Fix #1216

[j-wags]

• Fixes Labelling fails if v-site handler added after library charge handler #1216
• Fixes Label molecules with v-sites only works if sites are last #1047
• Update docstrings/documentation, if applicable
• Lint codebase
• Update changelog

[codecov]

Codecov Report

Merging #1290 (99c7d29) into master (27ef1d7) will decrease coverage by 0.11%.
The diff coverage is 100.00%.

❗ Current head 99c7d29 differs from pull request most recent head b35f883. Consider uploading reports for the commit b35f883 to get more accurate results

[mattwthompson]

This passes the repros in #1216 and #1047, but we should add a test. The issues are roughly duplicates so I one test will suffice.

The parameters in #1047 aren't supported verbatim in after the rework so #1216 is probably quicker to throw in. (I didn't look into this further, it seems tangential to the focus of the fix.)

(openff-dev) [openff-toolkit] git checkout 0.10.6                                           7:18:28  ☁  2af5b53a ☂
Previous HEAD position was 2af5b53a Use `packaging.version` to manage SMIRNOFF section versions (#1279)
HEAD is now at 37d6806b Fix #1283 (#1284)
(openff-dev) [openff-toolkit] python 1047.py                                                7:18:32  ☁  37d6806b ☂
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
<openff.toolkit.topology.topology.ValenceDict object at 0x162a67370>
<openff.toolkit.topology.topology.ValenceDict object at 0x162c5db80>
<openff.toolkit.topology.topology.TagSortedDict object at 0x162c5dbe0>
[<openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler._Match object at 0x162c5dfa0>]
Traceback (most recent call last):
  File "/Users/mattthompson/software/openff-toolkit/1047.py", line 58, in <module>
    print(force_field.label_molecules(Molecule.from_smiles("CF").to_topology()))
  File "/Users/mattthompson/software/openff-toolkit/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1513, in label_molecules
    m.parameter_type for m in matches[match]
TypeError: list indices must be integers or slices, not _Match
(openff-dev) [openff-toolkit] python 1216.py                                                7:18:35  ☁  37d6806b ☂
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
<openff.toolkit.topology.topology.ValenceDict object at 0x164799580>
[<openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler._Match object at 0x16478d0a0>]
Traceback (most recent call last):
  File "/Users/mattthompson/software/openff-toolkit/1216.py", line 45, in <module>
    print(force_field.label_molecules(Molecule.from_smiles("CF").to_topology()))
  File "/Users/mattthompson/software/openff-toolkit/openff/toolkit/typing/engines/smirnoff/forcefield.py", line 1513, in label_molecules
    m.parameter_type for m in matches[match]
TypeError: list indices must be integers or slices, not _Match
(openff-dev) [openff-toolkit] git checkout fix-1216                                         7:18:39  ☁  37d6806b ☂
Previous HEAD position was 37d6806b Fix #1283 (#1284)
Switched to branch 'fix-1216'
(openff-dev) [openff-toolkit] python 1047.py                                                7:18:48  ☁  fix-1216 ☂
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
[{'Constraints': <openff.toolkit.topology.topology.ValenceDict object at 0x1629ec910>, 'Electrostatics': <openff.toolkit.topology.topology.ValenceDict object at 0x162d0dac0>, 'ChargeIncrementModel': <openff.toolkit.topology.topology.TagSortedDict object at 0x1629ec1c0>, 'VirtualSites': {(0,): [<VirtualSiteType with smirks: [#6:1][#9:2]  epsilon: 0.0 kcal/mol  type: BondCharge  match: all_permutations  distance: 1.0 A  outOfPlaneAngle: None  inPlaneAngle: None  charge_increment1: 0.2 e  charge_increment2: 0.1 e  sigma: 1.0 A  name: EP  >]}, 'vdW': <openff.toolkit.topology.topology.ValenceDict object at 0x1629ec6a0>}]
(openff-dev) [openff-toolkit] python 1216.py                                                7:18:51  ☁  fix-1216 ☂
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
[{'Electrostatics': <openff.toolkit.topology.topology.ValenceDict object at 0x164f3d130>, 'VirtualSites': {(0,): [<VirtualSiteType with smirks: [#6:1][#9:2]  epsilon: 0.0 kcal/mol  type: BondCharge  match: all_permutations  distance: 1.0 A  outOfPlaneAngle: None  inPlaneAngle: None  charge_increment1: 0.2 e  charge_increment2: 0.1 e  sigma: 1.0 A  name: EP  >]}, 'LibraryCharges': {(0, 1, 2, 3, 4): <LibraryChargeType with smirks: [F:2][C:1]([H:3])([H:4])([H:5])  charge1: 0.3 e  charge2: -0.15 e  charge3: -0.05 e  charge4: -0.05 e  charge5: -0.05 e  >, (0, 1, 2, 4, 3): <LibraryChargeType with smirks: [F:2][C:1]([H:3])([H:4])([H:5])  charge1: 0.3 e  charge2: -0.15 e  charge3: -0.05 e  charge4: -0.05 e  charge5: -0.05 e  >, (0, 1, 3, 2, 4): <LibraryChargeType with smirks: [F:2][C:1]([H:3])([H:4])([H:5])  charge1: 0.3 e  charge2: -0.15 e  charge3: -0.05 e  charge4: -0.05 e  charge5: -0.05 e  >, (0, 1, 3, 4, 2): <LibraryChargeType with smirks: [F:2][C:1]([H:3])([H:4])([H:5])  charge1: 0.3 e  charge2: -0.15 e  charge3: -0.05 e  charge4: -0.05 e  charge5: -0.05 e  >, (0, 1, 4, 2, 3): <LibraryChargeType with smirks: [F:2][C:1]([H:3])([H:4])([H:5])  charge1: 0.3 e  charge2: -0.15 e  charge3: -0.05 e  charge4: -0.05 e  charge5: -0.05 e  >, (0, 1, 4, 3, 2): <LibraryChargeType with smirks: [F:2][C:1]([H:3])([H:4])([H:5])  charge1: 0.3 e  charge2: -0.15 e  charge3: -0.05 e  charge4: -0.05 e  charge5: -0.05 e  >}}]
(openff-dev) [openff-toolkit] cat 1*y                                                       7:18:55  ☁  fix-1216 ☂
from openff.toolkit.topology import Molecule
from openff.toolkit.typing.engines.smirnoff import ForceField
from openmm import unit as simtk_unit

# first build tip4p water with vsites before vdw
force_field = ForceField()
constraint_handler = force_field.get_parameter_handler("Constraints")
# Keep the H-O bond length fixed at 0.9572 angstroms.
constraint_handler.add_parameter(
    {"smirks": "[#1:1]-[#8X2H2+0:2]-[#1]", "distance": 0.9572 * simtk_unit.angstrom}
)
# Keep the H-O-H angle fixed at 104.52 degrees.
constraint_handler.add_parameter(
    {"smirks": "[#1:1]-[#8X2H2+0]-[#1:2]", "distance": 1.5139 * simtk_unit.angstrom}
)

force_field.get_parameter_handler("Electrostatics")

force_field.get_parameter_handler(
    "ChargeIncrementModel",
    {"version": "0.3", "partial_charge_method": "formal_charge"},
)
from openff.toolkit.typing.engines.smirnoff import ParameterList

virtual_site_handler = force_field.get_parameter_handler("VirtualSites")
virtual_site_handler.add_parameter(
    {
        "smirks": "[#6:1][#9:2]",
        "name": "EP",
        "type": "BondCharge",
        "distance": 1.0 * simtk_unit.angstrom,
        "match": "all_permutations",
        "charge_increment1": 0.2 * simtk_unit.elementary_charge,
        "charge_increment2": 0.1 * simtk_unit.elementary_charge,
        "sigma": 1.0 * simtk_unit.angstrom,
        "epsilon": 0.0 * simtk_unit.kilocalorie_per_mole,
    }
)
# Currently required due to OpenFF issue #884
virtual_site_handler._parameters = ParameterList(virtual_site_handler._parameters)

vdw_handler = force_field.get_parameter_handler("vdW")
vdw_handler.add_parameter(
    {
        "smirks": "[#6:1][#9:2]",
        "epsilon": 0.0 * simtk_unit.kilojoule_per_mole,
        "sigma": 1.0 * simtk_unit.angstrom,
    }
)
vdw_handler.add_parameter(
    {
        "smirks": "[#6:2][#9:1]",
        "epsilon": 0.155 * simtk_unit.kilocalorie_per_mole,
        "sigma": 3.15365 * simtk_unit.angstroms,
    }
)

print(force_field.label_molecules(Molecule.from_smiles("CF").to_topology()))
from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.topology import Molecule
from openff.toolkit.typing.engines.smirnoff.parameters import (
    LibraryChargeHandler,
    VirtualSiteHandler
)
from simtk import unit as simtk_unit

force_field = ForceField()
force_field.get_parameter_handler("Electrostatics")

vsite_handler: VirtualSiteHandler = force_field.get_parameter_handler(
    "VirtualSites"
)
vsite_handler.add_parameter(
    {
        "smirks": "[#6:1][#9:2]",
        "name": "EP",
        "type": "BondCharge",
        "distance": 1.0 * simtk_unit.angstrom,
        "match": "all_permutations",
        "charge_increment1": 0.2 * simtk_unit.elementary_charge,
        "charge_increment2": 0.1 * simtk_unit.elementary_charge,
        "sigma": 1.0 * simtk_unit.angstrom,
        "epsilon": 0.0 * simtk_unit.kilocalorie_per_mole,
    }
)

library_handler: LibraryChargeHandler = force_field.get_parameter_handler(
    "LibraryCharges"
)
library_handler.add_parameter(
    {
        "smirks": "[F:2][C:1]([H:3])([H:4])([H:5])",
        "charge": [
            0.3 * simtk_unit.elementary_charge,
            -0.15 * simtk_unit.elementary_charge,
            -0.05 * simtk_unit.elementary_charge,
            -0.05 * simtk_unit.elementary_charge,
            -0.05 * simtk_unit.elementary_charge
        ]
    }
)

print(force_field.label_molecules(Molecule.from_smiles("CF").to_topology()))

[j-wags]

Thanks @mattwthompson - I will add a test for this and then merge.