Add small molecule repex consistency tests

perses/app/relative_setup.py

@@ -78,7 +78,7 @@ def __init__(self,
 
         Parameters
         ----------
-        ligand_input : str
+        ligand_input : str or list of str
             the name of the ligand file (any openeye supported format)
             this can either be an .sdf or list of .sdf files, or a list of SMILES strings
         forcefield_files : list of str
@@ -303,6 +303,12 @@ def __init__(self,
         self._ligand_md_topology_new = md.Topology.from_openmm(self._ligand_topology_new)
         _logger.info(f"Created mdtraj topologies for both ligands.")
 
+        # We must generate the complex topology and positions before the SystemGenerator is created because if the
+        # receptor is a mol2, it must be added to mol_list, which is use to create self._molecules, which is fed to the SystemGenerator
+        if 'complex' in phases:
+            _logger.info(f"setting up complex phase...")
+            self._setup_complex_phase(protein_pdb_filename,receptor_mol2_filename,mol_list)
+
         # Select barostat
         NONPERIODIC_NONBONDED_METHODS = [app.NoCutoff, app.CutoffNonPeriodic]
         if pressure is not None:
@@ -318,7 +324,7 @@ def __init__(self,
 
         # Create openforcefield Molecule objects for old and new molecules
         from openff.toolkit.topology import Molecule
-        molecules = [ Molecule.from_openeye(oemol,allow_undefined_stereo=True) for oemol in [self._ligand_oemol_old, self._ligand_oemol_new] ]
+        self._molecules = [Molecule.from_openeye(oemol, allow_undefined_stereo=True) for oemol in mol_list]
 
         # Handle spectator molecules
         if self._spectator_filenames is not None:
@@ -335,7 +341,7 @@ def __init__(self,
                 spectator_mol = generate_unique_atom_names(spectator_mol)
                 self._spectator_molecules.append(spectator_mol)
                 # add this to a small molecule register
-                molecules.append(Molecule.from_openeye(spectator_mol,allow_undefined_stereo=True))
+                self._molecules.append(Molecule.from_openeye(spectator_mol,allow_undefined_stereo=True))
                 self._spectator_positions.append(extractPositionsFromOEMol(spectator_mol))
                 spectator_topology = forcefield_generators.generateTopologyFromOEMol(spectator_mol)
                 self._spectator_md_topologies.append(md.Topology.from_openmm(spectator_topology))
@@ -351,7 +357,7 @@ def __init__(self,
                                       periodic_forcefield_kwargs = {'nonbondedMethod': self._nonbonded_method})
         else:
             self._system_generator = SystemGenerator(forcefields=forcefield_files, barostat=barostat, forcefield_kwargs=forcefield_kwargs,
-                                                     small_molecule_forcefield=small_molecule_forcefield, molecules=molecules, cache=small_molecule_parameters_cache, periodic_forcefield_kwargs = {'nonbondedMethod': self._nonbonded_method})
+                                                     small_molecule_forcefield=small_molecule_forcefield, molecules=self._molecules, cache=small_molecule_parameters_cache, periodic_forcefield_kwargs = {'nonbondedMethod': self._nonbonded_method})
         _logger.info("successfully created SystemGenerator to create ligand systems")
 
         _logger.info(f"executing SmallMoleculeSetProposalEngine...")

perses/data/host-guest/a1.sybyl.mol2

@@ -0,0 +1,67 @@
+@<TRIPOS>MOLECULE
+A1
+   27    29     1     0     0
+SMALL
+No Charge or Current Charge
+
+
+@<TRIPOS>ATOM
+      1 C1           7.0000     7.0750    17.8360 C.3        2 A1       -0.060033
+      2 C2           4.6200     7.7880    18.0300 C.3        2 A1        0.150800
+      3 C3           5.1260     5.4360    17.3950 C.3        2 A1       -0.060033
+      4 C4           5.5620     7.3250    15.7700 C.3        2 A1       -0.060033
+      5 C5           6.0290     7.9800    18.6280 C.3        2 A1       -0.086067
+      6 C6           6.5490     5.6030    17.9710 C.3        2 A1       -0.071733
+      7 C7           6.9870     7.4880    16.3460 C.3        2 A1       -0.071733
+      8 C8           4.1480     6.3330    18.1870 C.3        2 A1       -0.086067
+      9 C9           4.5950     8.2360    16.5550 C.3        2 A1       -0.086067
+     10 C10          5.1130     5.8540    15.9070 C.3        2 A1       -0.071733
+     11 O1           3.6560     8.5860    18.7650 O.3        2 A1       -0.593800
+     12 H1           8.0250     7.1980    18.2550 H          2 A1        0.050367
+     13 H2           4.8080     4.3730    17.4870 H          2 A1        0.050367
+     14 H3           5.5560     7.6180    14.6960 H          2 A1        0.050367
+     15 H4           6.3500     9.0340    18.5690 H          2 A1        0.049367
+     16 H5           6.0340     7.7120    19.6990 H          2 A1        0.049367
+     17 H6           7.2470     4.9290    17.4460 H          2 A1        0.041867
+     18 H7           6.5690     5.2950    19.0320 H          2 A1        0.041867
+     19 H8           7.6920     6.8740    15.7640 H          2 A1        0.041867
+     20 H9           7.3280     8.5330    16.2350 H          2 A1        0.041867
+     21 H10          3.1210     6.2050    17.8100 H          2 A1        0.049367
+     22 H11          4.1220     6.0500    19.2550 H          2 A1        0.049367
+     23 H12          3.5760     8.1740    16.1390 H          2 A1        0.049367
+     24 H13          4.8910     9.2950    16.4650 H          2 A1        0.049367
+     25 H14          4.1010     5.7240    15.4840 H          2 A1        0.041867
+     26 H15          5.7800     5.1970    15.3210 H          2 A1        0.041867
+     27 H16          4.0340     9.4700    18.9770 H          2 A1        0.397000
+@<TRIPOS>BOND
+     1     1     5 1   
+     2     1     6 1   
+     3     1     7 1   
+     4     1    12 1   
+     5     2     5 1   
+     6     2     8 1   
+     7     2     9 1   
+     8     2    11 1   
+     9     3     6 1   
+    10     3     8 1   
+    11     3    10 1   
+    12     3    13 1   
+    13     4     7 1   
+    14     4     9 1   
+    15     4    10 1   
+    16     4    14 1   
+    17     5    15 1   
+    18     5    16 1   
+    19     6    17 1   
+    20     6    18 1   
+    21     7    19 1   
+    22     7    20 1   
+    23     8    21 1   
+    24     8    22 1   
+    25     9    23 1   
+    26     9    24 1   
+    27    10    25 1   
+    28    10    26 1   
+    29    11    27 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 A1          1 TEMP              0 ****  ****    0 ROOT

perses/data/host-guest/a2.sybyl.mol2

@@ -0,0 +1,71 @@
+@<TRIPOS>MOLECULE
+A2
+   29    31     1     0     0
+SMALL
+No Charge or Current Charge
+
+
+@<TRIPOS>ATOM
+      1 C1           6.2630     5.8810    17.7440 C.3        2 A2       -0.057700
+      2 C2           3.8870     6.6370    17.5750 C.3        2 A2        0.137200
+      3 C3           5.4000     6.9240    15.6130 C.3        2 A2       -0.057700
+      4 C4           5.7070     8.3430    17.6780 C.3        2 A2       -0.057700
+      5 C5           4.8130     5.5640    18.1840 C.3        2 A2       -0.091400
+      6 C6           6.3400     5.8520    16.2030 C.3        2 A2       -0.084400
+      7 C7           6.6560     7.2780    18.2690 C.3        2 A2       -0.084400
+      8 C8           3.9450     6.6130    16.0370 C.3        2 A2       -0.091400
+      9 C9           4.2540     8.0320    18.1150 C.3        2 A2       -0.091400
+     10 C10          5.7970     8.3190    16.1370 C.3        2 A2       -0.084400
+     11 N1           2.4380     6.2850    18.0010 N.4        2 A2       -0.846600
+     12 H1           6.9410     5.1080    18.1730 H          2 A2        0.087700
+     13 H2           5.4650     6.9090    14.5010 H          2 A2        0.087700
+     14 H3           5.9940     9.3510    18.0550 H          2 A2        0.087700
+     15 H4           4.7510     5.5540    19.2880 H          2 A2        0.063700
+     16 H5           4.5360     4.5490    17.8420 H          2 A2        0.063700
+     17 H6           7.3750     6.0280    15.8610 H          2 A2        0.067200
+     18 H7           6.0640     4.8510    15.8220 H          2 A2        0.067200
+     19 H8           7.6990     7.5160    17.9960 H          2 A2        0.067200
+     20 H9           6.6200     7.3030    19.3730 H          2 A2        0.067200
+     21 H10          3.2630     7.3600    15.5870 H          2 A2        0.063700
+     22 H11          3.6290     5.6310    15.6300 H          2 A2        0.063700
+     23 H12          3.5750     8.8200    17.7340 H          2 A2        0.063700
+     24 H13          4.1750     8.0730    19.2180 H          2 A2        0.063700
+     25 H14          5.1410     9.0940    15.7020 H          2 A2        0.067200
+     26 H15          6.8220     8.5720    15.8100 H          2 A2        0.067200
+     27 H16          2.3120     6.3790    19.0330 H          2 A2        0.453800
+     28 H17          2.2160     5.2980    17.7500 H          2 A2        0.453800
+     29 H18          1.7410     6.8920    17.5430 H          2 A2        0.453800
+@<TRIPOS>BOND
+     1     1     5 1   
+     2     1     6 1   
+     3     1     7 1   
+     4     1    12 1   
+     5     2     5 1   
+     6     2     8 1   
+     7     2     9 1   
+     8     2    11 1   
+     9     3     6 1   
+    10     3     8 1   
+    11     3    10 1   
+    12     3    13 1   
+    13     4     7 1   
+    14     4     9 1   
+    15     4    10 1   
+    16     4    14 1   
+    17     5    15 1   
+    18     5    16 1   
+    19     6    17 1   
+    20     6    18 1   
+    21     7    19 1   
+    22     7    20 1   
+    23     8    21 1   
+    24     8    22 1   
+    25     9    23 1   
+    26     9    24 1   
+    27    10    25 1   
+    28    10    26 1   
+    29    11    27 1   
+    30    11    28 1   
+    31    11    29 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 A2          1 TEMP              0 ****  ****    0 ROOT