From d45b2f376fc410ea974eb3ec4b21d5e8bb3ab84a Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 21 Jul 2023 13:43:43 +0200
Subject: [PATCH] Merge branch 'develop'
---
modules/io/pymod/export_omf_io.cc | 1 +
modules/mol/alg/pymod/ligand_scoring.py | 47 +++++++++++---------
modules/mol/alg/tests/test_ligand_scoring.py | 1 -
3 files changed, 26 insertions(+), 23 deletions(-)
diff --git a/modules/io/pymod/export_omf_io.cc b/modules/io/pymod/export_omf_io.cc
index 43355a4a9..d2df0e475 100644
--- a/modules/io/pymod/export_omf_io.cc
+++ b/modules/io/pymod/export_omf_io.cc
@@ -61,6 +61,7 @@ void export_omf_io() {
.value("ROUND_BFACTORS", OMF::ROUND_BFACTORS)
.value("SKIP_SS", OMF::SKIP_SS)
.value("INFER_PEP_BONDS", OMF::INFER_PEP_BONDS)
+ .value("INFER_AA_POS", OMF::INFER_AA_POS)
;
class_<OMF, OMFPtr>("OMF",no_init)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index cc54c2f5f..ac1e1fb1f 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -498,28 +498,29 @@ class LigandScorer:
ref_res.qualified_name, ligand.qualified_name))
ignored_residue_hashes.add(h)
+ if ref_residues_hashes:
+ # reason for doing that separately is to guarantee same ordering of
+ # residues as in underlying entity. (Reorder by ResNum seems only
+ # available on ChainHandles)
+ ref_bs = self.target.CreateEmptyView()
+ for ch in self.target.chains:
+ for r in ch.residues:
+ if r.handle.GetHashCode() in ref_residues_hashes:
+ ref_bs.AddResidue(r, mol.ViewAddFlag.INCLUDE_ALL)
+ if len(ref_bs.residues) == 0:
+ LogWarning("No residue in proximity of target ligand "
+ "%s" % str(ligand))
+
+ # Find the representations
+ if self.global_chain_mapping:
+ self._binding_sites[ligand.hash_code] = self.chain_mapper.GetRepr(
+ ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
+ global_mapping=self._model_mapping)
+ else:
+ self._binding_sites[ligand.hash_code] = self.chain_mapper.GetRepr(
+ ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
+ topn=self.binding_sites_topn)
- # reason for doing that separately is to guarantee same ordering of
- # residues as in underlying entity. (Reorder by ResNum seems only
- # available on ChainHandles)
- ref_bs = self.target.CreateEmptyView()
- for ch in self.target.chains:
- for r in ch.residues:
- if r.handle.GetHashCode() in ref_residues_hashes:
- ref_bs.AddResidue(r, mol.ViewAddFlag.INCLUDE_ALL)
- if len(ref_bs.residues) == 0:
- LogWarning("No residue in proximity of target ligand "
- "%s" % str(ligand))
-
- # Find the representations
- if self.global_chain_mapping:
- self._binding_sites[ligand.hash_code] = self.chain_mapper.GetRepr(
- ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
- global_mapping = self._model_mapping)
- else:
- self._binding_sites[ligand.hash_code] = self.chain_mapper.GetRepr(
- ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
- topn=self.binding_sites_topn)
return self._binding_sites[ligand.hash_code]
@staticmethod
@@ -825,6 +826,7 @@ class LigandScorer:
trg_idx, mdl_idx][main_key]
out_details[mdl_cname][mdl_resnum] = data[
trg_idx, mdl_idx]
+
return out_main, out_details
def _assign_matrix(self, mat, data1, main_key1, data2, main_key2):
@@ -985,7 +987,8 @@ class LigandScorer:
"""Get a dictionary of RMSD score details (dictionaries), keyed by
model ligand (chain name, :class:`~ost.mol.ResNum`).
- Each sub-dictionary contains the following information:
+ The value is a dictionary. For ligands that were assigned (mapped) to
+ the target, the dictionary contain the following information:
* `rmsd`: the RMSD score value.
* `lddt_lp`: the lDDT score of the ligand pocket (lDDT-LP).
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 0ec50a4b6..948941c69 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -388,7 +388,6 @@ class TestLigandScoring(unittest.TestCase):
assert sc.rmsd_details["L_2"][1]["chain_mapping"] == {'A': 'A'}
assert sc.lddt_pli_details["L_2"][1]["chain_mapping"] == {'C': 'A'}
-
def test_rmsd_assignment(self):
"""Test that the RMSD-based assignment works.
--
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