diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 0014f7dd3802ba1f97dee4d26142e02bc64e2cec..629a1de7d61b5a434963b4c375e9fdb1af3a6fa5 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -487,11 +487,15 @@ def _Main():
PushVerbosityLevel(opts.verbosity)
#
# Read the input files
- ost.LogInfo("Reading model from %s" % opts.model)
+ ost.LogInfo("#" * 80)
+ ost.LogInfo("Reading input files")
+ ost.LogInfo(" --> reading model from %s" % opts.model)
models = _ReadStructureFile(opts.model)
- ost.LogInfo("Reading reference from %s" % opts.reference)
+ ost.LogInfo(" --> reading reference from %s" % opts.reference)
references = _ReadStructureFile(opts.reference)
if opts.molck:
+ ost.LogInfo("#" * 80)
+ ost.LogInfo("Cleaning up input with Molck")
for i in range(len(references)):
_MolckEntity(references[i], opts)
references[i] = references[i].CreateFullView()
@@ -504,28 +508,32 @@ def _Main():
for i in range(len(models)):
models[i] = models[i].CreateFullView()
if opts.structural_checks:
+ ost.LogInfo("#" * 80)
+ ost.LogInfo("Performing structural checks")
stereochemical_parameters = ReadStereoChemicalPropsFile(
opts.parameter_file)
- ost.LogInfo("Performing structural checks for reference(s)")
+ ost.LogInfo(" --> for reference(s)")
for reference in references:
+ ost.LogInfo("Checking %s" % reference.GetName())
CheckStructure(reference,
stereochemical_parameters.bond_table,
stereochemical_parameters.angle_table,
stereochemical_parameters.nonbonded_table,
opts.bond_tolerance,
opts.angle_tolerance)
- ost.LogInfo("Performing structural checks for model(s)")
+ ost.LogInfo(" --> for model(s)")
for model in models:
+ ost.LogInfo("Checking %s" % model.GetName())
CheckStructure(model,
stereochemical_parameters.bond_table,
stereochemical_parameters.angle_table,
stereochemical_parameters.nonbonded_table,
opts.bond_tolerance,
opts.angle_tolerance)
-
if len(models) > 1 or len(references) > 1:
+ ost.LogInfo("#" * 80)
ost.LogInfo(
- "Multiple complexes detected. All combinations will be tried.")
+ "Multiple complexes mode ON. All combinations will be tried.")
result = {
"result": {},
@@ -533,13 +541,15 @@ def _Main():
result["options"]["cwd"] = os.path.abspath(os.getcwd())
#
# Perform scoring
+ ost.LogInfo("Performing 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" % (
+ ost.LogInfo("#" * 80)
+ ost.LogInfo("Comparing %s to %s" % (
model_name,
reference_name))
qs_scorer = qsscoring.QSscorer(reference,
@@ -551,7 +561,7 @@ def _Main():
opts.chain_mapping))
qs_scorer.chain_mapping = opts.chain_mapping
if opts.qs_score:
- ost.LogInfo("Computing QS-score")
+ ost.LogInfo("-> Computing QS-score")
try:
reference_results["qs_score"] = {
"status": "SUCCESS",
@@ -576,7 +586,6 @@ def _Main():
}
# Calculate lDDT
if opts.lddt:
- ost.LogInfo("Computing lDDT")
lddt_results = {
"single_chain_lddt": list()
}
@@ -604,14 +613,26 @@ def _Main():
model_chain = lddt_scorer.model.chains[0].GetName()
reference_chain = \
lddt_scorer.references[0].chains[0].GetName()
+ ost.LogInfo((" --> Computing lDDT between model "
+ "chain %s and reference chain %s") % (
+ model_chain,
+ reference_chain))
lddt_results["single_chain_lddt"].append({
"status": "SUCCESS",
"error": "",
"model_chain": model_chain,
"reference_chain": reference_chain,
"global_score": lddt_scorer.global_score,
- "conserved_contacts": lddt_scorer.conserved_contacts,
+ "conserved_contacts":
+ lddt_scorer.conserved_contacts,
"total_contacts": lddt_scorer.total_contacts})
+ ost.LogInfo("Global LDDT score: %.4f" %
+ lddt_scorer.global_score)
+ ost.LogInfo(
+ "(%i conserved distances out of %i checked, over "
+ "%i thresholds)" % (lddt_scorer.conserved_contacts,
+ lddt_scorer.total_contacts,
+ len(lddt_settings.cutoffs)))
except Exception as ex:
ost.LogError('Single chain lDDT failed:', str(ex))
lddt_results["single_chain_lddt"].append({
@@ -624,10 +645,14 @@ def _Main():
"total_contacts": 0.0})
# perform oligo lddt scoring
try:
+ ost.LogInfo(' --> Computing oligomeric lDDT score')
lddt_results["oligo_lddt"] = {
"status": "SUCCESS",
"error": "",
"global_score": oligo_lddt_scorer.oligo_lddt}
+ ost.LogInfo(
+ "Oligo lDDT score: %.4f" %
+ oligo_lddt_scorer.oligo_lddt)
except Exception as ex:
ost.LogError('Oligo lDDT failed:', str(ex))
lddt_results["oligo_lddt"] = {
@@ -635,11 +660,16 @@ def _Main():
"error": str(ex),
"global_score": 0.0}
try:
+ ost.LogInfo(' --> Computing weighted lDDT score')
lddt_results["weighted_lddt"] = {
"status": "SUCCESS",
"error": "",
"global_score": oligo_lddt_scorer.weighted_lddt}
+ ost.LogInfo(
+ "Weighted lDDT score: %.4f" %
+ oligo_lddt_scorer.weighted_lddt)
except Exception as ex:
+ ost.LogError('Weighted lDDT failed:', str(ex))
lddt_results["weighted_lddt"] = {
"status": "FAILURE",
"error": str(ex),
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 9c1da337832d290bb497001e4d5dd921d55cada2..16e4357c8cf4d9e03ba9be3253fe8ad04fc8c37d 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -16,7 +16,7 @@ Scoring of quaternary structures as in Martino's 2017 paper.
Authors: Gerardo Tauriello, Martino Bertoni
"""
-from ost import mol, geom, conop, seq, settings
+from ost import mol, geom, conop, seq, settings, PushVerbosityLevel
from ost import LogError, LogWarning, LogScript, LogInfo, LogVerbose, LogDebug
from ost.bindings.clustalw import ClustalW
from ost.mol.alg import lDDTScorer
@@ -870,7 +870,6 @@ class OligoLDDTScorer(object):
def oligo_lddt(self):
"""Fills cached lddt_score, lddt_mdl and lddt_ref."""
if self._oligo_lddt is None:
- LogInfo('Computing oligomeric lDDT score')
LogInfo('Reference %s has: %s chains' % (self.ref.GetName(), self.ref.chain_count))
LogInfo('Model %s has: %s chains' % (self.mdl.GetName(), self.mdl.chain_count))
@@ -893,12 +892,8 @@ class OligoLDDTScorer(object):
self._sc_lddt_scorers = list()
for aln in self.alignments:
# Get chains and renumber according to alignment (for lDDT)
- ch_ref = aln.GetSequence(0).GetName()
reference = Renumber(aln.GetSequence(0)).CreateFullView()
- ch_mdl = aln.GetSequence(1).GetName()
model = Renumber(aln.GetSequence(1)).CreateFullView()
- LogInfo(("Computing lDDT between model chain %s and "
- "reference chain %s") % (ch_mdl, ch_ref))
lddt_scorer = lDDTScorer(
references=[reference],
model=model,
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 29d1aabfb395304464c8013a2207c590dd7902aa..19c24c01882d5bcb9fc3fcea09d779fbd81a16c1 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -291,6 +291,11 @@ int main (int argc, char **argv)
}
}
CleanlDDTReferences(ref_list);
+ if (ref_list.size()==1) {
+ std::cout << "Multi-reference mode: Off" << std::endl;
+ } else {
+ std::cout << "Multi-reference mode: On" << std::endl;
+ }
glob_dist_list = PreparelDDTGlobalRDMap(ref_list,
settings.cutoffs,
settings.sequence_separation,
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 321f27e28a60a485c407021df3274d8db4ecd319..949e2fb5af8211cd43a8e7482ea3c984c9af8a8d 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -655,13 +655,14 @@ void lDDTScorer::_CheckConsistency(){
void lDDTScorer::_ComputelDDT(){
std::pair<int,int> cov = ComputeCoverage(model_view,glob_dist_list);
if (cov.second == -1) {
- std::cout << "Coverage: 0 (0 out of 0 residues)" << std::endl;
+ LOG_INFO("Coverage: 0 (0 out of 0 residues)");
} else {
- std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+ std::stringstream sout;
+ sout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)";
+ LOG_INFO(sout.str());
}
if (cov.first == 0) {
- std::cout << "Global LDDT score: 0.0" << std::endl;
_num_tot_con = 0;
_num_cons_con = 0;
_global_score = 0.0;
@@ -671,9 +672,6 @@ void lDDTScorer::_ComputelDDT(){
std::pair<int,int> total_ov=alg::LocalDistDiffTest(model_view, glob_dist_list, settings.cutoffs, settings.sequence_separation, settings.label);
Real lddt = static_cast<Real>(total_ov.first)/(static_cast<Real>(total_ov.second) ? static_cast<Real>(total_ov.second) : 1);
- std::cout << "Global LDDT score: " << std::setprecision(4) << lddt << std::endl;
- std::cout << "(" << std::fixed << total_ov.first << " conserved distances out of " << total_ov.second
- << " checked, over " << settings.cutoffs.size() << " thresholds)" << std::endl;
_num_tot_con = total_ov.second ? total_ov.second : 1;
_num_cons_con = total_ov.first;
_global_score = lddt;
@@ -943,10 +941,8 @@ GlobalRDMap PreparelDDTGlobalRDMap(const std::vector<EntityView>& ref_list,
Real max_dist){
GlobalRDMap glob_dist_list;
if (ref_list.size()==1) {
- std::cout << "Multi-reference mode: Off" << std::endl;
glob_dist_list = CreateDistanceList(ref_list[0], max_dist);
} else {
- std::cout << "Multi-reference mode: On" << std::endl;
glob_dist_list = CreateDistanceListFromMultipleReferences(ref_list,
cutoff_list,
sequence_separation,