Merge remote-tracking branch 'origin/develop' into cli_flags_output_d…

…esign
forlilab · Oct 14, 2024 · f3fa133 · f3fa133
2 parents b60ae0b + 89ba874
commit f3fa133
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/meeko/linked_rdkit_chorizo.py b/meeko/linked_rdkit_chorizo.py
@@ -178,6 +178,12 @@ def find_inter_mols_bonds(mols_dict):
             for a2 in mols_dict[keys[j]][0].GetAtoms():
                 vec = p1[a1.GetIdx()] - p2[a2.GetIdx()]
                 distsqr = np.dot(vec, vec)
+
+                # check if atom has implemented covalent radius
+                for atom in [a1, a2]:
+                    if atom.GetAtomicNum() not in covalent_radius:
+                        raise RuntimeError(f"Element {periodic_table.GetElementSymbol(atom.GetAtomicNum())} doesn't have an implemented covalent radius, which was required for the perception of intermolecular bonds. ")
+
                 cov_dist = (
                     covalent_radius[a1.GetAtomicNum()]
                     + covalent_radius[a2.GetAtomicNum()]
@@ -1130,6 +1136,8 @@ def _get_residues(
             elif len(ambiguous[input_resname]) == 1:
                 template_key = ambiguous[input_resname][0]
                 template = residue_templates[template_key]
+                candidate_template_keys = [template_key]
+                candidate_templates = [template]
             else:
                 candidate_template_keys = []
                 candidate_templates = []

diff --git a/meeko/utils/rdkitutils.py b/meeko/utils/rdkitutils.py
@@ -184,13 +184,13 @@ def _aux_altloc_mol_build(atom_field_list, requested_altloc, default_altloc):
     elif requested_altloc and requested_altloc not in mols_dict:
         pdbmol = None
         missed_altloc = True
-        needed_altoc = False
+        needed_altloc = False
     elif default_altloc and default_altloc in mols_dict:
         pdbmol, idx_to_rdkit = mols_dict[default_altloc]
     elif has_altloc and default_altloc not in mols_dict:
         pdbmol = None
-        needed_altloc = True
-        missed_altloc = False
+        missed_altloc = True
+        needed_altloc = False
     elif not has_altloc and requested_altloc is None:
         pdbmol, idx_to_rdkit = mols_dict[None]
     else:

diff --git a/scripts/mk_prepare_receptor.py b/scripts/mk_prepare_receptor.py
@@ -573,7 +573,7 @@ def get_args():
         if input_resname in reactive_atom:
             reactive_flexres_name[res_id] = reactive_atom[input_resname]
         else:
-            print("no default reactive name for %s, " % resname)
+            print("no default reactive name for %s, " % input_resname)
             print("use --reactive_name or --reactive_name_specific" + os_linesep)
             sys.exit(2)