120,7 +131,10 @@ class StateDataReporter(object):
 
         # Write the values.
         print >>self._out, self._separator.join(str(v) for v in values)
+        try:
             self._out.flush()
+        except AttributeError:
+            pass
 
     def _constructReportValues(self, simulation, state):
         """Query the simulation for the current state of our observables of interest.