diff --git a/actions/ost-compare-structures-new b/actions/ost-compare-structures-new
index adb998504e42cfad385f7d36ec5fefb898216bd9..f4e562d5dc58ca2ce44b1a2202d14d61e2a11368 100644
--- a/actions/ost-compare-structures-new
+++ b/actions/ost-compare-structures-new
@@ -168,10 +168,11 @@ def _ParseArgs():
help=("Compute per-residue lDDT scores with default parameterization "
"and store as key \"local_lddt\". Score for model residue with "
"number 42 in chain X can be extracted with: "
- "data[\"local_lddt\"][\"X\"][\"42\"]. Stereochemical irregularities "
- "affecting lDDT are reported as keys \"model_clashes\", "
- "\"model_bad_bonds\", \"model_bad_angles\" and the respective "
- "reference counterparts."))
+ "data[\"local_lddt\"][\"X\"][\"42\"]. If there is an insertion "
+ "code, lets say A, the last key becomes \"42A\" Stereochemical "
+ "irregularities affecting lDDT are reported as keys "
+ "\"model_clashes\", \"model_bad_bonds\", \"model_bad_angles\" "
+ "and the respective reference counterparts."))
parser.add_argument(
"--cad-score",
@@ -269,7 +270,8 @@ def _ParseArgs():
"the full patches are represented by the reference are set to "
"None. Model interface residues are available as key "
"\"model_interface_residues\", reference interface residues as "
- "key \"reference_interface_residues\". The respective scores are "
+ "key \"reference_interface_residues\". Residues are represented "
+ "as string in form <num><inscode>. The respective scores are "
"available as keys \"patch_qs\" and \"patch_dockq\""))
return parser.parse_args()
@@ -330,6 +332,26 @@ def _GetInconsistentResidues(alns):
lst = [f"{x[0].GetQualifiedName()}-{x[1].GetQualifiedName()}" for x in lst]
return lst
+def _LocalScoresToJSONDict(score_dict):
+ """ Score for model residue with number rnum in chain X can be extracted
+ with: data["local_cad_score"]["X"][rnum]. Convert ResNum object to str for
+ JSON serialization
+ """
+ json_dict = dict()
+ for ch, ch_scores in score_dict.items():
+ json_dict[ch] = {str(rnum): s for rnum, s in ch_scores.items()}
+ return json_dict
+
+def _InterfaceResiduesToJSONDict(interface_dict):
+ """ Interface residues are stored as
+ data["model_interface_residues"]["A"][rnum1, rnum2,...]. Convert ResNum
+ object to str for JSON serialization.
+ """
+ json_dict = dict()
+ for ch, ch_nums in interface_dict.items():
+ json_dict[ch] = [str(rnum) for rnum in ch_nums]
+ return json_dict
+
def _Process(model, reference, args):
@@ -350,7 +372,7 @@ def _Process(model, reference, args):
out["lddt"] = scorer.lddt
if args.local_lddt:
- out["local_lddt"] = scorer.local_lddt
+ out["local_lddt"] = _LocalScoresToJSONDict(scorer.local_lddt)
if args.lddt or args.local_lddt:
out["model_clashes"] = [x.ToJSON() for x in scorer.model_clashes]
@@ -364,7 +386,7 @@ def _Process(model, reference, args):
out["cad_score"] = scorer.cad_score
if args.local_cad_score:
- out["local_cad_score"] = scorer.local_cad_score
+ out["local_cad_score"] = _LocalScoresToJSONDict(scorer.local_cad_score)
if args.qs_score:
out["qs_global"] = scorer.qs_global
@@ -394,8 +416,10 @@ def _Process(model, reference, args):
out["dockq_wave_full"] = scorer.dockq_wave_full
if args.patch_scores:
- out["model_interface_residues"] = scorer.model_interface_residues
- out["reference_interface_residues"] = scorer.target_interface_residues
+ out["model_interface_residues"] = \
+ _InterfaceResiduesToJSONDict(scorer.model_interface_residues)
+ out["reference_interface_residues"] = \
+ _InterfaceResiduesToJSONDict(scorer.target_interface_residues)
out["patch_qs"] = scorer.patch_qs
out["patch_dockq"] = scorer.patch_dockq
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 2b8ecb3bcabbc3af8ddb41ed2e12a4c386ca348a..73d42464ffc54395aee3e77fb43abb007a927a10 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -974,14 +974,14 @@ class Scorer:
local_lddt[cname] = dict()
if r.HasProp("lddt"):
score = round(r.GetFloatProp("lddt"), 3)
- local_lddt[cname][r.GetNumber().GetNum()] = score
+ local_lddt[cname][r.GetNumber()] = score
else:
# rsc => residue stereo checked...
mdl_res = self.stereochecked_model.FindResidue(cname, r.GetNumber())
if mdl_res.IsValid():
# not covered by trg or skipped in chain mapping procedure
# the latter happens if its part of a super short chain
- local_lddt[cname][r.GetNumber().GetNum()] = None
+ local_lddt[cname][r.GetNumber()] = None
else:
# opt 1: removed by stereochecks => assign 0.0
# opt 2: removed by stereochecks AND not covered by ref
@@ -997,9 +997,9 @@ class Scorer:
trg_r = col.GetResidue(0)
break
if trg_r is None:
- local_lddt[cname][r.GetNumber().GetNum()] = None
+ local_lddt[cname][r.GetNumber()] = None
else:
- local_lddt[cname][r.GetNumber().GetNum()] = 0.0
+ local_lddt[cname][r.GetNumber()] = 0.0
self._lddt = lddt_score
self._local_lddt = local_lddt
@@ -1149,9 +1149,9 @@ class Scorer:
local_cad[cname] = dict()
if r.HasProp("localcad"):
score = round(r.GetFloatProp("localcad"), 3)
- local_cad[cname][r.GetNumber().GetNum()] = score
+ local_cad[cname][r.GetNumber()] = score
else:
- local_cad[cname][r.GetNumber().GetNum()] = None
+ local_cad[cname][r.GetNumber()] = None
self._cad_score = cad_result.globalAA
self._local_cad_score = local_cad
@@ -1187,7 +1187,7 @@ class Scorer:
for ch in ent.chains:
cname = ch.GetName()
sel = repr_ent.Select(f"(cname={cname} and 8 <> [cname!={cname}])")
- result[cname] = [r.GetNumber().GetNum() for r in sel.residues]
+ result[cname] = [r.GetNumber() for r in sel.residues]
return result
def _do_stereochecks(self):
@@ -1229,7 +1229,7 @@ class Scorer:
:param mdl_ch: Name of chain in *self.model* of residue of interest
:type mdl_ch: :class:`str`
:param mdl_rnum: Residue number of residue of interest
- :type mdl_rnum: :class:`int`
+ :type mdl_rnum: :class:`ost.mol.ResNum`
:returns: Tuple with 5 elements: 1) :class:`bool` flag whether all residues
in *mdl* patches are covered in *trg* 2) mtl_patch_one
3) mdl_patch_two 4) trg_patch_one 5) trg_patch_two
@@ -1238,7 +1238,7 @@ class Scorer:
repr_mdl = self._get_repr_view(self.model.Select("peptide=true"))
# get position for specified residue
- r = self.model.FindResidue(mdl_ch, mol.ResNum(mdl_rnum))
+ r = self.model.FindResidue(mdl_ch, mdl_rnum)
if not r.IsValid():
raise RuntimeError(f"Cannot find residue {mdl_rnum} in chain {mdl_ch}")
if r.GetName() == "GLY":
@@ -1332,7 +1332,7 @@ class Scorer:
scores = list()
for rnum in rnums:
score = None
- r = self.model.FindResidue(cname, mol.ResNum(rnum))
+ r = self.model.FindResidue(cname, rnum)
if r.IsValid() and r.GetChemType() == mol.ChemType.AMINOACIDS:
full_trg_coverage, mdl_patch_one, mdl_patch_two, \
trg_patch_one, trg_patch_two = \
@@ -1349,7 +1349,7 @@ class Scorer:
scores = list()
for rnum in rnums:
score = None
- r = self.model.FindResidue(cname, mol.ResNum(rnum))
+ r = self.model.FindResidue(cname, rnum)
if r.IsValid() and r.GetChemType() == mol.ChemType.AMINOACIDS:
full_trg_coverage, mdl_patch_one, mdl_patch_two, \
trg_patch_one, trg_patch_two = \