Pose Analysis MD

Pose-analysis MD accepts selectable small-molecule, protein, and water force fields. Mean and medoid structures are available through the same result helpers as protein MD.

Pose-analysis MD workflow - molecular dynamics simulations for ligand-protein complexes.

TrajectoryResult `dataclass`

TrajectoryResult(
    uuid: str,
    ligand_rmsd: list[float],
    contacts: list[BindingPoseContact],
    sasa: list[float | None],
    polar_sasa: list[float | None],
    isotropic_radius_of_gyration: list[float],
    cluster_centroid_indices: list[int],
    cluster_indices_by_frame: list[int],
    mean_structure_uuid: str | None = None,
    median_structure_frame_index: int | None = None,
)

Results from a single MD trajectory replicate.

Parameters:

Name	Type	Description	Default
`uuid`	`str`	UUID of the trajectory calculation.	required
`ligand_rmsd`	`list[float]`	Ligand RMSD values over time (Angstrom).	required
`contacts`	`list[BindingPoseContact]`	Ligand-protein contacts with occupancy over the trajectory.	required
`sasa`	`list[float \| None]`	Solvent-accessible surface area per analyzed frame (populated when analysis_interval_ps is set).	required
`polar_sasa`	`list[float \| None]`	Polar solvent-accessible surface area per analyzed frame (populated when analysis_interval_ps is set).	required
`isotropic_radius_of_gyration`	`list[float]`	Radius of gyration per analyzed frame.	required
`cluster_centroid_indices`	`list[int]`	Frame indices of the cluster centroids (populated when clustering is set).	required
`cluster_indices_by_frame`	`list[int]`	Cluster assignment for each frame (populated when clustering is set).	required
`mean_structure_uuid`	`str \| None`	UUID of the coordinate-averaged structure.	`None`
`median_structure_frame_index`	`int \| None`	Frame index of the medoid structure.	`None`

PoseAnalysisMDResult `dataclass`

PoseAnalysisMDResult(
    workflow_data: dict[str, Any],
    workflow_type: str,
    workflow_uuid: str,
    complete: bool = True,
)

Bases: _MolecularDynamicsResult

Result from a Pose-Analysis Molecular Dynamics (MD) workflow.

trajectories `property`

trajectories: list[TrajectoryResult]

Results from each trajectory replicate.

Each trajectory contains RMSD values, contact analysis, and cluster assignments.

hydration_sites `property`

hydration_sites: list[HydrationSite]

Hydration sites identified across all trajectories.

average_rmsds `property`

average_rmsds: list[float | None]

Average ligand RMSD per trajectory (Angstrom).

messages `property`

messages: list[Message]

Any messages or warnings from the workflow.

submit_pose_analysis_md_workflow

submit_pose_analysis_md_workflow(
    protein: Protein | ProteinUUID,
    initial_smiles: str,
    num_trajectories: int = 4,
    small_molecule_ff: Literal[
        "off_sage_2_0_0",
        "off_sage_2_2_1",
        "off_sage_2_3_0",
        "mango_1_0_0",
    ] = "off_sage_2_3_0",
    protein_ff: ProteinForceField
    | str = ProteinForceField.FF14SB,
    water_ff: WaterForceField | str = WaterForceField.TIP3P,
    equilibration_time_ns: float = 0.5,
    simulation_time_ns: float = 10,
    temperature: float = 300,
    pressure_atm: float = 1.0,
    langevin_timescale_ps: float = 1.0,
    timestep_fs: float = 4,
    hydrogen_mass: float = 3,
    constrain_hydrogens: bool = True,
    nonbonded_cutoff: float = 8.0,
    ionic_strength_M: float = 0.0,
    water_buffer: float = 8.0,
    ligand_residue_name: str = "LIG",
    protein_restraint_cutoff: float | None = 7.0,
    protein_restraint_constant: float = 100,
    save_solvent: bool = False,
    num_solvent_to_save: int | None = None,
    analysis_interval_ps: float | None = None,
    clustering: KMeansClusteringSettings
    | GreedyClusteringSettings
    | None = None,
    validate_forcefield: bool = True,
    name: str = "Pose-Analysis MD Workflow",
    folder_uuid: str | None = None,
    folder: Folder | None = None,
    max_credits: int | None = None,
    webhook_url: str | None = None,
    is_draft: bool = False,
) -> Workflow

Submits a Pose-Analysis Molecular Dynamics (MD) workflow to the API.

Parameters:

Name	Type	Description	Default
`protein`	`Protein \| ProteinUUID`	Holo protein on which MD will be run. Can be input as a UUID or a Protein object.	required
`initial_smiles`	`str`	SMILES for the ligand.	required
`num_trajectories`	`int`	Number of trajectories to run.	`4`
`small_molecule_ff`	`Literal['off_sage_2_0_0', 'off_sage_2_2_1', 'off_sage_2_3_0', 'mango_1_0_0']`	Force field for the ligand.	`'off_sage_2_3_0'`
`protein_ff`	`ProteinForceField \| str`	Force field for proteins.	`FF14SB`
`water_ff`	`WaterForceField \| str`	Force field for water.	`TIP3P`
`equilibration_time_ns`	`float`	Equilibration time per trajectory, in ns.	`0.5`
`simulation_time_ns`	`float`	Simulation time per trajectory, in ns.	`10`
`temperature`	`float`	Temperature, in K.	`300`
`pressure_atm`	`float`	Pressure, in atm.	`1.0`
`langevin_timescale_ps`	`float`	Timescale for the Langevin integrator, in ps⁻¹.	`1.0`
`timestep_fs`	`float`	Timestep, in femtoseconds.	`4`
`hydrogen_mass`	`float`	Hydrogen mass, in atomic mass units.	`3`
`ligand_residue_name`	`str`	Name of the residue corresponding to the ligand.	`'LIG'`
`constrain_hydrogens`	`bool`	Whether to use SHAKE to freeze bonds to hydrogen.	`True`
`nonbonded_cutoff`	`float`	Nonbonded cutoff for particle-mesh Ewald, in Å.	`8.0`
`ionic_strength_M`	`float`	Ionic strength of the solution, in M (molar).	`0.0`
`water_buffer`	`float`	Amount of water to add around the protein, in Å.	`8.0`
`protein_restraint_cutoff`	`float \| None`	Cutoff past which alpha-carbons will be constrained, in Å, measured from the ligand. None applies no restraints.	`7.0`
`protein_restraint_constant`	`float`	Force constant for backbone restraints, in kcal/mol/Å².	`100`
`save_solvent`	`bool`	Whether to save solvent molecules.	`False`
`num_solvent_to_save`	`int \| None`	Number of solvent molecules to save (the N nearest the ligand each frame). None saves all solvent when save_solvent is True.	`None`
`analysis_interval_ps`	`float \| None`	Interval at which to compute per-frame SASA and polar SASA, in ps. None disables those analyses.	`None`
`clustering`	`KMeansClusteringSettings \| GreedyClusteringSettings \| None`	How to cluster trajectory frames. None disables clustering; pass a KMeansClusteringSettings (num_clusters) or GreedyClusteringSettings (cutoff_angstrom).	`None`
`validate_forcefield`	`bool`	if True (default), validate the protein forcefield compatibility before submitting. Raises an error early if the protein cannot be parameterized or has clashing residues.	`True`
`name`	`str`	Name of the workflow.	`'Pose-Analysis MD Workflow'`
`folder_uuid`	`str \| None`	UUID of the folder to place the workflow in.	`None`
`folder`	`Folder \| None`	Folder object to store the workflow in.	`None`
`max_credits`	`int \| None`	Maximum number of credits to use for the workflow.	`None`
`webhook_url`	`str \| None`	URL that Rowan will POST to when the workflow completes.	`None`
`is_draft`	`bool`	If True, submit the workflow as a draft without starting execution.	`False`

Returns:

Type	Description
`Workflow`	Workflow object representing the submitted workflow.

Raises:

Type	Description
`requests.HTTPError`	if the request to the API fails.

Pose Analysis MD

TrajectoryResult dataclass

PoseAnalysisMDResult dataclass

trajectories property

hydration_sites property

average_rmsds property

messages property