From 818da844e44951930fdb2dd710df4ed041445e88 Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Wed, 24 Jan 2018 17:02:13 +0000
Subject: [PATCH] Fixed several bugs related to topology info in MDDataAccess
---
.../nomadcore/md_data_access/MDDataAccess.py | 27 ++++++++++++-------
1 file changed, 18 insertions(+), 9 deletions(-)
diff --git a/common/python/nomadcore/md_data_access/MDDataAccess.py b/common/python/nomadcore/md_data_access/MDDataAccess.py
index 9e9d0e3..09fddf2 100644
--- a/common/python/nomadcore/md_data_access/MDDataAccess.py
+++ b/common/python/nomadcore/md_data_access/MDDataAccess.py
@@ -1062,7 +1062,7 @@ class MDDataAccess(object):
if self.topohandler is None:
if self.topofile:
- self.check_topology_format_support("traj")
+ self.check_topology_format_support()
if self.trajhandler is None:
self.check_trajectory_format_support("traj")
@@ -1288,9 +1288,8 @@ class MDDataAccess(object):
filetrajformat = re.sub('[.]', '', chkformat)
trajhandler_check = None
if self.topohandler is not None:
- numatoms = self.get_natoms_from_topo(topocode="pymolfile")
- if(isinstance(self.topohandler, pym.OpenMolfile)
- or isinstance(self.topohandler, pym.OpenMolfile.topology)):
+ numatoms = self.get_natoms_from_topo(topocode=self.topocode)
+ if isinstance(self.topohandler, pym.OpenMolfile):
molfile_traj = pym.OpenMolfile(chkfile, file_format=filetrajformat, topology=self.topohandler, silent=False)
elif numatoms is not None:
if numatoms > 0:
@@ -1409,7 +1408,7 @@ class MDDataAccess(object):
self.natoms = numatoms
usedefault=False
break
- except (AttributeError, IOError, OSError, ValueError, TypeError):
+ except (AttributeError, IOError, OSError, ValueError, TypeError, KeyError):
try:
universe = mda_u.Universe(self.topohandler, self.trajfile, format=mdanalysis_format)
trajhandler = None
@@ -1447,8 +1446,8 @@ class MDDataAccess(object):
self.natoms = numatoms
usedefault=False
break
- #except (AttributeError, IOError, OSError, ValueError, TypeError):
- except IOError:
+ except (IOError, ValueError, TypeError, KeyError):
+ #except IOError:
pass
# if topology handler is not a MDAnalysis Universe
# or is not initialized, we can try accessing only
@@ -2799,11 +2798,21 @@ class MDDataAccess(object):
if __name__ == "__main__":
topo_file = sys.argv[1]
- traj_file = sys.argv[2]
+ topo_format = sys.argv[2]
+ traj_file = sys.argv[3]
+ traj_format = sys.argv[4]
MDdata = MDDataAccess()
MDdata.trajfile = traj_file
MDdata.topofile = topo_file
- #MDdata.interfaceorder = ["mdanalysis", "pymolfile", "mdtraj", "ase"]
+ if 'None' in topo_format:
+ pass
+ else:
+ MDdata.topoformat = topo_format
+ if 'None' in traj_format:
+ pass
+ else:
+ MDdata.trajformat = traj_format
+ MDdata.interfaceorder = ["mdanalysis", "pymolfile", "mdtraj", "ase"]
#MDdata.interfaceorder = ["pymolfile", "mdanalysis", "mdtraj", "ase"]
MDdata.interfacematch = False
traj_iterator = MDdata.load()
--
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