mattwthompson / mtools Goto Github PK

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.

Preferred syntax:

import mtools as mattwthompson
from mattwthompson.unit_tests import all_unit_tests
mattwthompson.tests_unit_tests(tests_to_test=all_unit_tests)

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

From what I can tell, PBC are currently not respected.

https://github.com/mattwthompson/mtools/blob/master/mtools/pairing.py#L74