Merge branch 'bugfix-inconsistent_behavior_between_dcd_like_converters' into 'develop'

Bugfix inconsistent behavior between dcd like converters

See merge request !32

CHANGELOG

@@ -2,6 +2,7 @@ version 1.2.0
 --------------
 * ADDED issue #27 Better error handling when an error occurs when running an analysis from the GUI
 * ADDED issue #10 Implemented Gromacs trajectory converter
+* FIXED issue #28 The time step is now part of the settings for DCD based converters
 * FIXED issue #26 Data can be deleted from the GUI
 * FIXED issue #25 The plotter is now compliant with all matplotlib versions (was crashing on ubuntu-xenial)
 * FIXED issue #25 The plotter is now compliant with all matplotlib versions (was crashing on ubuntu-xenial)

MDANSE/Framework/Jobs/DCDConverter.py

@@ -229,7 +229,8 @@ class DCDFile(FortranBinaryFile, dict):
             # This file was generated by CHARMM, or by NAMD > 2.5, with the angle
             # cosines of the periodic cell angles written to the DCD file.       
             # This formulation improves rounding behavior for orthogonal cells   
-            # so that the angles end up at precisely 90 degrees, unlike acos().            
+            # so that the angles end up at precisely 90 degrees, unlike acos(). 
+            # See https://github.com/MDAnalysis/mdanalysis/wiki/FileFormats for info           
             if numpy.all(abs(unitCell[3:]) <= 1):
                 unitCell[3:] = PI_2 - numpy.arcsin(unitCell[3:])
             else:
@@ -280,8 +281,9 @@ class DCDConverter(Converter):
     settings = collections.OrderedDict()
     settings['pdb_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.pdb')})
     settings['dcd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.dcd')})
-    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
+    settings['time_step'] = ('float', {'default':1.0,'label':"Time step (ps)"})    
     settings['fold'] = ('boolean', {'default':False,'label':"Fold coordinates in to box"})    
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
 
     def initialize(self):
         """
@@ -343,7 +345,7 @@ class DCDConverter(Converter):
             self._universe.foldCoordinatesIntoBox()
                                                    
         # The current time.
-        t = (index+1)*self.configuration["dcd_file"]["instance"]['time_step']
+        t = (index+1)*self.configuration["time_step"]["value"]
 
         # Store a snapshot of the current configuration in the output trajectory.
         self._snapshot(data={'time': t})