diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index fdc61c75f968d90245de2e53b2f5fd07903cedba..fa20a448ca81708d75649ef66790beca4103e596 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -391,8 +391,11 @@ class LigandScorer:
return bs_ent
def _compute_scores(self):
- """"""
- # Create the matrix
+ """
+ Compute the RMSD and lDDT-PLI scores for every possible target-model
+ ligand pair and store the result in internal matrices.
+ """
+ # Create the result matrices
rmsd_full_matrix = np.empty(
(len(self.target_ligands), len(self.model_ligands)), dtype=dict)
lddt_pli_full_matrix = np.empty(
@@ -447,14 +450,14 @@ class LigandScorer:
rmsd_full_matrix[target_i, model_i]["rmsd"] > rmsd:
rmsd_full_matrix[target_i, model_i] = {
"rmsd": rmsd,
- "chain_mapping": binding_site.GetFlatChainMapping(),
"lddt_bs": binding_site.lDDT,
- "bb_rmsd": binding_site.bb_rmsd,
- "transform": binding_site.transform,
"bs_num_res": len(binding_site.substructure.residues),
"bs_num_overlap_res": len(binding_site.ref_residues),
+ "bb_rmsd": binding_site.bb_rmsd,
"target_ligand": target_ligand,
"model_ligand": model_ligand,
+ "chain_mapping": binding_site.GetFlatChainMapping(),
+ "transform": binding_site.transform,
"substructure_match": substructure_match,
}
LogDebug("Saved RMSD")
@@ -484,7 +487,6 @@ class LigandScorer:
LogDebug("lDDT-PLI for symmetry %d: %.4f" % (i, global_lddt))
# Save results?
-
if not lddt_pli_full_matrix[target_i, model_i]:
# First iteration
save_lddt = True
@@ -505,17 +507,16 @@ class LigandScorer:
if save_lddt:
lddt_pli_full_matrix[target_i, model_i] = {
"lddt_pli": global_lddt,
- "lddt_pli_n_contacts": lddt_tot,
"rmsd": rmsd,
- # "symmetry_number": i,
- "chain_mapping": binding_site.GetFlatChainMapping(),
"lddt_bs": binding_site.lDDT,
- "bb_rmsd": binding_site.bb_rmsd,
- "transform": binding_site.transform,
+ "lddt_pli_n_contacts": lddt_tot,
"bs_num_res": len(binding_site.substructure.residues),
"bs_num_overlap_res": len(binding_site.ref_residues),
+ "bb_rmsd": binding_site.bb_rmsd,
"target_ligand": target_ligand,
"model_ligand": model_ligand,
+ "chain_mapping": binding_site.GetFlatChainMapping(),
+ "transform": binding_site.transform,
"substructure_match": substructure_match,
}
LogDebug("Saved lDDT-PLI")
@@ -713,17 +714,17 @@ class LigandScorer:
Each sub-dictionary contains the following information:
- * `rmsd`: the RMSD score value
- * `lddt_bs`: the lDDT-BS score of the binding site
- * `bs_num_res`: number of residues in the target binding site
+ * `rmsd`: the RMSD score value.
+ * `lddt_bs`: the lDDT-BS score of the binding site.
+ * `bs_num_res`: number of residues in the target binding site.
* `bs_num_overlap_res`: number of residues in the model overlapping
with the target binding site.
* `bb_rmsd`: the RMSD of the binding site backbone after superposition
- * `transform`: transformation to superpose the model onto the target
- * `target_ligand`: residue handle of the target ligand
- * `model_ligand`: residue handle of the model ligand
+ * `target_ligand`: residue handle of the target ligand.
+ * `model_ligand`: residue handle of the model ligand.
* `chain_mapping`: local chain mapping as a dictionary, with target
chain name as key and model chain name as value.
+ * `transform`: transformation to superpose the model onto the target.
* `substructure_match`: whether the score is the result of a partial
(substructure) match. A value of `True` indicates that the target
ligand covers only part of the model, while `False` indicates a
@@ -753,23 +754,24 @@ class LigandScorer:
Each sub-dictionary contains the following information:
- * `lddt_pli`: the lDDT-PLI score value
+ * `lddt_pli`: the lDDT-PLI score value.
+ * `rmsd`: the RMSD score value corresponding to the lDDT-PLI
+ assignment. This may differ from the RMSD-based assignment.
+ * `lddt_bs`: the lDDT-BS score of the binding site.
* `lddt_pli_n_contacts`: number of total contacts used in lDDT-PLI,
summed over all thresholds. Can be divided by 8 to obtain the number
of atomic contacts.
- * `rmsd`: the RMSD score value corresponding to the lDDT-PLI
- assignment. This may differ from the RMSD-based assignment.
- * `lddt_bs`: the lDDT-BS score of the binding site
- * `bs_num_res`: number of residues in the target binding site
+ * `bs_num_res`: number of residues in the target binding site.
* `bs_num_overlap_res`: number of residues in the model overlapping
with the target binding site.
* `bb_rmsd`: the RMSD of the binding site backbone after superposition.
Note: not used for lDDT-PLI computation.
- * `transform`: transformation to superpose the model onto the target
- * `target_ligand`: residue handle of the target ligand
- * `model_ligand`: residue handle of the model ligand
+ * `target_ligand`: residue handle of the target ligand.
+ * `model_ligand`: residue handle of the model ligand.
* `chain_mapping`: local chain mapping as a dictionary, with target
chain name as key and model chain name as value.
+ * `transform`: transformation to superpose the model onto the target
+ (for RMSD only).
* `substructure_match`: whether the score is the result of a partial
(substructure) match. A value of `True` indicates that the target
ligand covers only part of the model, while `False` indicates a