Permit fits with virtual sites

devtools/conda-envs/test_env.yaml

@@ -28,4 +28,4 @@ dependencies:
  - openff-evaluator-base >= 0.4.1
  - pint =0.20
  # - openff-recharge
- # - openeye-toolkits (Don't have a license file to use with GH Actions.)
+ - openeye-toolkits

src/smirnoffio.py

@@ -249,7 +249,27 @@ def smirnoff_update_pgrads(target):
 
 class SMIRNOFF(OpenMM):
 
- """ Derived from Engine object for carrying out OpenMM calculations that use the SMIRNOFF force field. """
+ """
+ Derived from Engine object for carrying out OpenMM calculations that use the SMIRNOFF force field.
+
+ Parameters
+ ----------
+ name : str
+ ffxml : str
+ pdb : str
+ mol :
+ mol2 : list[str]
+ mol : Molecule
+ coords : str
+ platname : string
+ precision : string
+ nonbonded_cutoff
+ mmopts : dict
+ vsite_bonds : list
+ implicit_solvent : string
+ restrain_k : float
+ freeze_atoms : list
+ """
 
  def __init__(self, name="openmm", **kwargs):
  self.valkwd = ['ffxml', 'pdb', 'mol2', 'platname', 'precision', 'mmopts', 'vsite_bonds', 'implicit_solvent', 'restrain_k', 'freeze_atoms']
@@ -419,8 +439,8 @@ def prepare(self, pbc=False, mmopts={}, **kwargs):
 
  n_virtual_sites = 0
  self._has_virtual_sites = False
- if 'VirtualSites' in interchange.handlers:
- n_virtual_sites = len(interchange['VirtualSites'].slot_map)
+ if 'VirtualSites' in interchange.collections:
+ n_virtual_sites = len(interchange['VirtualSites'].key_map)
  if n_virtual_sites > 0:
  self._has_virtual_sites = True
 
@@ -504,15 +524,6 @@ def update_simulation(self, **kwargs):
  # delattr(self, 'simulation')
  # self.vsprm = vsprm.copy()
 
- has_vsites = False
- for particle_idx in range(self.system.getNumParticles()):
- if self.system.isVirtualSite(particle_idx):
- has_vsites = True
-
- if has_vsites:
- raise Exception("ForceBalance can't currently handle SMIRNOFF vsites. "
- "Downgrade to ForceBalance 1.9.3 or earlier to handle those.")
-
  if hasattr(self, 'simulation'):
  UpdateSimulationParameters(self.system, self.simulation)
  else:

src/tests/files/opc/dimer.mol2

@@ -0,0 +1,21 @@
+@<TRIPOS>MOLECULE
+*****
+ 8 5 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+ 1 O 11.9600 8.3530 7.6660 O.3 1 HOH1 0.0000
+ 2 H 11.8800 7.4390 7.3960 H 0 HOH0 0.0000
+ 3 H 11.5470 8.8500 6.9600 H 0 HOH0 0.0000
+ 4 M 10.0920 10.1310 9.5470 Du 1 HOH1 0.0000
+ 5 O 9.3160 9.6510 9.8370 O.3 1 HOH1 0.0000
+ 6 H 10.7430 9.4520 9.3730 H 1 HOH1 0.0000
+ 7 H 11.8930 8.2960 7.5330 H 2 UNK2 0.0000
+ 8 M 10.0750 9.9730 9.5630 Du 1 HOH1 0.0000
+@<TRIPOS>BOND
+ 1 1 2 1
+ 2 1 3 1
+ 3 4 5 1
+ 4 5 8 1
+ 5 6 8 1

src/tests/files/opc/dimer.pdb

@@ -0,0 +1,13 @@
+REMARK 1 CREATED WITH OPENMM 8.1, 2023-12-05
+CRYST1 93.604 93.604 93.604 90.00 90.00 90.00 P 1 1 
+HETATM 1 O HOH A 1 11.960 8.353 7.666 1.00 0.00 O 
+HETATM 2 H1 HOH A 1 11.880 7.439 7.396 1.00 0.00 H 
+HETATM 3 H2 HOH A 1 11.547 8.850 6.960 1.00 0.00 H 
+HETATM 4 EP HOH A 1 10.092 10.131 9.547 1.00 0.00 EP 
+TER 5 HOH A 1
+HETATM 6 O HOH B 1 9.316 9.651 9.837 1.00 0.00 O 
+HETATM 7 H1 HOH B 1 10.743 9.452 9.373 1.00 0.00 H 
+HETATM 8 H2 HOH B 1 11.893 8.296 7.533 1.00 0.00 H 
+HETATM 9 EP HOH B 1 10.075 9.973 9.563 1.00 0.00 EP 
+TER 10 HOH B 1
+END