diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 3560bf4a05c514228b1d4e888f4d70fdd0cd6504..2e685cd685bc894dca4d4858885acc1d9b1a4d42 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -12,11 +12,10 @@ import argparse
import ost
from ost.io import (LoadPDB, LoadMMCIF, MMCifInfoBioUnit, MMCifInfo,
- MMCifInfoTransOp, StereoChemicalParamsReader)
+ MMCifInfoTransOp, ReadStereoChemicalPropsFile)
from ost import PushVerbosityLevel
-from ost.mol.alg import (qsscoring, Molck, MolckSettings, CleanlDDTReferences,
- PreparelDDTGlobalRDMap, lDDTSettings, CheckStructure,
- LocalDistDiffTest)
+from ost.mol.alg import (qsscoring, Molck, MolckSettings, lDDTSettings,
+ lDDTScorer)
from ost.conop import CompoundLib
from ost.seq.alg.renumber import Renumber
@@ -220,7 +219,9 @@ def _ParseArgs():
dest="sequence_separation",
type=int,
default=0,
- help=("Sequence separation."))
+ help=("Sequence separation. Only distances between residues whose "
+ "separation is higher than the provided parameter are "
+ "considered when computing the score"))
parser.add_argument(
"-cc",
"--consistency-checks",
@@ -363,22 +364,6 @@ def _ReadStructureFile(path):
return entities
-def _ComputelDDT(model, references, settings):
- CleanlDDTReferences(references)
- rdmap = PreparelDDTGlobalRDMap(references, settings)
- stereochemical_parameters = StereoChemicalParamsReader(
- settings.parameter_file_path)
- stereochemical_parameters.Read()
- CheckStructure(ent=model,
- bond_table=stereochemical_parameters.bond_table,
- angle_table=stereochemical_parameters.angle_table,
- nonbonded_table=stereochemical_parameters.nonbonded_table,
- bond_tolerance=settings.bond_tolerance,
- angle_tolerance=settings.angle_tolerance)
- global_score = LocalDistDiffTest(model, references, rdmap, settings)
- return global_score
-
-
def _MolckEntity(entity, options):
"""Molck the entity."""
lib = CompoundLib.Load(options.compound_library)
@@ -417,14 +402,21 @@ def _Main():
ost.LogInfo(
"Multiple complexes detected. All combinations will be tried.")
- result = {"result": []}
+ result = {
+ "result": {},
+ "options": vars(opts)}
+ result["options"]["cwd"] = os.path.abspath(os.getcwd())
#
# Perform scoring
for model in models:
+ model_name = model.GetName()
+ model_results = dict()
for reference in references:
+ reference_name = reference.GetName()
+ reference_results = dict()
ost.LogInfo("#\nComparing %s to %s" % (
- model.GetName(),
- reference.GetName()))
+ model_name,
+ reference_name))
qs_scorer = qsscoring.QSscorer(reference, model)
if opts.qs_score:
ost.LogInfo("Computing QS-score")
@@ -434,42 +426,46 @@ def _Main():
"Using custom chain mapping: %s" % str(
opts.chain_mapping))
qs_scorer.chain_mapping = opts.chain_mapping
- result["result"].append({
+ reference_results["qs_score"] = {
"status": "SUCCESS",
"error": "",
- "model_name": model.GetName(),
- "reference_name": reference.GetName(),
+ "model_name": model_name,
+ "reference_name": reference_name,
"global_score": qs_scorer.global_score,
- "lddt_score": qs_scorer.lddt_score,
+ "oligo_lddt_score": qs_scorer.lddt_score,
"best_score": qs_scorer.best_score,
"chain_mapping": qs_scorer.chain_mapping
- })
+ }
except qsscoring.QSscoreError as ex:
# default handling: report failure and set score to 0
ost.LogError('QSscore failed:', str(ex))
- result["result"].append({
+ reference_results["qs-score"] = {
"status": "FAILURE",
"error": str(ex),
- "model_name": model.GetName(),
+ "model_name": model_name,
"reference_name": reference.GetName(),
"global_score": 0.0,
- "lddt_score": 0.0,
+ "oligo_lddt_score": 0.0,
"best_score": 0.0,
"chain_mapping": None
- })
+ }
# Calculate lDDT
if opts.lddt:
ost.LogInfo("Computing lDDT")
+ lddt_results = {
+ "single_chain_lddt": list()
+ }
lddt_settings = lDDTSettings(
bond_tolerance=opts.bond_tolerance,
angle_tolerance=opts.angle_tolerance,
radius=opts.inclusion_radius,
sequence_separation=opts.sequence_separation,
sel=opts.selection,
- parameter_file_path=opts.parameter_file,
structural_checks=opts.structural_checks,
consistency_checks=opts.consistency_checks,
label="lddt")
+ stereochemical_parameters = ReadStereoChemicalPropsFile(
+ opts.parameter_file)
if opts.verbosity > 3:
lddt_settings.PrintParameters()
# Perform scoring
@@ -477,13 +473,23 @@ def _Main():
for aln in qs_scorer.alignments:
# Get chains and renumber according to alignment (for lDDT)
ch_ref = aln.GetSequence(0).GetName()
- reference_view = Renumber(
- aln.GetSequence(0)).CreateFullView()
+ reference = Renumber(aln.GetSequence(0))
ch_mdl = aln.GetSequence(1).GetName()
- model_view = Renumber(aln.GetSequence(1)).CreateFullView()
+ model = Renumber(aln.GetSequence(1))
ost.LogInfo(("Computing lDDT between model chain %s and "
"reference chain %s") % (ch_mdl, ch_ref))
- _ComputelDDT(model_view, [reference_view], lddt_settings)
+ lddt_scorer = lDDTScorer(
+ references=[reference],
+ model=model,
+ settings=lddt_settings,
+ stereochemical_params=stereochemical_parameters)
+ lddt_results["single_chain_lddt"].append({
+ "model_chain": ch_mdl,
+ "reference_chain": ch_ref,
+ "global_score": lddt_scorer.global_score})
+ reference_results["lddt"] = lddt_results
+ model_results[reference_name] = reference_results
+ result["result"][model_name] = model_results
if opts.output is not None:
with open(opts.output, "w") as outfile:
diff --git a/actions/ost-qs-score b/actions/ost-qs-score
index ffdc76b03d6b7a27e3e55ec9f468fae18bf674a3..0a92262a70688ba535ee902a6599a14ff0f10c29 100644
--- a/actions/ost-qs-score
+++ b/actions/ost-qs-score
@@ -159,7 +159,7 @@ def _Main():
"model_name": model.GetName(),
"reference_name": reference.GetName(),
"global_score": qs_scorer.global_score,
- "lddt_score": qs_scorer.lddt_score,
+ "oligo_lddt_score": qs_scorer.lddt_score,
"best_score": qs_scorer.best_score,
"chain_mapping": qs_scorer.chain_mapping
})
@@ -172,7 +172,7 @@ def _Main():
"model_name": model.GetName(),
"reference_name": reference.GetName(),
"global_score": 0.0,
- "lddt_score": 0.0,
+ "oligo_lddt_score": 0.0,
"best_score": 0.0,
"chain_mapping": None
})