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Update ParmEd converter for new components #45

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merged 16 commits into from
Nov 17, 2020
Merged

Update ParmEd converter for new components #45

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c0229a9
INTEROP: Update ParmEd converter for new components
mattwthompson Nov 11, 2020
b186b99
ENH: Better handling of box data
mattwthompson Nov 11, 2020
4ee0d76
INTEROP: Fix parsing of partial charges in ParmEd conversion
mattwthompson Nov 11, 2020
98b4146
TST: Update interoperability testing functions
mattwthompson Nov 12, 2020
3a0bb81
LINT: Flake8
mattwthompson Nov 12, 2020
c6b8d8d
TST: Fix false positives in InterMol tests
mattwthompson Nov 12, 2020
1490e98
INTEROP: Overhaul ParmEd conversions
mattwthompson Nov 12, 2020
14bb7b6
TST: Treat everything dependent on temperature as flaky
mattwthompson Nov 12, 2020
2f84806
ENH: Update Potential to allow int parameter-like data
mattwthompson Nov 13, 2020
7fc98fa
ENH: Store intramolecular scaling factors in non-bonded handlers
mattwthompson Nov 13, 2020
dd786d5
INTEROP: Improvements to ParmEd conversion
mattwthompson Nov 13, 2020
d4f2a56
ENH: More ParmEd conversion changes
mattwthompson Nov 16, 2020
f0f2a0a
ENH: Clear matches/potentials when assigning new pairs
mattwthompson Nov 16, 2020
fbd9956
Merge remote-tracking branch 'upstream/master' into parmed-2
mattwthompson Nov 17, 2020
a28c7ff
LINT: Cleanup
mattwthompson Nov 17, 2020
530261f
MAIN: goanpeca/setup-miniconda@v1 -> conda-incubator/setup-miniconda@v2
mattwthompson Nov 17, 2020
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ENH: Clear matches/potentials when assigning new pairs
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@mattwthompson
mattwthompson committed Nov 16, 2020
commit f0f2a0ac951d69fe4bf3b5307274f45e029a3082
4 changes: 4 additions & 0 deletions openff/system/components/smirnoff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@ def store_matches(self, parameter_handler: BondHandler, topology: Topology) -> N
and unique potential identifiers

"""
if self.slot_map:
self.slot_map = dict()
matches = parameter_handler.find_matches(topology)
for key, val in matches.items():
self.slot_map[key] = val.parameter_type.smirks
Expand All @@ -39,6 +41,8 @@ def store_potentials(self, parameter_handler: BondHandler) -> None:
identifiers and their associated Potential objects

"""
if self.potentials:
self.potentials = dict()
for smirks in self.slot_map.values():
parameter_type = parameter_handler.get_parameter({"smirks": smirks})[0]
potential = Potential(
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