diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 75972640de0c7dd4869470593ab00628962beb97..fbae451dcb0dcaf34f906674b84d22c3063ad67a 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -494,6 +494,13 @@ def _ParseArgs():
return parser.parse_args()
+def _RoundOrNone(num, decimals = 3):
+ """ Helper to create valid JSON output
+ """
+ if num is None:
+ return None
+ return round(num, decimals)
+
def _Rename(ent):
"""Revert chain names to original names.
@@ -614,7 +621,7 @@ def _LocalScoresToJSONDict(score_dict):
for ch, ch_scores in score_dict.items():
for num, s in ch_scores.items():
ins_code = num.ins_code.strip("\u0000")
- json_dict[f"{ch}.{num.num}.{ins_code}"] = s
+ json_dict[f"{ch}.{num.num}.{ins_code}"] = _RoundOrNone(s)
return json_dict
def _InterfaceResiduesToJSONList(interface_dict):
@@ -635,7 +642,8 @@ def _PatchScoresToJSONList(interface_dict, score_dict):
"""
json_list = list()
for ch, ch_nums in interface_dict.items():
- json_list += score_dict[ch]
+ for item in score_dict[ch]:
+ json_list.append(_RoundOrNone(item))
return json_list
def _GetAlignedResidues(aln):
@@ -711,7 +719,7 @@ def _Process(model, reference, args):
out["pepnuc_aligned_residues"] = _GetAlignedResidues(scorer.pepnuc_aln)
if args.lddt:
- out["lddt"] = scorer.lddt
+ out["lddt"] = _RoundOrNone(scorer.lddt)
if args.local_lddt:
out["local_lddt"] = _LocalScoresToJSONDict(scorer.local_lddt)
@@ -725,7 +733,7 @@ def _Process(model, reference, args):
out["reference_bad_angles"] = [x.ToJSON() for x in scorer.target_bad_angles]
if args.bb_lddt:
- out["bb_lddt"] = scorer.bb_lddt
+ out["bb_lddt"] = _RoundOrNone(scorer.bb_lddt)
if args.bb_local_lddt:
out["bb_local_lddt"] = _LocalScoresToJSONDict(scorer.bb_local_lddt)
@@ -737,13 +745,15 @@ def _Process(model, reference, args):
out["local_cad_score"] = _LocalScoresToJSONDict(scorer.local_cad_score)
if args.qs_score:
- out["qs_global"] = scorer.qs_global
- out["qs_best"] = scorer.qs_best
+ out["qs_global"] = _RoundOrNone(scorer.qs_global)
+ out["qs_best"] = _RoundOrNone(scorer.qs_best)
out["qs_reference_interfaces"] = scorer.qs_target_interfaces
out["qs_model_interfaces"] = scorer.qs_model_interfaces
out["qs_interfaces"] = scorer.qs_interfaces
- out["per_interface_qs_global"] = scorer.per_interface_qs_global
- out["per_interface_qs_best"] = scorer.per_interface_qs_best
+ out["per_interface_qs_global"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_qs_global]
+ out["per_interface_qs_best"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_qs_best]
if args.ics or args.ips:
out["reference_contacts"] = scorer.native_contacts
@@ -751,39 +761,45 @@ def _Process(model, reference, args):
out["contact_reference_interfaces"] = scorer.contact_target_interfaces
if args.ics:
- out["ics_precision"] = scorer.ics_precision
- out["ics_recall"] = scorer.ics_recall
- out["ics"] = scorer.ics
- out["per_interface_ics_precision"] = scorer.per_interface_ics_precision
- out["per_interface_ics_recall"] = scorer.per_interface_ics_recall
- out["per_interface_ics"] = scorer.per_interface_ics
+ out["ics_precision"] = _RoundOrNone(scorer.ics_precision)
+ out["ics_recall"] = _RoundOrNone(scorer.ics_recall)
+ out["ics"] = _RoundOrNone(scorer.ics)
+ out["per_interface_ics_precision"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ics_precision]
+ out["per_interface_ics_recall"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ics_recall]
+ out["per_interface_ics"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ics]
if args.ips:
- out["ips_precision"] = scorer.ips_precision
- out["ips_recall"] = scorer.ips_recall
- out["ips"] = scorer.ips
- out["per_interface_ips_precision"] = scorer.per_interface_ips_precision
- out["per_interface_ips_recall"] = scorer.per_interface_ips_recall
- out["per_interface_ips"] = scorer.per_interface_ips
+ out["ips_precision"] = _RoundOrNone(scorer.ips_precision)
+ out["ips_recall"] = _RoundOrNone(scorer.ips_recall)
+ out["ips"] = _RoundOrNone(scorer.ips)
+ out["per_interface_ips_precision"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ips_precision]
+ out["per_interface_ips_recall"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ips_recall]
+ out["per_interface_ips"] = \
+ [_RoundOrNone(x) for x in scorer.per_interface_ips]
if args.dockq:
out["dockq_reference_interfaces"] = scorer.dockq_target_interfaces
out["dockq_interfaces"] = scorer.dockq_interfaces
- out["dockq"] = scorer.dockq_scores
- out["fnat"] = scorer.fnat
- out["irmsd"] = scorer.irmsd
- out["lrmsd"] = scorer.lrmsd
+ out["dockq"] = [_RoundOrNone(x) for x in scorer.dockq_scores]
+ out["fnat"] = [_RoundOrNone(x) for x in scorer.fnat]
+ out["irmsd"] = [_RoundOrNone(x) for x in scorer.irmsd]
+ out["lrmsd"] = [_RoundOrNone(x) for x in scorer.lrmsd]
out["nnat"] = scorer.nnat
out["nmdl"] = scorer.nmdl
- out["dockq_ave"] = scorer.dockq_ave
- out["dockq_wave"] = scorer.dockq_wave
- out["dockq_ave_full"] = scorer.dockq_ave_full
- out["dockq_wave_full"] = scorer.dockq_wave_full
+ out["dockq_ave"] = _RoundOrNone(scorer.dockq_ave)
+ out["dockq_wave"] = _RoundOrNone(scorer.dockq_wave)
+ out["dockq_ave_full"] = _RoundOrNone(scorer.dockq_ave_full)
+ out["dockq_wave_full"] = _RoundOrNone(scorer.dockq_wave_full)
if args.rigid_scores:
- out["oligo_gdtts"] = scorer.gdtts
- out["oligo_gdtha"] = scorer.gdtha
- out["rmsd"] = scorer.rmsd
+ out["oligo_gdtts"] = _RoundOrNone(scorer.gdtts)
+ out["oligo_gdtha"] = _RoundOrNone(scorer.gdtha)
+ out["rmsd"] = _RoundOrNone(scorer.rmsd)
data = scorer.transform.data
out["transform"] = [data[i:i + 4] for i in range(0, len(data), 4)]
@@ -794,11 +810,12 @@ def _Process(model, reference, args):
_InterfaceResiduesToJSONList(scorer.target_interface_residues)
out["patch_qs"] = _PatchScoresToJSONList(scorer.model_interface_residues,
scorer.patch_qs)
+
out["patch_dockq"] = _PatchScoresToJSONList(scorer.model_interface_residues,
scorer.patch_dockq)
if args.tm_score:
- out["tm_score"] = scorer.tm_score
+ out["tm_score"] = _RoundOrNone(scorer.tm_score)
out["usalign_mapping"] = scorer.usalign_mapping
if args.dump_structures:
diff --git a/modules/mol/alg/pymod/stereochemistry.py b/modules/mol/alg/pymod/stereochemistry.py
index b3708648bf26a4e331f683e9fe7309196450f72c..b6aa98a58406036ede61eb3a072d5982fd0b50f7 100644
--- a/modules/mol/alg/pymod/stereochemistry.py
+++ b/modules/mol/alg/pymod/stereochemistry.py
@@ -365,7 +365,7 @@ class ClashInfo:
self.dist = dist
self.tolerated_dist = tolerated_dist
- def ToJSON(self):
+ def ToJSON(self, decimals = 3):
""" Return JSON serializable dict
Atoms are represented by a string in format:
@@ -373,8 +373,8 @@ class ClashInfo:
"""
return {"a1": _AtomToQualifiedName(self.a1),
"a2": _AtomToQualifiedName(self.a2),
- "dist": self.dist,
- "tolerated_dist": self.tolerated_dist}
+ "dist": round(self.dist, decimals),
+ "tolerated_dist": round(self.tolerated_dist, decimals)}
class BondViolationInfo:
@@ -395,7 +395,7 @@ class BondViolationInfo:
self.exp_length = exp_length
self.std = std
- def ToJSON(self):
+ def ToJSON(self, decimals = 3):
""" Return JSON serializable dict
Atoms are represented by a string in format:
@@ -403,9 +403,9 @@ class BondViolationInfo:
"""
return {"a1": _AtomToQualifiedName(self.a1),
"a2": _AtomToQualifiedName(self.a2),
- "length": self.length,
- "exp_length": self.exp_length,
- "std": self.std}
+ "length": round(self.length, decimals),
+ "exp_length": round(self.exp_length, decimals),
+ "std": round(self.std, decimals)}
class AngleViolationInfo:
@@ -428,7 +428,7 @@ class AngleViolationInfo:
self.exp_angle = exp_angle
self.std = std
- def ToJSON(self):
+ def ToJSON(self, decimals = 3):
""" Return JSON serializable dict
Atoms are represented by a string in format:
@@ -437,9 +437,9 @@ class AngleViolationInfo:
return {"a1": _AtomToQualifiedName(self.a1),
"a2": _AtomToQualifiedName(self.a2),
"a3": _AtomToQualifiedName(self.a3),
- "angle": self.angle,
- "exp_angle": self.exp_angle,
- "std": self.std}
+ "angle": round(self.angle, decimals),
+ "exp_angle": round(self.exp_angle, decimals),
+ "std": round(self.std, decimals)}
def GetClashes(ent, vdw_radii = None, tolerance = 1.5, disulfid_dist = 2.03,