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terminate called after throwing an instance of 'std::out_of_range'
what(): Bad index for an atom
Aborted (core dumped)
from trying to read to the end of a trajectory defined with the multipose pdb
To Reproduce
I attached an example pdb test-pose.txt (change the extension, obviously). When I try to read it like this:
import loos
from loos import pyloos
m = loos.createSystem('test-pose.pdb')
t = pyloos.Trajectory('test-pose.pdb', m)
print(len(t))
t[len(t) - 1]
I get the segfault. When I delete the last ENDMDL record, the file can be read through the final frame and the iterator exhausts normally. The issues don't arise until trying to reference the 'final' frame.
Expected behavior
Reading all 20 frames, then having the iterator know it's empty instead of thinking there are 21 and segfaulting.
LOOS version and platform
conda install 4.04
linux
Additional context
Alan and I slacked about this. It looks like the ENDMDL record queues the reader to expect another frame, but this PDB (created from a multipose sdf using openbabel) ends with:
ENDMDL
END
The text was updated successfully, but these errors were encountered:
Describe the bug
I get a:
from trying to read to the end of a trajectory defined with the multipose pdb
To Reproduce
I attached an example pdb test-pose.txt (change the extension, obviously). When I try to read it like this:
I get the segfault. When I delete the last ENDMDL record, the file can be read through the final frame and the iterator exhausts normally. The issues don't arise until trying to reference the 'final' frame.
Expected behavior
Reading all 20 frames, then having the iterator know it's empty instead of thinking there are 21 and segfaulting.
LOOS version and platform
conda install 4.04
linux
Additional context
Alan and I slacked about this. It looks like the ENDMDL record queues the reader to expect another frame, but this PDB (created from a multipose sdf using openbabel) ends with:
The text was updated successfully, but these errors were encountered: