schrodinger.application.bioluminate.pose_filtering.hdx_analysis module

Pose scoring based on Hydrogen Deuterium eXchange mass spec (HDX-MS) data.

schrodinger.application.bioluminate.pose_filtering.hdx_analysis.calc_delta_sasa_by_res_id(st: schrodinger.structure._structure.Structure, sasa_by_res_id_bound: Dict[str, float], substructure_res_ids: List[str]) → Dict[str, float]

Return a map of each residue ID in substructure_res_ids to its delta SASA i.e. the difference between its bound and unbound SASA. Residue ID is in the form of <chain_name>:<residue number>.

Parameters

  • st – The structure to use for SASA calculations

  • sasa_by_res_id_bound – The SASA per residue ID of the bound state.

  • substructure_res_ids – Residue IDs for the substructure to use for the unbound state.

Raises

RuntimeError if we cannot extract any of the supplied residues from the structure.

schrodinger.application.bioluminate.pose_filtering.hdx_analysis.calc_sasa_by_res_id(st: schrodinger.structure._structure.Structure) → Dict[str, float]

Return a map of each residue ID in st to its SASA.

Parameters

st – Structure for which SASA is desired.

schrodinger.application.bioluminate.pose_filtering.hdx_analysis.calc_substructure_scores(pose: schrodinger.structure._structure.Structure, delta_pd_by_res_id_recep: Dict[str, float], delta_pd_by_res_id_lig: Dict[str, float], chain_names_recep: Set[str], chain_names_lig: Set[str], delta_d_cutoff: float) → Tuple[float, Optional[float]]

Return receptor and ligand scores.

Parameters

  • pose – The pose to score

  • delta_pd_by_res_id_recep – The delta %D by residue ID for the receptor

  • delta_pd_by_res_id_lig – The delta %D by residue ID for the ligand

  • chain_names_recep – The receptor chain names

  • chain_names_lig – The ligand chain names

  • delta_d_cutoff – Minimum delta d value for use in pose scoring

schrodinger.application.bioluminate.pose_filtering.hdx_analysis.calc_substructure_score(pose: schrodinger.structure._structure.Structure, delta_pd_by_res_id: Dict[str, float], other_chains: Set[str], delta_d_cutoff: float) → float

Calculate a score for the receptor or ligand by summing up (delta %D * #neighbors) for each residue that has delta %D >= 10. #neighbors is the number of residues from the other substructure whose backbones are within 10A of backbone of the residue in question.

Parameters

  • pose – The pose structure.

  • delta_pd_by_res_id – Delta %D by residue ID for either the receptor or ligand.

  • other_chains – Set of chain names for either the receptor or ligand. This corresponds to the substructure not represented in delta_pd_by_res_id e.g. if delta_pd_by_res_id is for the receptor, then this parameter contains chain names for the ligand.

  • delta_d_cutoff – Minimum delta d value for use in pose scoring