Protein MD

Protein MD workflow - molecular dynamics simulations for proteins.

ProteinMDTrajectory dataclass

ProteinMDTrajectory(
    uuid: str,
    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],
)

Results from a single protein-MD trajectory replicate.

Parameters:

Name	Type	Description	Default
uuid	str	UUID of the trajectory calculation.	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

ProteinMDResult dataclass

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

Bases: WorkflowResult

Result from a Protein Molecular Dynamics (MD) workflow.

trajectory_uuids property

trajectory_uuids: list[str]

UUIDs of all trajectory calculations.

trajectories property

trajectories: list[ProteinMDTrajectory]

Per-replicate trajectory results (SASA, radius of gyration, cluster assignments).

minimized_protein_uuid property

minimized_protein_uuid: str | None

UUID of the energy-minimized protein structure.

bonds property

bonds: list[tuple[int, int]]

Bond connectivity as pairs of atom indices.

messages property

messages: list[Message]

Any messages or warnings from the workflow.

get_minimized_protein

get_minimized_protein() -> Protein | None

Fetch the energy-minimized protein structure.

.. note:: Makes one API call on first access. Results are cached. Call clear_cache() to refresh.

Returns:

Type	Description
Protein | None	Protein object or None if not available.

get_atom_distances

get_atom_distances(
    atom_pairs: list[tuple[int, int]], replicate: int = 0
) -> list[list[float]]

Fetch interatomic distances over the trajectory for specified atom pairs.

Parameters:

Name	Type	Description	Default
atom_pairs	list[tuple[int, int]]	List of (atom_i, atom_j) index pairs (0-indexed).	required
replicate	int	Trajectory replicate index (default 0).	0

Returns:

Type	Description
list[list[float]]	List of distance arrays, one per pair, over all frames (Angstrom).

Raises:

Type	Description
HTTPError	If the API request fails.

download_trajectories

download_trajectories(
    replicates: list[int],
    name: str | None = None,
    path: Path | str | None = None,
) -> Path

Download DCD trajectory files for specified replicates.

Parameters:

Name	Type	Description	Default
replicates	list[int]	List of replicate indices to download.	required
name	str | None	Custom name for the tar.gz file (without extension).	None
path	Path | str | None	Directory to save the file to. Defaults to current directory.	None

Returns:

Type	Description
Path	Path to the downloaded tar.gz file.

Raises:

Type	Description
HTTPError	If the API request fails.

submit_protein_md_workflow

submit_protein_md_workflow(
    protein: Protein | ProteinUUID,
    num_trajectories: int = 4,
    equilibration_time_ns: float = 1,
    simulation_time_ns: float = 10,
    temperature: float = 300,
    pressure_atm: float = 1.0,
    langevin_timescale_ps: float = 1.0,
    timestep_fs: float = 2,
    constrain_hydrogens: bool = True,
    nonbonded_cutoff: float = 8.0,
    ionic_strength_M: float = 0.0,
    water_buffer: float = 10.0,
    save_solvent: bool = False,
    num_solvent_to_save: int | None = None,
    binder: Binder | None = None,
    protein_restraint_cutoff: float | None = None,
    protein_restraint_constant: float = 100,
    analysis_interval_ps: float | None = None,
    clustering: KMeansClusteringSettings
    | GreedyClusteringSettings
    | None = None,
    validate_forcefield: bool = True,
    name: str = "Protein 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 Protein 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
num_trajectories	int	Number of trajectories to run.	4
equilibration_time_ns	float	how long to equilibrate trajectories for, in ns	1
simulation_time_ns	float	how long to run trajectories for, 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	2
constrain_hydrogens	bool	whether or not to use SHAKE to freeze bonds to hydrogen	True
nonbonded_cutoff	float	nonbonded cutoff for particle-mesh Ewald, in A	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 A	10.0
save_solvent	bool	whether solvent should be saved	False
num_solvent_to_save	int | None	keep this many solvent molecules nearest the binder, or all if None; only meaningful when save_solvent is True and a binder is present	None
binder	Binder | None	optional binder specification (protein chains and/or small molecules). When set, per-frame MM/GBSA scores are computed against the whole binder. Per-frame binder RMSD is populated only when the binder is a single component (one small molecule → heavy-atom RMSD; one binder chain → backbone N/CA/C/O RMSD); it is empty for multi-molecule, multi-chain, or combined chain+molecule binders.	None
protein_restraint_cutoff	float | None	cutoff distance from the binder past which Cα atoms are harmonically restrained, in Å; None disables restraints	None
protein_restraint_constant	float	force constant for Cα backbone restraints, in kcal/mol/Ų	100
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. Binder small molecules are skipped, whether given by residue name or by index, since they are parameterized from their SMILES rather than the protein forcefield; cofactors, metals, and glycans outside the binder are still validated.	True
name	str	Name of the workflow.	'Protein 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.