deepdrivemd.sim.openmm.config
- pydantic settings deepdrivemd.sim.openmm.config.OpenMMConfig
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{ "title": "OpenMMConfig", "description": "Auto-generates configuration file for MD tasks.", "type": "object", "properties": { "experiment_directory": { "title": "Experiment Directory", "default": "set_by_deepdrivemd", "env_names": "{'experiment_directory'}", "type": "string", "format": "path" }, "stage_idx": { "title": "Stage Idx", "default": 0, "env_names": "{'stage_idx'}", "type": "integer" }, "task_idx": { "title": "Task Idx", "default": 0, "env_names": "{'task_idx'}", "type": "integer" }, "output_path": { "title": "Output Path", "default": "set_by_deepdrivemd", "env_names": "{'output_path'}", "type": "string", "format": "path" }, "node_local_path": { "title": "Node Local Path", "default": "set_by_deepdrivemd", "env_names": "{'node_local_path'}", "type": "string", "format": "path" }, "pdb_file": { "title": "Pdb File", "default": "set_by_deepdrivemd", "env_names": "{'pdb_file'}", "type": "string", "format": "path" }, "initial_pdb_dir": { "title": "Initial Pdb Dir", "env_names": "{'initial_pdb_dir'}", "type": "string", "format": "path" }, "solvent_type": { "default": "implicit", "env_names": "{'solvent_type'}", "allOf": [ { "$ref": "#/definitions/MDSolvent" } ] }, "top_suffix": { "title": "Top Suffix", "default": ".top", "env_names": "{'top_suffix'}", "type": "string" }, "simulation_length_ns": { "title": "Simulation Length Ns", "default": 10, "env_names": "{'simulation_length_ns'}", "type": "number" }, "report_interval_ps": { "title": "Report Interval Ps", "default": 50, "env_names": "{'report_interval_ps'}", "type": "number" }, "dt_ps": { "title": "Dt Ps", "default": 0.002, "env_names": "{'dt_ps'}", "type": "number" }, "temperature_kelvin": { "title": "Temperature Kelvin", "default": 310.0, "env_names": "{'temperature_kelvin'}", "type": "number" }, "heat_bath_friction_coef": { "title": "Heat Bath Friction Coef", "default": 1.0, "env_names": "{'heat_bath_friction_coef'}", "type": "number" }, "wrap": { "title": "Wrap", "default": false, "env_names": "{'wrap'}", "type": "boolean" }, "reference_pdb_file": { "title": "Reference Pdb File", "env_names": "{'reference_pdb_file'}", "type": "string", "format": "path" }, "openmm_selection": { "title": "Openmm Selection", "default": [ "CA" ], "env_names": "{'openmm_selection'}", "type": "array", "items": { "type": "string" } }, "mda_selection": { "title": "Mda Selection", "default": "protein and name CA", "env_names": "{'mda_selection'}", "type": "string" }, "threshold": { "title": "Threshold", "default": 8.0, "env_names": "{'threshold'}", "type": "number" }, "contact_map": { "title": "Contact Map", "default": true, "env_names": "{'contact_map'}", "type": "boolean" }, "point_cloud": { "title": "Point Cloud", "default": true, "env_names": "{'point_cloud'}", "type": "boolean" }, "fraction_of_contacts": { "title": "Fraction Of Contacts", "default": true, "env_names": "{'fraction_of_contacts'}", "type": "boolean" }, "in_memory": { "title": "In Memory", "default": true, "env_names": "{'in_memory'}", "type": "boolean" } }, "required": [ "initial_pdb_dir" ], "definitions": { "MDSolvent": { "title": "MDSolvent", "description": "An enumeration.", "enum": [ "implicit", "explicit" ], "type": "string" } } }
- Config
extra: str = allow
- Fields
- field contact_map: bool = True
- Validated by
- field dt_ps: float = 0.002
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- field fraction_of_contacts: bool = True
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- field heat_bath_friction_coef: float = 1.0
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- field in_memory: bool = True
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- field mda_selection: str = 'protein and name CA'
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- field openmm_selection: List[str] = ['CA']
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- field point_cloud: bool = True
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- field reference_pdb_file: Optional[pathlib.Path] = PydanticUndefined
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- field report_interval_ps: float = 50
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- field simulation_length_ns: float = 10
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- field solvent_type: deepdrivemd.sim.openmm.config.OpenMMConfig.MDSolvent = MDSolvent.implicit
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- field temperature_kelvin: float = 310.0
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- field threshold: float = 8.0
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- field top_suffix: Optional[str] = '.top'
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- field wrap: bool = False
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- validator explicit_solvent_requires_top_suffix » all fields