diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index e91457d689304560db9771f6fc6f07a1b44796fb..95e89e58a775495064f1f9ac1b26eefd22cd0994 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -73,7 +73,7 @@ from ost.io import (LoadPDB, LoadMMCIF, SavePDB, MMCifInfoBioUnit, MMCifInfo,
MMCifInfoTransOp, ReadStereoChemicalPropsFile)
from ost import PushVerbosityLevel
from ost.mol.alg import (qsscoring, Molck, MolckSettings, lDDTSettings,
- CheckStructure)
+ CheckStructure, ResidueNamesMatch)
from ost.conop import CompoundLib
@@ -214,10 +214,10 @@ def _ParseArgs():
nargs="+",
type=lambda x: x.split(":"),
dest="chain_mapping",
- help=("Mapping of chains between the model and the reference.\n"
+ help=("Mapping of chains between the reference and the model.\n"
"Each separate mapping consist of key:value pairs where key\n"
- "is the chain name in model and value is the chain name in\n"
- "reference."))
+ "is the chain name in reference and value is the chain name in\n"
+ "model."))
parser.add_argument(
"-rna",
"--residue-number-alignment",
@@ -304,12 +304,19 @@ def _ParseArgs():
"separation is higher than the provided parameter are\n"
"considered when computing the score"))
parser.add_argument(
- "-cc",
- "--consistency-checks",
- dest="consistency_checks",
+ "-ic",
+ "--ignore-consistency-checks",
+ dest="ignore_consistency_checks",
default=False,
action="store_true",
- help=("Residue name consistency checks."))
+ help=("Ignore consistency checks. By default residue name\n"
+ "consistency between a model-reference pair would be checked\n"
+ "and an error will be rised if no valid pair is found (For\n"
+ "mmCIF there could be more than one biounit in one file).\n"
+ "The pair that does not conform to the check will be skipped.\n"
+ "If the option is selected consistency checks will also be\n"
+ "performed but only a warning will be shown and the pair will\b"
+ "evaluated."))
parser.add_argument(
"-spr",
"--save-per-residue-scores",
@@ -397,9 +404,15 @@ def _ParseArgs():
def _RevertChainNames(ent):
- """Revert chain names to original names."""
+ """Revert chain names to original names.
+
+ By default the first chain with given name will not have any number
+ attached to it ie. if there are two chains mapping to chain A the resulting
+ chain names will be: A and A2.
+ """
editor = ent.EditXCS()
suffix = "_tmp" # just a suffix for temporary chain name
+ separator = "" # dot causes selection error
used_names = dict()
reverted_chains = dict()
for chain in ent.chains:
@@ -414,12 +427,13 @@ def _RevertChainNames(ent):
continue
new_name = original_name
if new_name not in used_names:
- used_names[original_name] = 1
+ used_names[original_name] = 2
reverted_chains[chain.name] = new_name
editor.RenameChain(chain, chain.name + suffix)
else:
- new_name = "%s_%i" % (original_name, # dot causes selection error
- used_names[original_name])
+ new_name = "%s%s%i" % (original_name,
+ separator,
+ used_names[original_name])
reverted_chains[chain.name] = new_name
editor.RenameChain(chain, chain.name + suffix)
used_names[original_name] += 1
@@ -429,6 +443,15 @@ def _RevertChainNames(ent):
ost.LogInfo("Reverted chains: %s" % ", ".join(rev_out))
+def _CheckConsistency(reference, model, chain_mapping, log_error):
+ is_cons = True
+ for ref_cname, mdl_cname in chain_mapping.iteritems():
+ ref_chain = reference.Select("cname=%s" % ref_cname)
+ mdl_chain = model.Select("cname=%s" % mdl_cname)
+ is_cons = ResidueNamesMatch(ref_chain, mdl_chain, log_error)
+ return is_cons
+
+
def _ReadStructureFile(path):
"""Safely read structure file into OST entity.
@@ -566,6 +589,7 @@ def _Main():
result["options"]["cwd"] = os.path.abspath(os.getcwd())
#
# Perform scoring
+ skipped = list()
for model in models:
model_name = model.GetName()
model_results = dict()
@@ -584,6 +608,39 @@ def _Main():
"Using custom chain mapping: %s" % str(
opts.chain_mapping))
qs_scorer.chain_mapping = opts.chain_mapping
+ else:
+ qs_scorer.chain_mapping # just to initialize it
+ ost.LogInfo("-" * 80)
+ ost.LogInfo("Checking consistency between %s and %s" % (
+ model_name, reference_name))
+ is_cons = _CheckConsistency(
+ reference,
+ model,
+ qs_scorer.chain_mapping,
+ not opts.ignore_consistency_checks)
+ if not opts.ignore_consistency_checks:
+ if not is_cons:
+ msg = (("Residue names in model %s and in reference "
+ "%s are inconsistent. Skipping.") % (
+ model_name,
+ reference_name))
+ ost.LogError(msg)
+ skipped.append(True)
+ continue
+ else:
+ ost.LogInfo("Consistency check: OK")
+ skipped.append(False)
+ else:
+ skipped.append(False)
+ if not is_cons:
+ msg = (("Residue names in model %s and in reference "
+ "%s are inconsistent.\nThis might lead to "
+ "corrupted results.") % (
+ model_name,
+ reference_name))
+ ost.LogWarning(msg)
+ else:
+ ost.LogInfo("Consistency check: OK")
if opts.qs_score:
ost.LogInfo("-" * 80)
ost.LogInfo("Computing QS-score")
@@ -622,8 +679,8 @@ def _Main():
radius=opts.inclusion_radius,
sequence_separation=opts.sequence_separation,
sel=opts.selection,
- structural_checks=False,
- consistency_checks=opts.consistency_checks,
+ structural_checks=False, # These are performed elsewhere
+ consistency_checks=False, # These are performed elsewhere
label="lddt")
ost.LogInfo("lDDT settings: ")
ost.LogInfo(str(lddt_settings).rstrip())
@@ -725,6 +782,7 @@ def _Main():
reference_results["lddt"] = lddt_results
model_results[reference_name] = reference_results
if opts.dump_structures:
+ ost.LogInfo("-" * 80)
ref_output_path = os.path.join(
os.path.dirname(opts.reference),
reference_name + opts.dump_suffix)
@@ -747,7 +805,12 @@ def _Main():
ost.LogError("Cannot save model: %s" % str(ex))
result["result"][model_name] = model_results
+ if all(skipped) and len(skipped) > 0:
+ raise RuntimeError("Consistency check failed for all model-reference "
+ "pairs.")
if opts.output is not None:
+ ost.LogInfo("#" * 80)
+ ost.LogInfo("Saving output into %s" % opts.output)
with open(opts.output, "w") as outfile:
outfile.write(json.dumps(result, indent=4))
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 949e2fb5af8211cd43a8e7482ea3c984c9af8a8d..4e4545f4579232d29f4b227c5cda38294f10ded9 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -566,6 +566,9 @@ void lDDTScorer::_Init(){
throw std::runtime_error(errstr.str());
}
}
+ if (settings.consistency_checks) {
+ _CheckConsistency();
+ }
}
Real lDDTScorer::GetGlobalScore(){
@@ -641,13 +644,9 @@ bool lDDTScorer::IsValid(){
void lDDTScorer::_CheckConsistency(){
for (std::vector<EntityView>::const_iterator ref_list_it = references_view.begin();
ref_list_it != references_view.end(); ++ref_list_it) {
- bool cons_check = ResidueNamesMatch(model_view, *ref_list_it, settings.consistency_checks);
+ bool cons_check = ResidueNamesMatch(model_view, *ref_list_it, true);
if (cons_check == false) {
- if (settings.consistency_checks == true) {
- throw std::runtime_error("Residue names in model and in reference structure(s) are inconsistent.");
- } else {
- LOG_WARNING("Residue names in model and in reference structure(s) are inconsistent.");
- }
+ throw std::runtime_error("Residue names in model and in reference structure(s) are inconsistent.");
}
}
}