From 120b10349a053c9b9d7cdccd589f1943ea4931dc Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Thu, 15 Jun 2017 16:11:25 +0100
Subject: [PATCH] Handle trajectories that don't return box dims with MDTraj
---
pycgtool/framereader.py | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/pycgtool/framereader.py b/pycgtool/framereader.py
index c843f77..337d909 100644
--- a/pycgtool/framereader.py
+++ b/pycgtool/framereader.py
@@ -39,9 +39,10 @@ def get_frame_reader(top, traj=None, frame_start=0, name=None):
for name, reader in readers.items(): # Return first reader that accepts given files
try:
return reader(top, traj, frame_start)
- except (UnsupportedFormatException, ImportError):
+ except (UnsupportedFormatException, ImportError) as e:
+ print(e)
continue
- raise UnsupportedFormatException("None of the available readers support the trajector format provided")
+ raise UnsupportedFormatException("None of the available readers support the trajector format provided, {0} {1}".format(top, traj))
class FrameReader(metaclass=abc.ABCMeta):
@@ -65,6 +66,8 @@ class FrameReader(metaclass=abc.ABCMeta):
def read_frame_number(self, number, frame):
try:
time, coords, box = self._read_frame_number(number)
+ if box is None:
+ box = np.zeros(3)
frame.time = time
frame.box = box
@@ -114,6 +117,10 @@ class FrameReaderSimpleTraj(FrameReader):
raise FileNotFoundError(trajname) from e
e.args = ("Error opening file '{0}'".format(trajname),)
raise
+ except Exception as e:
+ if "extension" in repr(e) and "not supported" in repr(e):
+ raise UnsupportedFormatException from e
+ raise
if self._traj.numatoms != self.num_atoms:
raise UnsupportedFormatException
@@ -233,7 +240,10 @@ class FrameReaderMDTraj(FrameReader):
"""
Read next frame from XTC using mdtraj library.
"""
- return self._traj.time[number], self._traj.xyz[number], self._traj.unitcell_lengths[number]
+ try:
+ return self._traj.time[number], self._traj.xyz[number], self._traj.unitcell_lengths[number]
+ except TypeError:
+ return self._traj.time[number], self._traj.xyz[number], None
class FrameReaderMDAnalysis(FrameReader):
--
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