Fix tests YamlBuilder
@@ -367,7 +367,7 @@ def test_validation_correct_solvents():
{'nonbonded_method': 'NoCutoff', 'implicit_solvent': 'OBC2'},
{'nonbonded_method': 'CutoffPeriodic', 'nonbonded_cutoff': '9*angstroms',
'clearance': '9*angstroms', 'positive_ion': 'Na+', 'negative_ion': 'Cl-'},
- {'implicit_solvent': 'OBC2', 'implicit_solvent_salt_conc': '1.0*(nano*mole)/liter'},
+ {'implicit_solvent': 'OBC2', 'implicit_solvent_salt_conc': '1.0*nanomolar'},
{'nonbonded_method': 'PME', 'clearance': '3*angstroms', 'ewald_error_tolerance': 0.001},
]
for solvent in solvents:
@@ -764,9 +764,12 @@ def test_clashing_atoms():
prmtop = openmm.app.AmberPrmtopFile(os.path.join(system_dir, 'complex.prmtop'))
inpcrd = openmm.app.AmberInpcrdFile(os.path.join(system_dir, 'complex.inpcrd'))
positions = inpcrd.getPositions(asNumpy=True).value_in_unit(unit.angstrom)
- atom_indices = pipeline.find_components(prmtop.createSystem(), prmtop.topology, 'resname TOL')
- benzene_pos2 = positions.take(atom_indices['receptor'], axis=0)
- toluene_pos2 = positions.take(atom_indices['ligand'], axis=0)
+ topography = Topography(prmtop.topology, ligand_atoms='resname TOL')
+ benzene_pos2 = positions.take(topography.receptor_atoms, axis=0)
+ toluene_pos2 = positions.take(topography.ligand_atoms, axis=0)
+ # atom_indices = pipeline.find_components(prmtop.createSystem(), prmtop.topology, 'resname TOL')
+ # benzene_pos2 = positions.take(atom_indices['receptor'], axis=0)
+ # toluene_pos2 = positions.take(atom_indices['ligand'], axis=0)
# Test that clashes are resolved in the system
min_dist, max_dist = pipeline.compute_min_max_dist(toluene_pos2, benzene_pos2)
