mtools's People
mtools's Issues
Allow post-processing functions to accept mdtraj.Trajectory objects
Generalize reading itp files
Currently itp files are read in with the assumption that the file name is the same as the resname, which will fail for water, and most code written by others, molecules with multiple abbreviations, e.g.
emim, NULL = read_charges('../../forcefields/emim.itp')
tfsi, NULL = read_charges('../../forcefields/Tf2N.itp')
charges = dict(emim, **tfsi)
This may require reading the topology file.
PBC accounting in pairing module
From what I can tell, PBC are currently not respected.
https://github.com/mattwthompson/mtools/blob/master/mtools/pairing.py#L74
[Feature request] Testing the unit testing framework
Preferred syntax:
import mtools as mattwthompson
from mattwthompson.unit_tests import all_unit_tests
mattwthompson.tests_unit_tests(tests_to_test=all_unit_tests)
make_comtrj is too slow
In hindsight it should be written to do all frames of a given residue at once instead of doing a residue loop inside of a frame loop
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