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