schrodinger.application.desmond.solubility_utils module

schrodinger.application.desmond.solubility_utils.extract_solute_ct(cms_model: schrodinger.application.desmond.cms.Cms) → Optional[schrodinger.structure._structure.Structure][source]

Returns a structure representing the solute component of the input cms file. The solute should come before the solvent if there are custom charges present.

Parameters

cms_model – Input cms object to extract the solute from.

Returns

Solute structure object or None if no solute is found

schrodinger.application.desmond.solubility_utils.get_transfer_free_energy(cms_model: schrodinger.application.desmond.cms.Cms) → Optional[schrodinger.application.desmond.measurement.Measurement][source]

Returns the transfer free energy as a Measurement or None if the property could not be found. Depending on the leg that the cmd corresponds to, this could be sublimation, solvation, or hydration dGs.

Parameters

cms_model – Input cms object to extract the transfer free energy from.

schrodinger.application.desmond.solubility_utils.median_sublimation_free_energy(sublimation_dgs: List[schrodinger.application.desmond.measurement.Measurement]) → schrodinger.application.desmond.measurement.Measurement[source]

Returns the median sublimation free energy. For an odd number this is the median, for an even number this is the one closest to the average.

Parameters

sublimation_dgs – List of sublimation transfer free energy measurements.

schrodinger.application.desmond.solubility_utils.calculate_solubility_free_energy(hydration_dg: schrodinger.application.desmond.measurement.Measurement, sublimation_dg: schrodinger.application.desmond.measurement.Measurement) → schrodinger.application.desmond.measurement.Measurement[source]

Returns the dissolution free energy.

NOTE:

  • “Sublimation” leg actually simulates deposition (gas -> solid)

  • Solvation/hydration legs simulate solvation (solid -> solvated)

  • Dissolution (“solubility”) free energy = Hydration - “Sublimation”

Parameters

  • hydration_dg – Hydration transfer free energy measurement.

  • sublimation_dg – Sublimation transfer free energy measurement.

schrodinger.application.desmond.solubility_utils.set_structure_soluble(ct: schrodinger.structure._structure.Structure) → None[source]

Update the fep solubility property to mark the structure as being soluble. The input ct is modified in place.

Parameters

ct – Structure to mark as soluble.

schrodinger.application.desmond.solubility_utils.is_structure_soluble(ct: schrodinger.structure._structure.Structure) → bool[source]

Return True if the structure has been marked as soluble, False otherwise.

Parameters

ct – Structure to check if marked as soluble.

schrodinger.application.desmond.solubility_utils.is_soluble(exposures: List[float]) → bool[source]

If more than 10% of the solute molecules have a exposure greater than 90.0, flag the molecule as soluble (< 5 kcal/mol transfer energy).

Parameters

exposures – List of exposure for each molecule in the structure.

Returns

True if this molecule is considered soluble, False otherwise.

schrodinger.application.desmond.solubility_utils.get_molecule_exposures(baseline_ct: schrodinger.structure._structure.Structure, exposure_ct: schrodinger.structure._structure.Structure, delete_h_atoms=True) → List[float][source]

Calculates the exposure of each molecule in a structure based on SASA and returns a list of exposure of each molecule by index of each molecule in the structure - 1 (since structure.molecule is a 1-indexed list). By default this functiion deletes all H atoms from the specified structure. To retain H atoms set delete_h_atoms to False.

Parameters

  • baseline_ct – Structure of an individual molecule used as the reference.

  • exposure_ct – Structure used for the list of molecule exposures.

  • delete_h_atoms – Set to True to delete all H atoms from the structure when calculating SASA.

Returns

List of exposure for each molecule in the structure.

schrodinger.application.desmond.solubility_utils.extract_most_exposed_solute_molecules(solute_ct: schrodinger.structure._structure.Structure, exposures: List[float], extract_count=5) → List[schrodinger.structure._structure.Structure][source]

Takes the solute component of an input system and returns the extract_count most exposed molecules ordered by exposure.

If less than extract_count solute molecules are present, the returned list contains all solute molecules sorted by exposure.

Parameters

  • solute_ct – Input ct file containing the system to process.

  • exposures – Input ct file containing the system to process.

  • extract_count – The number of molecules to extract.

Returns

List of extract_count most exposed solute mols.

schrodinger.application.desmond.solubility_utils.get_header(max_num_sublimation: int)[source]
schrodinger.application.desmond.solubility_utils.get_header_solvation(max_num_solvation: int)[source]
schrodinger.application.desmond.solubility_utils.get_report(title: str, hydration_dg: Optional[schrodinger.application.desmond.measurement.Measurement] = None, sublimation_dgs: Optional[List[schrodinger.application.desmond.measurement.Measurement]] = None, solvation_dgs: Optional[List[schrodinger.application.desmond.measurement.Measurement]] = None, is_soluble: bool = False) → str[source]

Returns the formatted results as csv file contents.

Parameters

  • title – Title of the ligand.

  • hydration_dg – Hydration transfer free energy measurement. Must be specified if is_soluble is False.

  • sublimation_dgs – List of sublimation transfer free energy measurements. Must be specified if is_soluble is False.

  • solvation_dgs – List of solvation transfer free energy measurements.

  • is_soluble – Set to True if this ligand was determined to be soluble in the MD stage.

schrodinger.application.desmond.solubility_utils.parse_report(csv_contents: str) → Dict[str, Dict][source]

Parse a report csv and return a ParsedReport mapping the ligand to the result. Each result is a dictionary where the keys are the columns from the csv.

schrodinger.application.desmond.solubility_utils.calculate_report_rmse(ref_data: Dict[str, Dict], test_data: Dict[str, Dict]) → Dict[str, float][source]

Calculate the rsme between the parsed reference data and the test data. Missing data is treated as infinite difference

Used in STU and SCIVAL tests.

Returns

Dictionary where the keys are the column names and the values are the rmse for that column.

schrodinger.application.desmond.solubility_utils.parse_output_structure_properties(sts: List[schrodinger.structure._structure.Structure]) → Dict[str, Dict][source]

Parse the ct level solubility properties from report structures and return the dictionary of {compound: {property: value}}. Missing values are set to None.

Used in STU and SCIVAL tests.

schrodinger.application.desmond.solubility_utils.bootstrapped_solvation_free_energy(solvation_dgs: List[schrodinger.application.desmond.measurement.Measurement]) → schrodinger.application.desmond.correlation_tau.ConfidenceInterval[source]