From c8f36bb6f624cafb9738a5fcf01c4b0d7bfe1731 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Wed, 25 May 2016 16:19:53 +0100
Subject: [PATCH] Better error messages when xtc fails
---
pycgtool/frame.py | 25 ++++++++++++++++++++++---
1 file changed, 22 insertions(+), 3 deletions(-)
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index c0a9ba1..53578c3 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -5,6 +5,8 @@ The Frame class may contain multiple Residues which may each contain multiple At
Both Frame and Residue are iterable. Residue is indexable with either atom numbers or names.
"""
+import os
+
import numpy as np
from simpletraj import trajectory
@@ -15,6 +17,15 @@ from .parsers.cfg import CFG
np.seterr(all="raise")
+try:
+ raise FileNotFoundError
+except FileNotFoundError:
+ pass
+except NameError:
+ class FileNotFoundError(OSError):
+ pass
+
+
class Atom:
"""
Hold data for a single atom
@@ -112,9 +123,17 @@ class Frame:
self.numframes += 1
if xtc is not None:
- self.xtc = trajectory.XtcTrajectory(xtc)
- assert self.xtc.numatoms == self.natoms
- self.numframes += self.xtc.numframes
+ try:
+ self.xtc = trajectory.XtcTrajectory(xtc)
+ except OSError as e:
+ if not os.path.isfile(xtc):
+ raise FileNotFoundError(xtc) from e
+ e.args = ("Error opening file '{0}'".format(xtc),)
+ raise
+ else:
+ if self.xtc.numatoms != self.natoms:
+ raise AssertionError("Number of atoms does not match between gro and xtc files.")
+ self.numframes += self.xtc.numframes
if itp is not None:
self._parse_itp(itp)
--
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