schrodinger.application.desmond.msj_generator.workflow_params module¶

class schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None)¶

Bases: object

Parameters for the simulation. Normally, this is used to set the simulation parameters for the subjobs.

Variables

forcefield – The name of the forcefield to use.
sim_time – The simulation time for the production stage in ps.
sim_time_complex – The simulation time for the complex leg in ps
sim_time_solvent – The simulation time for the solvent leg in ps
rand_seed – The random seed.
ensemble – The ensemble, NPT or NVT.
buffer_width – The buffer width in Angstrom determines how much solvent is added to the solute. This is only used if it is larger than the default buffer width.
lambda_windows – Number of lambda replicas to use for the FEP stages.
custom_charge_mode – Set to CUSTOM_CHARGE_MODE.ASSIGN to assign custom charges. Set to CUSTOM_CHARGE_MODE.CLEAR to clear custom charges if present, without reassigning. Set to CUSTOM_CHARGE_MODE.KEEP to keep existing custom charges if present.
h_mass – Set to True to enable hydrogen mass repartitioning and False to disable it. Default is True.
concatenate – Set to True to concatenate the equilibration FEP stages. Default is True.
max_walltime – Maximum walltime in seconds before the subjobs are automatically checkpointed and restarted. The default of 0 means to not set a maximum walltime.

forcefield: str = 'S-OPLS'¶

rand_seed: int = 2014¶

ensemble: str = 'NPT'¶

buffer_width: float = 0.0¶

molecules: int = 64¶

water_model: Optional[str] = None¶

salt_concentration: Optional[float] = 0.0¶

membrane: Optional[str] = None¶

sim_time: Optional[int] = 5000¶

equilibration_time: Optional[int] = None¶

sim_time_complex: Optional[int] = None¶

sim_time_solvent: Optional[int] = None¶

sim_time_vacuum: Optional[int] = None¶

sim_time_fragment: Optional[int] = None¶

max_walltime: int = 0¶

lambda_windows: Optional[int] = None¶

custom_charge_mode: str = 'assign'¶

charged_lambda_windows: Optional[int] = None¶

core_hopping_lambda_windows: Optional[int] = None¶

h_mass: bool = True¶

concatenate: bool = True¶

skip_legs: List¶

ffbuilder: bool = False¶

modify_dihe: bool = False¶

minimize_volume: bool = False¶

rest_asl: str = 'asl: atom.%s 1'¶

ff_host: Optional[str] = None¶

ff_structure_file: Optional[str] = None¶

restraints_file: Optional[str] = None¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams(graph_file: str = '')¶

Bases: object

graph_file: str = ''¶

__init__(graph_file: str = '') → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.MapperParams(graph_file: str = '', atom_mapping: str = '', align_core_only: bool = False, ats: bool = False)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams

atom_mapping: str = ''¶

align_core_only: bool = False¶

ats: bool = False¶

__init__(graph_file: str = '', atom_mapping: str = '', align_core_only: bool = False, ats: bool = False) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>)¶

Bases: object

Parameters for the workflow that params for main job and subjobs.

sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams¶

classmethod from_dict(params: Dict[str, Any]) → schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.MapperWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MapperParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

Parameters for the mapper workflow that params for main job and subjobs.

mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MapperParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MapperParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.SmallMoleculeWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MapperParams = <factory>)¶: Bases: schrodinger.application.desmond.msj_generator.workflow_params.MapperWorkflowParams

class schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinMapperParams(graph_file: str = '', atom_mapping: str = '', align_core_only: bool = False, ats: bool = False, mp: list[str] = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.MapperParams

A data class that holds simulation parameters for metal simulations.

Variables: mp – The list of metal parameters.

mp: list[str]¶

__init__(graph_file: str = '', atom_mapping: str = '', align_core_only: bool = False, ats: bool = False, mp: list[str] = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinMapperParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

A data class that holds simulation parameters for metal simulations.

Variables: mp – The list of metal parameters.

mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinMapperParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.MetalloproteinMapperParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams(graph_file: str = '', atom_mapping: str = '', align_core_only: bool = False, ats: bool = False, solvent_asl: Optional[str] = None, mutation_filename: str = 'mutations.txt', residue_file: str = '', neighbor: Optional[int] = None, structure_file: str = '', enable_one_graph_stage: bool = False, fep_type: str = None)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.MapperParams

A data class that holds simulation parameters specific for protein FEP.

Variables

solvent_asl – ASL expression to specify the chain where the mutation(s) occur
mutation_filename – Path of text file that contains a list of protein mutations
residue_file – Path of a structure file with non-standard amino acids
neighbor – Number of residues to flank the mutated residue when creating the mutant peptides
structure_file – The filename for the structure input.
enable_one_graph_stage – If True, use CombinedProteinFepMapper stage for the graph generation, only supported for three combined protein FEP workflows. (FEP_TYPES: PRM_LIGAND_BINDING, PRM_PROTEIN_BINDING, PRM_THERMOSTABILITY)

solvent_asl: Optional[str] = None¶

mutation_filename: str = 'mutations.txt'¶

residue_file: str = ''¶

neighbor: Optional[int] = None¶

structure_file: str = ''¶

enable_one_graph_stage: bool = False¶

fep_type: str = None¶

__init__(graph_file: str = '', atom_mapping: str = '', align_core_only: bool = False, ats: bool = False, solvent_asl: Optional[str] = None, mutation_filename: str = 'mutations.txt', residue_file: str = '', neighbor: Optional[int] = None, structure_file: str = '', enable_one_graph_stage: bool = False, fep_type: str = None) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.ProteinWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.ProteinMapperParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, md_sim_time: int = 1000, ligand_restraint: typing.Dict[str, bool] = <factory>, adaptive_ligand_restraint: typing.Dict[str, bool] = <factory>, use_representative_structure: bool = True, use_centroid: bool = True, use_pl_interactions: bool = True, min_angle: int = 45, ligand_asl: str = 'a.i_fep_absolute_binding_ligand 1', receptor_asl: str = 'protein or nucleic_acids', graph_file: str = '', skip_fep_cutoff_rmsd: int = 4)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams

Variables

md_sim_time – The simulation time for the md production stage.
ligand_asl – Set the ASL used to identify the ligand.
ligand_restraint – Set to the parameters for the ligand restraints.
ligand_restraint – Dictionary with the keys: ‘enable’, ‘name’, ‘sigma’, ‘alpha’, ‘fc’.
adaptive_ligand_restraint – Set to the parameters for the adaptive ligand restraints.
adaptive_ligand_restraint – Dictionary with the keys: ‘enable’, ‘name’, ‘sigma’, ‘alpha’, ‘fc’.
use_representative_structure – Set to True to use the representative structure from MD to prepare the FEP simulations. The default of False means to use the last frame from MD.
skip_fep_cutoff_rmsd – If the RMSD of the ligand aligned on the receptor’s input coordinates goes above this value in Angstroms during the MD production stage, the ligand is considered unstable in the binding pocket, and FEP will be skipped. Set to None to disable skipping FEP.

md_sim_time: int = 1000¶

ligand_restraint: Dict[str, bool]¶

adaptive_ligand_restraint: Dict[str, bool]¶

use_representative_structure: bool = True¶

use_centroid: bool = True¶

use_pl_interactions: bool = True¶

min_angle: int = 45¶

ligand_asl: str = 'a.i_fep_absolute_binding_ligand 1'¶

receptor_asl: str = 'protein or nucleic_acids'¶

graph_file: str = ''¶

skip_fep_cutoff_rmsd: int = 4¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, md_sim_time: int = 1000, ligand_restraint: typing.Dict[str, bool] = <factory>, adaptive_ligand_restraint: typing.Dict[str, bool] = <factory>, use_representative_structure: bool = True, use_centroid: bool = True, use_pl_interactions: bool = True, min_angle: int = 45, ligand_asl: str = 'a.i_fep_absolute_binding_ligand 1', receptor_asl: str = 'protein or nucleic_acids', graph_file: str = '', skip_fep_cutoff_rmsd: int = 4) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.MapperWorkflowParams

sim_params: schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams¶

mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.AbsoluteBindingSimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, hydration_fep_sim_time: int = 5000, sublimation_fep_sim_time: int = 10000, solvation_fep_sim_time: int = 10000, hydration_only: bool = False, solvation_only: bool = False, crystal_structure: None = None, graph_file: str = '', solvent_composition: str = '', solvent_template_structure: None = None, rest_enabled: bool = True, num_solvation_legs: int = 20)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams

A data class that holds simulation parameters for solubility simulations.

Variables

hydration_fep_sim_time – The simulation time for hydration free energy perturbation.
sublimation_fep_sim_time – The simulation time for sublimation free energy perturbation.
solvation_fep_sim_time – The simulation time for solvation free energy perturbation.
hydration_only – Whether to perform only hydration simulation.
solvation_only – Whether to perform only solvation simulation.
crystal_structure – The crystal structure for the simulation.
graph_file – The filename for the FMP file.
solvent_composition – The composition of the solvent.
solvent_template_structure – The template structure for the solvent.
rest_enabled – Whether REST is enabled.
num_solvation_legs – Number of solvation legs run in the solvation-only workflow

hydration_fep_sim_time: int = 5000¶

sublimation_fep_sim_time: int = 10000¶

solvation_fep_sim_time: int = 10000¶

hydration_only: bool = False¶

solvation_only: bool = False¶

crystal_structure: None = None¶

graph_file: str = ''¶

solvent_composition: str = ''¶

solvent_template_structure: None = None¶

rest_enabled: bool = True¶

num_solvation_legs: int = 20¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, hydration_fep_sim_time: int = 5000, sublimation_fep_sim_time: int = 10000, solvation_fep_sim_time: int = 10000, hydration_only: bool = False, solvation_only: bool = False, crystal_structure: None = None, graph_file: str = '', solvent_composition: str = '', solvent_template_structure: None = None, rest_enabled: bool = True, num_solvation_legs: int = 20) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.SolubilityWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.MapperWorkflowParams

sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams¶

mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.SolubilitySimLegParams = <factory>, mapper_params: schrodinger.application.desmond.msj_generator.workflow_params.BaseMapperParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, subhost: str = 'localhost', equilibrate_time: float = 15000.0, custom_probe_dir: typing.Optional[str] = None)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams

A data class that holds simulation parameters for mixed solvent simulations.

Variables

subhost – The subhost for the simulation.
equilibrate_time – The equilibration time for the simulation.
custom_probe_dir – The directory for custom probes.
membrane – The membrane for the simulation.

subhost: str = 'localhost'¶

equilibrate_time: float = 15000.0¶

custom_probe_dir: Optional[str] = None¶

membrane: Optional[str] = None¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, subhost: str = 'localhost', equilibrate_time: float = 15000.0, custom_probe_dir: typing.Optional[str] = None) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

sim_params: schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.MixedSolventSimLegParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'muVT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, phs: typing.List[float] = <factory>, ph_md: float = 7.0, order: str = 5, site_info: typing.Dict = <factory>, softcore_enabled: bool = False, linear_schedule: bool = True, adapt_iterations: int = 6, app_type_override: str = 'adaptive_remd', adapt_interval: float = 1000.0, n_blocks: int = 1, n_segments: int = 20)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams

A data class that holds simulation parameters for constant pH simulations.

Variables

phs – List of pH values for the simulation.
ph_md – The pH value for molecular dynamics simulation. Default is 7.0.
order – The order of the constant pH potential of mean force. Default is defined by CONSTANT_PH_PMF_ORDER.
site_info – Information about the site. Default is an empty dictionary.
modify_dihe – Whether to modify the dihedral. Default is False.
softcore_enabled – Whether softcore is enabled. Default is False.
linear_schedule – Whether to use a linear schedule. Default is True.
adapt_iterations – The number of adaptive iterations. Default is 6.
app_type_override – The type of application to override. Default is ‘adaptive_remd’.
adapt_interval – The interval for adaptation. Default is 1000.0.
n_blocks – The number of blocks. Default is 1.
n_segments – The number of segments. Default is 20.

phs: List[float]¶

ph_md: float = 7.0¶

order: str = 5¶

site_info: Dict¶

modify_dihe: bool = False¶

softcore_enabled: bool = False¶

linear_schedule: bool = True¶

adapt_iterations: int = 6¶

app_type_override: str = 'adaptive_remd'¶

adapt_interval: float = 1000.0¶

n_blocks: int = 1¶

n_segments: int = 20¶

ensemble: str = 'muVT'¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'muVT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, phs: typing.List[float] = <factory>, ph_md: float = 7.0, order: str = 5, site_info: typing.Dict = <factory>, softcore_enabled: bool = False, linear_schedule: bool = True, adapt_iterations: int = 6, app_type_override: str = 'adaptive_remd', adapt_interval: float = 1000.0, n_blocks: int = 1, n_segments: int = 20) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

sim_params: schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.ConstantpHSimLegParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, subhost: str = 'localhost', asl_receptor: str = 'protein or dna', asl_ligand: str = 'ligand', rmsd_cutoff: float = 5.0, mindist_cutoff: float = 8.0, stability_sim_time: int = 10000, ramd_only: bool = False, nreplicas_ramd: int = 30, ramd_spring_fk: float = 15.0, ramd_fk_increase_rate: float = 0.005, nreplicas_mtd: int = 10, mtd_time: int = 200000, residence_time_cutoff: float = 1000000000000.0, pathcv_z_wall: float = 250.0)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams

A data class that holds simulation parameters for unbinding kinetics simulations.

Variables

subhost – The subhost for the simulation.
asl_receptor – Atom selection language for the receptor.
asl_ligand – Atom selection language for the ligand.
custom_charge_mode – Set to CUSTOM_CHARGE_MODE.ASSIGN to assign custom charges. Set to CUSTOM_CHARGE_MODE.CLEAR to clear custom charges if present, without reassigning. Set to CUSTOM_CHARGE_MODE.KEEP to keep existing custom charges if present.
membrane – The membrane for the simulation.
rmsd_cutoff – RMSD cutoff to consider the ligand unbound in Å.
mindist_cutoff – MinDist (minimum distance between ligand heavy atoms and receptor carbon alphas) cutoff to consider the ligand unbound in Å.
stability_sim_time – Length of simulation (in ps) to establish the ligand’s stability within the binding pocket. A value of 0 will skip the stability validation stage.
ramd_only – Option to only run RAMD and not metadynamics.
nreplicas_ramd – Number of RAMD simulations to submit.
ramd_spring_fk – Initial force constant for RAMD simulations in kcal/mol/Å^2.
ramd_fk_increase_rate – Rate at which the RAMD force constant increases in kcal/mol/Å^2/ns.
nreplicas_mtd – Number of infrequent metadynamics simulations to submit.
mtd_time – Maximum metadynamics simulation time.
residence_time_cutoff – Maximum accelerated time before metadynamics jobs are terminated.
pathcv_z_wall – Width of flat bottom restraints on the Z path CV which measures distance from the path waypoints in Å^2.

subhost: str = 'localhost'¶

asl_receptor: str = 'protein or dna'¶

asl_ligand: str = 'ligand'¶

custom_charge_mode: str = 'assign'¶

membrane: Optional[str] = None¶

rmsd_cutoff: float = 5.0¶

mindist_cutoff: float = 8.0¶

stability_sim_time: int = 10000¶

ramd_only: bool = False¶

nreplicas_ramd: int = 30¶

ramd_spring_fk: float = 15.0¶

ramd_fk_increase_rate: float = 0.005¶

nreplicas_mtd: int = 10¶

mtd_time: int = 200000¶

residence_time_cutoff: float = 1000000000000.0¶

pathcv_z_wall: float = 250.0¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, subhost: str = 'localhost', asl_receptor: str = 'protein or dna', asl_ligand: str = 'ligand', rmsd_cutoff: float = 5.0, mindist_cutoff: float = 8.0, stability_sim_time: int = 10000, ramd_only: bool = False, nreplicas_ramd: int = 30, ramd_spring_fk: float = 15.0, ramd_fk_increase_rate: float = 0.005, nreplicas_mtd: int = 10, mtd_time: int = 200000, residence_time_cutoff: float = 1000000000000.0, pathcv_z_wall: float = 250.0) → None¶

class schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

sim_params: schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.workflow_params.UnbindingKineticsSimLegParams = <factory>) → None¶