PBSA

PBSA module for the Rush Python client.

Computes solvation energies using the Poisson-Boltzmann Surface Area method.

Usage:

from rush import pbsa

result = pbsa.solvation_energy("mol.json", ...).fetch()
print(result.solvation_energy)

class rush.pbsa.Result(solvation_energy, polar_solvation_energy, nonpolar_solvation_energy)

Bases: object

Parsed PBSA solvation energy results (all values in Hartrees).

Parameters:

• solvation_energy (float)

• polar_solvation_energy (float)

• nonpolar_solvation_energy (float)

nonpolar_solvation_energy: float

polar_solvation_energy: float

solvation_energy: float

class rush.pbsa.ResultPaths(output)

Bases: object

Workspace path for saved PBSA output.

Parameters:

output (Path)

output: Path

class rush.pbsa.ResultRef(solvation_energy, polar_solvation_energy, nonpolar_solvation_energy)

Bases: object

Lightweight reference to PBSA output.

PBSA results are small enough to be returned inline (three floats), so no object store download is needed.

Parameters:

• solvation_energy (float)

• polar_solvation_energy (float)

• nonpolar_solvation_energy (float)

classmethod from_raw_output(res)

Parse raw collect_run output into a ResultRef.

Parameters:

res (Any)

Return type:

ResultRef

fetch()

Return parsed PBSA results (no download needed — data is inline).

Return type:

Result

save()

Save PBSA results as JSON to the workspace.

Return type:

ResultPaths

nonpolar_solvation_energy: float

polar_solvation_energy: float

solvation_energy: float

rush.pbsa.solvation_energy(mol, solute_dielectric, solvent_dielectric, solvent_radius, ion_concentration, temperature, spacing, sasa_gamma, sasa_beta, sasa_n_samples, convergence, box_size_factor, run_spec=RunSpec(gpus=1), run_opts=RunOpts())

Submit a PBSA solvation energy calculation for the topology at topology_path.

Returns a RushRun handle. Call .fetch() to get the parsed result, or .save() to write it to disk as JSON.

Parameters:

• mol (TRC | TRCRef | Path | str | RushObject | Topology)

• solute_dielectric (float)

• solvent_dielectric (float)

• solvent_radius (float)

• ion_concentration (float)

• temperature (float)

• spacing (float)

• sasa_gamma (float)

• sasa_beta (float)

• sasa_n_samples (int)

• convergence (float)

• box_size_factor (float)

• run_spec (RunSpec)

• run_opts (RunOpts)

Return type:

RushRun[ResultRef]