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Fix spectator support #1233

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merged 2 commits into from
Sep 12, 2023
Merged

Fix spectator support #1233

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9ad2cac
fix spectator support. Enabling test.
ijpulidos Sep 8, 2023
c34c734
Test to run on GPU CI.
ijpulidos Sep 11, 2023
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8 changes: 1 addition & 7 deletions perses/app/relative_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -326,12 +326,6 @@ 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()

# Select barostat
NONPERIODIC_NONBONDED_METHODS = [app.NoCutoff, app.CutoffNonPeriodic]
if pressure is not None:
Expand Down Expand Up @@ -365,7 +359,7 @@ def __init__(self,
spectator_mol = generate_unique_atom_names(spectator_mol)
self._spectator_molecules.append(spectator_mol)
# add this to a small molecule register
self._molecules.append(Molecule.from_openeye(spectator_mol,allow_undefined_stereo=True))
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))
Expand Down
10 changes: 4 additions & 6 deletions perses/tests/test_relative_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,11 +204,11 @@ def warn(*args, **kwargs):

# TODO: Check output

#@skipIf(running_on_github_actions, "Skip analysis test on GH Actions. SLOW")
@pytest.mark.skip(reason="Skip analysis test on GH Actions. SLOW")
# Running it on gpu CI -- slow
@pytest.mark.gpu_needed
def test_run_bace_spectator():
"""
Ensure that we can instantiate and run a repex relative free energy calculation the cdk2 ligands in vacuum
Ensure that we can setup a simulation of BACE system with an spectator
"""
# Enter a temporary directory
from perses.tests.utils import enter_temp_directory
Expand Down Expand Up @@ -242,14 +242,12 @@ def warn(*args, **kwargs):
setup_options[parameter] = os.path.join(setup_directory, setup_options[parameter])
# only one spectator
setup_options['spectators'] = [ os.path.join(setup_directory, setup_options['spectators'][0])]
for parameter in ['trajectory_directory', 'trajectory_prefix', 'save_setup_pickle_as']:
for parameter in ['trajectory_directory', 'save_setup_pickle_as']:
setup_options[parameter] = os.path.join(tmpdirname, setup_options[parameter])


# Run setup
n_iterations = 2
setup_dict = setup_relative_calculation.run_setup(setup_options)
setup_dict['hybrid_samplers']['complex'].run(n_iterations=n_iterations)

# test that there is TLA in the complex system
found_tla = False
Expand Down