Commit c482b22f authored by Remi Perenon's avatar Remi Perenon

Merge branch 'bugfix-inconsistent_behavior_between_dcd_like_converters' into 'develop'

Bugfix inconsistent behavior between dcd like converters

See merge request !32
parents 13d3d99a 0fb98a17
Pipeline #4279 passed with stages
in 34 minutes and 18 seconds
...@@ -2,6 +2,7 @@ version 1.2.0 ...@@ -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 #27 Better error handling when an error occurs when running an analysis from the GUI
* ADDED issue #10 Implemented Gromacs trajectory converter * 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 #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)
* 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)
......
...@@ -229,7 +229,8 @@ class DCDFile(FortranBinaryFile, dict): ...@@ -229,7 +229,8 @@ class DCDFile(FortranBinaryFile, dict):
# This file was generated by CHARMM, or by NAMD > 2.5, with the angle # 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. # cosines of the periodic cell angles written to the DCD file.
# This formulation improves rounding behavior for orthogonal cells # 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): if numpy.all(abs(unitCell[3:]) <= 1):
unitCell[3:] = PI_2 - numpy.arcsin(unitCell[3:]) unitCell[3:] = PI_2 - numpy.arcsin(unitCell[3:])
else: else:
...@@ -280,8 +281,9 @@ class DCDConverter(Converter): ...@@ -280,8 +281,9 @@ class DCDConverter(Converter):
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['pdb_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.pdb')}) 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['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['fold'] = ('boolean', {'default':False,'label':"Fold coordinates in to box"})
settings['output_files'] = ('output_files', {'formats':["netcdf"]})
def initialize(self): def initialize(self):
""" """
...@@ -343,7 +345,7 @@ class DCDConverter(Converter): ...@@ -343,7 +345,7 @@ class DCDConverter(Converter):
self._universe.foldCoordinatesIntoBox() self._universe.foldCoordinatesIntoBox()
# The current time. # 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. # Store a snapshot of the current configuration in the output trajectory.
self._snapshot(data={'time': t}) self._snapshot(data={'time': t})
......
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