add option to specify charges and masses for .gro files

mdevaluate/__init__.py

@@ -15,7 +15,7 @@ __version__ = '22.6.dev1'
 
 
 def open(directory='', topology='*.tpr', trajectory='*.xtc', cached=False,
-         nojump=False, index_file=None):
+         nojump=False, index_file=None, charges=None, masses=None):
     """
     Open a simulation from a directory.
 
@@ -70,7 +70,8 @@ def open(directory='', topology='*.tpr', trajectory='*.xtc', cached=False,
         raise FileNotFoundError('Trajectory file could not be identified.')
         
     atom_set, frames = reader.open_with_mdanalysis(
-        top_file, traj_file, cached=cached, index_file=index_file
+        top_file, traj_file, cached=cached, index_file=index_file,
+        charges=charges, masses=masses
     )    
     coords = coordinates.Coordinates(frames, atom_subset=atom_set)
     if nojump:

mdevaluate/reader.py

@@ -34,7 +34,8 @@ class NojumpError(Exception):
 class WrongTopologyError(Exception):
     pass
 
-def open_with_mdanalysis(topology, trajectory, cached=False, index_file=None):
+def open_with_mdanalysis(topology, trajectory, cached=False, index_file=None, 
+                         charges=None, masses=None):
     """Open a the topology and trajectory with mdanalysis."""
     uni = mdanalysis.Universe(topology, trajectory, convert_units=False)
     if cached is not False:
@@ -50,8 +51,8 @@ def open_with_mdanalysis(topology, trajectory, cached=False, index_file=None):
         charges = uni.atoms.charges
         masses = uni.atoms.masses
     elif topology.endswith('.gro'):
-        charges = None
-        masses = None
+        charges = charges
+        masses = masses
     else:
         raise WrongTopologyError('Topology file should end with ".tpr" or ".gro"')
     indices = None