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Add compatibility with openforcefield 0.7.0 #121

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merged 6 commits into from
Jun 24, 2020
Merged

Add compatibility with openforcefield 0.7.0 #121

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0dbba06
Add compatibility with openforcefield 0.7.0
jchodera Jun 24, 2020
2f83069
Fix tests
jchodera Jun 24, 2020
5506300
Fix handling of Molecule.total_charge
jchodera Jun 24, 2020
654e2f3
Fix tests
jchodera Jun 24, 2020
a6670a1
Fix test failing with openforcefield < 0.7.0
jchodera Jun 24, 2020
3ee5655
Update changelog
jchodera Jun 24, 2020
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3 changes: 3 additions & 0 deletions README.md
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Expand Up @@ -269,6 +269,9 @@ See the corresponding directories for information on how to use the provided con

# Changelog

## 0.7.3 Bugfix release: Compatibility with openforcefield toolkit 0.7.0 and auto-detection of installed openforcefield force fields
* [(PR #121)](https://github.com/openmm/openmmforcefields/pull/121) Add compatibility with [`openforcefield 0.7.0`](https://github.com/openforcefield/openforcefield/releases/tag/0.7.0)

## 0.7.3 Bugfix release: Compatibility with openforcefield toolkit 0.7.0 and auto-detection of installed openforcefield force fields
* [(PR #119)](https://github.com/openmm/openmmforcefields/pull/119) Handle `None` partial charges in openforcefield `Molecule` objects (needed in `openforcefield` toolkit 0.7.0)
* [(PR #120)](https://github.com/openmm/openmmforcefields/pull/120) Auto-detect installed SMIRNOFF force fields
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6 changes: 5 additions & 1 deletion openmmforcefields/generators/template_generators.py
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Expand Up @@ -570,6 +570,10 @@ def generate_residue_template(self, molecule, residue_atoms=None):

# Compute net formal charge
net_charge = molecule.total_charge
from simtk import unit
if type(net_charge) != unit.Quantity:
# openforcefield toolkit < 0.7.0 did not return unit-bearing quantity
net_charge = float(net_charge) * unit.elementary_charge
_logger.debug(f'Total charge is {net_charge}')

# Compute partial charges if required
Expand Down Expand Up @@ -621,7 +625,7 @@ def generate_residue_template(self, molecule, residue_atoms=None):
residue_charge = 0.0 * unit.elementary_charge
total_charge = unit.sum(molecule.partial_charges)
sum_of_absolute_charge = unit.sum(abs(molecule.partial_charges))
charge_deficit = net_charge * unit.elementary_charge - total_charge
charge_deficit = net_charge - total_charge
if sum_of_absolute_charge / unit.elementary_charge > 0.0:
# Redistribute excess charge proportionally to absolute charge
molecule.partial_charges += charge_deficit * abs(molecule.partial_charges) / sum_of_absolute_charge
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13 changes: 9 additions & 4 deletions openmmforcefields/tests/test_template_generators.py
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Expand Up @@ -206,7 +206,7 @@ def test_charge(self):
from simtk import unit
molecule = self.molecules[0]
# Ensure partial charges are initially zero
assert np.all(molecule.partial_charges / unit.elementary_charge == 0)
assert (molecule.partial_charges is None) or np.all(molecule.partial_charges / unit.elementary_charge == 0)
# Add the molecule
generator.add_molecules(molecule)
# Create the System
Expand All @@ -231,9 +231,13 @@ def test_charge_from_molecules(self):
from simtk import unit
molecule = self.molecules[0]
charges = np.random.random([molecule.n_particles])
total_charge = molecule.total_charge
if type(total_charge) is unit.Quantity:
# Handle openforcefield >= 0.7.0
total_charge /= unit.elementary_charge
charges += (molecule.total_charge - charges.sum()) / molecule.n_particles
molecule.partial_charges = unit.Quantity(charges, unit.elementary_charge)
assert not np.all(molecule.partial_charges / unit.elementary_charge == 0)
assert (molecule.partial_charges is not None) and not np.all(molecule.partial_charges / unit.elementary_charge == 0)
# Add the molecule
generator.add_molecules(molecule)
# Create the System
Expand Down Expand Up @@ -707,7 +711,7 @@ def test_INSTALLED_FORCEFIELDS(self):
assert 'openff-1.1.0' in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
assert 'smirnoff99Frosst-1.1.0' in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS
assert 'openff_unconstrained-1.1.0' not in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS

def test_energies(self):
"""Test potential energies match between openforcefield and OpenMM ForceField"""
# DEBUG
Expand Down Expand Up @@ -753,7 +757,8 @@ def test_partial_charges_are_none(self):
from openforcefield.topology import Molecule
molecule = Molecule.from_smiles('C=O')
molecule.generate_conformers(n_conformers=1)
molecule._partial_charges = None
#molecule._partial_charges = None
assert (molecule.partial_charges is None) or np.all(molecule.partial_charges / unit.elementary_charge == 0)
# Test all supported SMIRNOFF force fields
for small_molecule_forcefield in SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS:
print(f'Testing energies for {small_molecule_forcefield}...')
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