diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 7302741a4d7f9e423dd5d1ad0d1edb69648535c4..2491a8a5cb0fcb4c873f295c1f6ee6f8489debf9 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -430,21 +430,26 @@ class LigandScorer:
str(model_ligand), str(target_ligand)))
continue
- #LogVerbose("Compute RMSD for model ligand %s" % model_ligand)
rmsd = SCRMSD(model_ligand, target_ligand,
transformation=binding_site.transform,
substructure_match=self.substructure_match)
- 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),
- "target_ligand": target_ligand,
- "model_ligand": model_ligand
- }
+ LogDebug("RMSD: %.4f" % rmsd)
+
+ # Save results?
+ if not rmsd_full_matrix[target_i, model_i] or \
+ 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),
+ "target_ligand": target_ligand,
+ "model_ligand": model_ligand
+ }
+ LogDebug("Saved RMSD")
mdl_bs_ent = self._build_binding_site_entity(
model_ligand, binding_site.mdl_residues, [])
@@ -459,20 +464,6 @@ class LigandScorer:
# LogWarning("Can't calculate backbone RMSD: %s"
# " - setting to Infinity" % str(err))
# bb_rmsd = float("inf")
- lddt_pli_full_matrix[target_i, model_i] = {
- "lddt_pli": np.nan,
- "lddt_pli_n_contacts": None,
- "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,
- "bs_num_res": len(binding_site.substructure.residues),
- "bs_num_overlap_res": len(binding_site.ref_residues),
- "target_ligand": target_ligand,
- "model_ligand": model_ligand
- }
# Now for each symmetry, loop and rename atoms according
# to ref.
@@ -492,15 +483,28 @@ class LigandScorer:
no_intrachain=True,
return_dist_test=True,
check_resnames=self.check_resnames)
+ LogDebug("lDDT-PLI for symmetry %d: %.4f" % (i, global_lddt))
# Save results?
- best_lddt = lddt_pli_full_matrix[
- target_i, model_i]["lddt_pli"]
- if global_lddt > best_lddt or np.isnan(best_lddt):
- lddt_pli_full_matrix[target_i, model_i].update({
+ if not lddt_pli_full_matrix[target_i, model_i] or \
+ global_lddt > lddt_pli_full_matrix[
+ target_i, model_i]["lddt_pli"] :
+ 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,
+ "bs_num_res": len(binding_site.substructure.residues),
+ "bs_num_overlap_res": len(binding_site.ref_residues),
+ "target_ligand": target_ligand,
+ "model_ligand": model_ligand
+ }
+ LogDebug("Saved lDDT-PLI")
+
self._rmsd_full_matrix = rmsd_full_matrix
self._lddt_pli_full_matrix = lddt_pli_full_matrix
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 7586a67fab5f0c0655df0972b1fdc6d62e2e6481..79b80751be3bc3767b8b5901fb3f2b76221af275 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -301,37 +301,37 @@ class TestLigandScoring(unittest.TestCase):
self.assertFalse(expected_keys.symmetric_difference(sc.lddt_pli_details.keys()))
# rmsd
- self.assertAlmostEqual(sc.rmsd["J"][(1, "\x00")], 3.8498, 3)
- self.assertAlmostEqual(sc.rmsd["F"][(1, "\x00")], 57.6295, 3)
+ self.assertAlmostEqual(sc.rmsd["J"][(1, "\x00")], 0.8016608357429504, 5)
+ self.assertAlmostEqual(sc.rmsd["F"][(1, "\x00")], 0.9286373257637024, 5)
# rmsd_details
- self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["chain_mapping"], {'A': 'B', 'H': 'C'})
- self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_res"], 16)
- self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_overlap_res"], 16)
- self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["target_ligand"].qualified_name, 'L.G3D1')
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["chain_mapping"], {'F': 'D', 'C': 'C'})
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_res"], 15)
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_overlap_res"], 15)
+ self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["target_ligand"].qualified_name, 'I.G3D1')
self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["model_ligand"].qualified_name, 'J.G3D1')
- self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["chain_mapping"], {'F': 'B', 'C': 'C'})
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["chain_mapping"], {'B': 'B', 'G': 'A'})
self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["bs_num_res"], 15)
self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["bs_num_overlap_res"], 15)
- self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["target_ligand"].qualified_name, 'I.G3D1')
+ self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["target_ligand"].qualified_name, 'K.G3D1')
self.assertEqual(sc.rmsd_details["F"][(1, "\x00")]["model_ligand"].qualified_name, 'F.G3D1')
# lddt_pli
- self.assertAlmostEqual(sc.lddt_pli["J"][(1, "\x00")], 0.91194, 5)
- self.assertAlmostEqual(sc.lddt_pli["F"][(1, "\x00")], 0.0014598, 6)
+ self.assertAlmostEqual(sc.lddt_pli["J"][(1, "\x00")], 0.9127105666156202, 5)
+ self.assertAlmostEqual(sc.lddt_pli["F"][(1, "\x00")], 0.915929203539823, 6)
# lddt_pli_details
- self.assertAlmostEqual(sc.lddt_pli_details["J"][(1, "\x00")]["rmsd"], 4.1008, 4)
+ self.assertAlmostEqual(sc.lddt_pli_details["J"][(1, "\x00")]["rmsd"], 0.8016608357429504, 4)
self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["lddt_pli_n_contacts"], 5224)
- self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["chain_mapping"], {'F': 'B', 'C': 'C'})
+ self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["chain_mapping"], {'F': 'D', 'C': 'C'})
self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["bs_num_res"], 15)
self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["bs_num_overlap_res"], 15)
self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["target_ligand"].qualified_name, 'I.G3D1')
self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["model_ligand"].qualified_name, 'J.G3D1')
- self.assertAlmostEqual(sc.lddt_pli_details["F"][(1, "\x00")]["rmsd"], 57.7868, 4)
- self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["lddt_pli_n_contacts"], 5480)
- self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["chain_mapping"], {'E': 'B', 'D': 'C'})
- self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["bs_num_res"], 16)
- self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["bs_num_overlap_res"], 16)
- self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["target_ligand"].qualified_name, 'J.G3D1')
+ self.assertAlmostEqual(sc.lddt_pli_details["F"][(1, "\x00")]["rmsd"], 0.9286373257637024, 4)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["lddt_pli_n_contacts"], 5424)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["chain_mapping"], {'B': 'B', 'G': 'A'})
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["bs_num_res"], 15)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["bs_num_overlap_res"], 15)
+ self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["target_ligand"].qualified_name, 'K.G3D1')
self.assertEqual(sc.lddt_pli_details["F"][(1, "\x00")]["model_ligand"].qualified_name, 'F.G3D1')