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IAlibayatravitz
IAlibay
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atravitz
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Update cookbooks for v1.7 (#237)
* Update cookbooks for v1.7 * not sure why it didn't delete the first time * review comments * bump version * rerun choose_protocol * rerun create_alchemical_network --------- Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
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‎cookbook/bespoke_parameters_showcase.ipynb‎

Lines changed: 32 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -49,23 +49,31 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# create the OpenFE RBFE protocol using our bespoke force field\n",
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"import copy\n",
58+
"from openff.units import unit\n",
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"from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol\n",
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"import openfe\n",
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"\n",
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"\n",
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"# create the default protocol settings\n",
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"settings = RelativeHybridTopologyProtocol.default_settings()\n",
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"base_settings = RelativeHybridTopologyProtocol.default_settings()\n",
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"\n",
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"# add our new force field as a string\n",
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"# this avoids the need to move the file around when executing the transformations\n",
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"settings.forcefield_settings.small_molecule_forcefield = bespoke_force_field.to_string()\n",
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"base_settings.forcefield_settings.small_molecule_forcefield = bespoke_force_field.to_string()\n",
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"\n",
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"# we create a copy of the settings for the complex leg so that we can reduce the solvation cutoff\n",
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"complex_settings = copy.deepcopy(base_settings)\n",
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"complex_settings.solvation_settings.solvent_padding = 1 * unit.nanometer\n",
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"\n",
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"# create the protocols\n",
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"solvent_protocol = RelativeHybridTopologyProtocol(base_settings)\n",
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"complex_protocol = RelativeHybridTopologyProtocol(complex_settings)\n",
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"\n",
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"# create the protocol\n",
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"protocol = RelativeHybridTopologyProtocol(settings)\n",
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"\n",
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"# create the solvent and protein components\n",
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"solvent = openfe.SolventComponent()\n",
@@ -82,8 +90,11 @@
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" 'solvent': solvent}\n",
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"\n",
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" if leg == 'complex':\n",
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" protocol = complex_protocol\n",
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" sysA_dict['protein'] = protein\n",
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" sysB_dict['protein'] = protein\n",
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" else:\n",
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" protocol = solvent_protocol\n",
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"\n",
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" # we don't have to name objects, but it can make things (like filenames) more convenient\n",
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" sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n",
@@ -94,7 +105,7 @@
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" transformation = openfe.Transformation(\n",
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" stateA=sysA,\n",
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" stateB=sysB,\n",
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" mapping={'ligand': mapping},\n",
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" mapping=mapping,\n",
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" protocol=protocol, # use protocol created above\n",
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" name=f\"{prefix}{sysA.name}_{sysB.name}\"\n",
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" )\n",
@@ -112,7 +123,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -123,7 +134,7 @@
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"\n",
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"# then we write out each transformation\n",
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"for transformation in network.edges:\n",
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" transformation.dump(transformation_dir / f\"{transformation.name}.json\")"
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" transformation.to_json(transformation_dir / f\"{transformation.name}.json\")"
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]
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},
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{
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"source": [
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"# Recap\n",
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"\n",
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"So to recap the workflow can be reduced to the following steps:\n\n",
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"So to recap the workflow can be reduced to the following steps:\n",
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"\n",
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"- Plan the RBFE network\n",
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"- Create a single SMIRNOFF style force field with all of the bespoke parameters for the network using the BespokeFit `combine` CLI\n",
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"- Store the force field as a string in the OpenFE protocol under the `settings.forcefield_settings.small_molecule_forcefield` field\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "asapdiscovery",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"version": "3.12.11"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {
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"state": {},
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"version_major": 2,
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"version_minor": 0
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}
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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"nbformat_minor": 4
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}

‎cookbook/choose_protocol.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -178,64 +178,82 @@
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"text": [
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"{'alchemical_settings': {'endstate_dispersion_correction': False,\n",
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" 'explicit_charge_correction': False,\n",
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" 'explicit_charge_correction_cutoff': <Quantity(0.8, 'nanometer')>,\n",
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" 'explicit_charge_correction_cutoff': {'unit': 'nanometer',\n",
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" 'val': 0.8},\n",
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" 'softcore_LJ': 'gapsys',\n",
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" 'softcore_alpha': 0.85,\n",
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" 'turn_off_core_unique_exceptions': False,\n",
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" 'use_dispersion_correction': False},\n",
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" 'engine_settings': {'compute_platform': None, 'gpu_device_index': None},\n",
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" 'engine_settings': {'compute_platform': 'cuda', 'gpu_device_index': None},\n",
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" 'forcefield_settings': {'constraints': 'hbonds',\n",
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" 'forcefields': ['amber/ff14SB.xml',\n",
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" 'amber/tip3p_standard.xml',\n",
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" 'amber/tip3p_HFE_multivalent.xml',\n",
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" 'amber/phosaa10.xml'],\n",
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" 'hydrogen_mass': 3.0,\n",
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" 'nonbonded_cutoff': <Quantity(1.0, 'nanometer')>,\n",
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" 'nonbonded_cutoff': {'unit': 'nanometer', 'val': 0.9},\n",
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" 'nonbonded_method': 'PME',\n",
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" 'rigid_water': True,\n",
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" 'small_molecule_forcefield': 'openff-2.1.1'},\n",
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" 'integrator_settings': {'barostat_frequency': <Quantity(25.0, 'timestep')>,\n",
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" 'small_molecule_forcefield': 'openff-2.2.1'},\n",
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" 'integrator_settings': {'barostat_frequency': {'unit': 'timestep',\n",
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" 'val': 25.0},\n",
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" 'constraint_tolerance': 1e-06,\n",
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" 'langevin_collision_rate': <Quantity(1.0, '1 / picosecond')>,\n",
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" 'langevin_collision_rate': {'unit': '1 / picosecond',\n",
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" 'val': 1.0},\n",
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" 'n_restart_attempts': 20,\n",
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" 'reassign_velocities': False,\n",
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" 'remove_com': False,\n",
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" 'timestep': <Quantity(4.0, 'femtosecond')>},\n",
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" 'timestep': {'unit': 'femtosecond', 'val': 4.0}},\n",
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" 'lambda_settings': {'lambda_functions': 'default', 'lambda_windows': 11},\n",
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" 'output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
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" 'output_settings': {'checkpoint_interval': {'unit': 'nanosecond', 'val': 1.0},\n",
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" 'checkpoint_storage_filename': 'checkpoint.chk',\n",
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" 'forcefield_cache': 'db.json',\n",
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" 'output_filename': 'simulation.nc',\n",
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" 'output_indices': 'not water',\n",
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" 'output_structure': 'hybrid_system.pdb',\n",
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" 'positions_write_frequency': <Quantity(100.0, 'picosecond')>,\n",
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" 'positions_write_frequency': {'unit': 'picosecond',\n",
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" 'val': 100.0},\n",
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" 'velocities_write_frequency': None},\n",
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" 'partial_charge_settings': {'nagl_model': None,\n",
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" 'number_of_conformers': None,\n",
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" 'off_toolkit_backend': 'ambertools',\n",
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" 'partial_charge_method': 'am1bcc'},\n",
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" 'protocol_repeats': 3,\n",
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" 'simulation_settings': {'early_termination_target_error': <Quantity(0.0, 'kilocalorie_per_mole')>,\n",
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" 'equilibration_length': <Quantity(1.0, 'nanosecond')>,\n",
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" 'simulation_settings': {'early_termination_target_error': {'unit': 'kilocalorie_per_mole',\n",
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" 'val': 0.0},\n",
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" 'equilibration_length': {'unit': 'nanosecond',\n",
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" 'val': 1.0},\n",
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" 'minimization_steps': 5000,\n",
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" 'n_replicas': 11,\n",
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" 'production_length': <Quantity(5.0, 'nanosecond')>,\n",
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" 'real_time_analysis_interval': <Quantity(250.0, 'picosecond')>,\n",
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" 'real_time_analysis_minimum_time': <Quantity(500.0, 'picosecond')>,\n",
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" 'production_length': {'unit': 'nanosecond',\n",
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" 'val': 5.0},\n",
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" 'real_time_analysis_interval': {'unit': 'picosecond',\n",
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" 'val': 250.0},\n",
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" 'real_time_analysis_minimum_time': {'unit': 'picosecond',\n",
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" 'val': 500.0},\n",
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" 'sampler_method': 'repex',\n",
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" 'sams_flatness_criteria': 'logZ-flatness',\n",
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" 'sams_gamma0': 1.0,\n",
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" 'time_per_iteration': <Quantity(1.0, 'picosecond')>},\n",
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" 'solvation_settings': {'box_shape': 'cube',\n",
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" 'time_per_iteration': {'unit': 'picosecond',\n",
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" 'val': 2.5}},\n",
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" 'solvation_settings': {'box_shape': 'dodecahedron',\n",
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" 'box_size': None,\n",
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" 'box_vectors': None,\n",
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" 'number_of_solvent_molecules': None,\n",
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" 'solvent_model': 'tip3p',\n",
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" 'solvent_padding': <Quantity(1.2, 'nanometer')>},\n",
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" 'solvent_padding': {'unit': 'nanometer', 'val': 1.5}},\n",
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" 'thermo_settings': {'ph': None,\n",
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" 'pressure': <Quantity(0.986923267, 'standard_atmosphere')>,\n",
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" 'pressure': {'unit': 'bar', 'val': 1},\n",
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" 'redox_potential': None,\n",
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" 'temperature': <Quantity(298.15, 'kelvin')>}}\n"
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" 'temperature': {'unit': 'kelvin', 'val': 298.15}}}\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Users/atravitz/micromamba/envs/openfe-conda/lib/python3.11/site-packages/gufe/settings/models.py:30: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/\n",
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" pprint.pprint(self.dict())\n"
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]
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}
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],
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" ],\n",
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" \n",
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" # Small molecule force field to use with OpenMM template generator:\n",
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" small_molecule_forcefield='openff-2.1.1',\n",
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" small_molecule_forcefield='openff-2.2.1',\n",
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" \n",
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" # Nonbonded settings\n",
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" nonbonded_method='PME', # Particle Mesh Ewald for long range electrostatics\n",
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" nonbonded_cutoff=1.0 * unit.nm, # Cut off Lennard-Jones interactions beyond 1 nm\n",
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" nonbonded_cutoff=0.9 * unit.nm, # Cut off Lennard-Jones interactions beyond 0.9 nm\n",
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" ),\n",
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" thermo_settings=equil_rfe_settings.ThermoSettings(\n",
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" temperature=298.15 * unit.kelvin, # Set thermostat temperature\n",
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" ),\n",
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" solvation_settings=equil_rfe_settings.OpenMMSolvationSettings(\n",
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" solvent_model='tip3p', # Solvent model to generate starting coords\n",
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" solvent_padding=1.2 * unit.nm, # Total distance between periodic image starting coords\n",
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" box_shape = 'cube', # Cubic water box\n",
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" solvent_padding=1.5 * unit.nm, # Minimum padding distance from the solute\n",
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" box_shape = 'dodecahedron', # Dodecahedron water box\n",
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" box_size = None, # Size of the water box\n",
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" box_vectors = None, # Box vectors\n",
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" number_of_solvent_molecules = None, # Number of solvent molecules\n",
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" # Alchemical Space Sampling settings\n",
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" n_replicas=11, # Number of replicas sampling alchemical space\n",
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" sampler_method='repex', # Sample lambda with Hamiltonian Replica Exchange\n",
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" time_per_iteration=1*unit.ps, # Time interval between state sampling (MCMC) attempts\n",
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" time_per_iteration=2.5*unit.ps, # Time interval between state sampling (MCMC) attempts\n",
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" \n",
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" # SAMS sampling settings (used if sampler_method='sams')\n",
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" sams_flatness_criteria='logZ-flatness', # Criteria for switch to asymptomatically optimal scheme\n",
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" early_termination_target_error=0.0*unit.kilocalorie_per_mole,\n",
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" ),\n",
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" engine_settings=equil_rfe_settings.OpenMMEngineSettings(\n",
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" compute_platform=None, # Let OpenMM choose the best platform for your hardware\n",
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" compute_platform=\"cuda\", # Force the usage of a CUDA device for compute\n",
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" ),\n",
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" integrator_settings=equil_rfe_settings.IntegratorSettings(\n",
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" timestep=4 * unit.femtosecond, # Integration timestep\n",
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"source": [
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"Unlike `ProtocolSettings`, a `Protocol` instance is immutable. The only way to safely change the settings of a `Protocol` is to recreate it from the modified `ProtocolSettings` object."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "91e223bc-5dc7-4533-ba5d-da112809be9a",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.10"
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"version": "3.11.14"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

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