diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 7104d26d7be36c9c545da89bf80a1bd056183112..6121d05103fce84047d159a4d485b8a07d1e5a57 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -15,7 +15,7 @@ from ost.io import (LoadPDB, LoadMMCIF, MMCifInfoBioUnit, MMCifInfo,
MMCifInfoTransOp, ReadStereoChemicalPropsFile)
from ost import PushVerbosityLevel
from ost.mol.alg import (qsscoring, Molck, MolckSettings, lDDTSettings,
- lDDTScorer)
+ lDDTScorer, CheckStructure)
from ost.conop import CompoundLib
from ost.seq.alg.renumber import Renumber
@@ -407,14 +407,34 @@ def _Main():
# Read the input files
ost.LogInfo("Reading model from %s" % opts.model)
models = _ReadStructureFile(opts.model)
- if opts.molck:
- for model in models:
- _MolckEntity(model, opts)
ost.LogInfo("Reading reference from %s" % opts.reference)
references = _ReadStructureFile(opts.reference)
if opts.molck:
+ for i in range(len(references)):
+ _MolckEntity(references[i], opts)
+ references[i] = references[i].CreateFullView()
+ for i in range(len(models)):
+ _MolckEntity(models[i], opts)
+ models[i] = models[i].CreateFullView()
+ if opts.structural_checks:
+ stereochemical_parameters = ReadStereoChemicalPropsFile(
+ opts.parameter_file)
+ ost.LogInfo("Performing structural checks for reference(s)")
for reference in references:
- _MolckEntity(reference, opts)
+ 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)")
+ for model in models:
+ 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(
@@ -479,11 +499,9 @@ def _Main():
radius=opts.inclusion_radius,
sequence_separation=opts.sequence_separation,
sel=opts.selection,
- structural_checks=opts.structural_checks,
+ structural_checks=False,
consistency_checks=opts.consistency_checks,
label="lddt")
- stereochemical_parameters = ReadStereoChemicalPropsFile(
- opts.parameter_file)
if opts.verbosity > 3:
lddt_settings.PrintParameters()
# Perform single chain scoring
@@ -492,16 +510,15 @@ def _Main():
for aln in qs_scorer.alignments:
# Get chains and renumber according to alignment (for lDDT)
ch_ref = aln.GetSequence(0).GetName()
- reference = Renumber(aln.GetSequence(0))
+ reference = Renumber(aln.GetSequence(0)).CreateFullView()
ch_mdl = aln.GetSequence(1).GetName()
- model = Renumber(aln.GetSequence(1))
+ model = Renumber(aln.GetSequence(1)).CreateFullView()
ost.LogInfo(("Computing lDDT between model chain %s and "
"reference chain %s") % (ch_mdl, ch_ref))
lddt_scorer = lDDTScorer(
references=[reference],
model=model,
- settings=lddt_settings,
- stereochemical_params=stereochemical_parameters)
+ settings=lddt_settings)
try:
lddt_results["single_chain_lddt"].append({
"status": "SUCCESS",
@@ -529,8 +546,7 @@ def _Main():
qs_scorer.qs_ent_2.ent,
qs_scorer.alignments,
qs_scorer.calpha_only,
- lddt_settings,
- stereochemical_parameters)
+ lddt_settings)
lddt_results["oligo_lddt"] = {
"status": "SUCCESS",
"error": "",
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index c57ff0820912c139121aedcd2bb8d2f987d65461..094d8b3aa701e6554d9a732afa91f2b7d883c7fc 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -828,7 +828,7 @@ def GetContacts(entity, calpha_only, dist_thr=12.0):
class OligoLDDTScorer(object):
"""A simple class to calculate oligomeric lDDT score."""
- def __init__(self, ref, mdl, alignments, calpha_only, settings, stereochemical_params):
+ def __init__(self, ref, mdl, alignments, calpha_only, settings):
if mdl.chain_count > ref.chain_count:
LogWarning('MODEL contains more chains than REFERENCE, '
'lDDT is not considering them')
@@ -838,15 +838,13 @@ class OligoLDDTScorer(object):
self.calpha_only = calpha_only
self.alignments = alignments
self.settings = settings
- self.stereochemical_params = stereochemical_params
self._lddt = None
self._lddt_ref = None
self._lddt_mdl = None
self.scorer = lDDTScorer(
- references=[self.lddt_ref],
- model=self.lddt_mdl,
- settings=self.settings,
- stereochemical_params=self.stereochemical_params)
+ references=[self.lddt_ref.Select("")],
+ model=self.lddt_mdl.Select(""),
+ settings=self.settings)
@property
def lddt_ref(self):
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 6ec8be1c33a46af1b8e1353476e1e399b9778fc7..efa15a5ea5c7302050d5612c8f7efed024c7c02b 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -211,21 +211,21 @@ object lDDTScorerInitWrapper(tuple args, dict kwargs){
object self = args[0];
args = tuple(args.slice(1, len(args)));
- std::vector<ost::mol::EntityHandle> reference_list_vector;
+ std::vector<ost::mol::EntityView> reference_list_vector;
if(kwargs.contains("references")){
list reference_list = boost::python::extract<list>(kwargs["references"]);
int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
for (int i=0; i<reference_list_length; i++) {
- reference_list_vector.push_back(boost::python::extract<ost::mol::EntityHandle>(reference_list[i]));
+ reference_list_vector.push_back(boost::python::extract<ost::mol::EntityView>(reference_list[i]));
}
kwargs["references"].del();
} else {
throw std::invalid_argument("'references' argument is required");
}
- ost::mol::EntityHandle model;
+ ost::mol::EntityView model;
if(kwargs.contains("model")){
- model = boost::python::extract<ost::mol::EntityHandle>(kwargs["model"]);
+ model = boost::python::extract<ost::mol::EntityView>(kwargs["model"]);
kwargs["model"].del();
} else {
throw std::invalid_argument("'model' argument is required");
@@ -294,7 +294,7 @@ ost::mol::alg::GlobalRDMap prepare_lddt_global_rdmap_wrapper(const list& referen
return mol::alg::PreparelDDTGlobalRDMap(reference_list_vector, cutoff_list_vector, sequence_separation, max_dist);
}
-list get_lddt_per_residue_stats_wrapper(mol::EntityHandle& model,
+list get_lddt_per_residue_stats_wrapper(mol::EntityView& model,
ost::mol::alg::GlobalRDMap& distance_list,
bool structural_checks,
String label) {
@@ -424,7 +424,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::lDDTScorer>("lDDTScorer", no_init)
.def("__init__", raw_function(lDDTScorerInitWrapper))
- .def(init<std::vector<mol::EntityHandle>&, mol::EntityHandle&, mol::alg::lDDTSettings&, mol::alg::StereoChemicalProps&>())
+ .def(init<std::vector<mol::EntityView>&, mol::EntityView&, mol::alg::lDDTSettings&, mol::alg::StereoChemicalProps&>())
.add_property("global_score", &mol::alg::lDDTScorer::GetGlobalScore)
.add_property("conserved_contacts", &mol::alg::lDDTScorer::GetNumConservedContacts)
.add_property("total_contacts", &mol::alg::lDDTScorer::GetNumTotalContacts)
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index e9117757b0696ca982561ca8f82dd5aad328f491..29d1aabfb395304464c8013a2207c590dd7902aa 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -356,7 +356,8 @@ int main (int argc, char **argv)
// prints the residue-by-residue statistics
std::vector<lDDTLocalScore> local_scores;
- local_scores = GetlDDTPerResidueStats(model, glob_dist_list, settings.structural_checks, settings.label);
+ EntityView outview = model.GetChainList()[0].Select("peptide=true");
+ local_scores = GetlDDTPerResidueStats(outview, glob_dist_list, settings.structural_checks, settings.label);
PrintlDDTPerResidueStats(local_scores, settings.structural_checks, settings.cutoffs.size());
}
return 0;
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index ff745714d213692be233e011319cc1ebb3908c6c..676c955e10651a7b7bc70165b9da24d1c133e095 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -517,81 +517,56 @@ String lDDTLocalScore::GetHeader(bool structural_checks, int cutoffs_length) {
return outstr.str();
}
-
-lDDTScorer::lDDTScorer(std::vector<EntityHandle>& init_references,
- ost::mol::EntityHandle& init_model,
+lDDTScorer::lDDTScorer(std::vector<EntityView>& init_references,
+ ost::mol::EntityView& init_model,
lDDTSettings& init_settings):
- references(init_references),
- model(init_model),
settings(init_settings),
- _score_calculated(false),
- _score_valid(false),
- _has_local_scores(false),
- _num_cons_con(-1),
- _num_tot_con(-1),
- _global_score(-1.0)
+ references_view(init_references),
+ model_view(init_model)
{
- model_view = model.GetChainList()[0].Select("peptide=true");
- _PrepareReferences();
- _PrepareGlobalRDMap();
- if (settings.structural_checks) {
- if (!stereochemical_params.is_valid) {
- throw std::runtime_error(
- "Structural checks are ON. Please provide stereochemical_params to enable structural checks.");
- }
- try {
- CheckStructure(model_view,
- stereochemical_params.bond_table,
- stereochemical_params.angle_table,
- stereochemical_params.nonbonded_table,
- settings.bond_tolerance,
- settings.angle_tolerance);
- } catch (std::exception& e) {
- std::cout << e.what() << std::endl;
- std::stringstream errstr;
- errstr << "Structure check failed: " << e.what();
- throw std::runtime_error(errstr.str());
- }
- }
+ _Init();
}
-lDDTScorer::lDDTScorer(std::vector<EntityHandle>& init_references,
- ost::mol::EntityHandle& init_model,
+lDDTScorer::lDDTScorer(std::vector<EntityView>& init_references,
+ ost::mol::EntityView& init_model,
lDDTSettings& init_settings,
StereoChemicalProps& init_stereochemical_params):
- references(init_references),
- model(init_model),
settings(init_settings),
- stereochemical_params(init_stereochemical_params),
- _score_calculated(false),
- _score_valid(false),
- _has_local_scores(false),
- _num_cons_con(-1),
- _num_tot_con(-1),
- _global_score(-1.0) {
- model_view = model.GetChainList()[0].Select("peptide=true");
- _PrepareReferences();
- _PrepareGlobalRDMap();
- if (settings.structural_checks) {
- if (!stereochemical_params.is_valid) {
- throw std::runtime_error(
- "Please provide stereochemical_params to enable structural_checks.");
- }
- try {
- CheckStructure(model_view,
- stereochemical_params.bond_table,
- stereochemical_params.angle_table,
- stereochemical_params.nonbonded_table,
- settings.bond_tolerance,
- settings.angle_tolerance);
- } catch (std::exception& e) {
- std::cout << e.what() << std::endl;
- std::stringstream errstr;
- errstr << "Structure check failed: " << e.what();
- throw std::runtime_error(errstr.str());
- }
- }
+ references_view(init_references),
+ model_view(init_model),
+ stereochemical_params(init_stereochemical_params) {
+ _Init();
+ }
+
+void lDDTScorer::_Init(){
+ _score_calculated = false;
+ _score_valid = false;
+ _has_local_scores = false;
+ _num_cons_con = -1;
+ _num_tot_con = -1;
+ _global_score = -1.0;
+ CleanlDDTReferences(references_view);
+ _PrepareGlobalRDMap();
+ if (settings.structural_checks) {
+ if (!stereochemical_params.is_valid) {
+ throw std::runtime_error(
+ "Please provide stereochemical_params to enable structural_checks.");
+ }
+ try {
+ CheckStructure(model_view,
+ stereochemical_params.bond_table,
+ stereochemical_params.angle_table,
+ stereochemical_params.nonbonded_table,
+ settings.bond_tolerance,
+ settings.angle_tolerance);
+ } catch (std::exception& e) {
+ std::cout << e.what() << std::endl;
+ std::stringstream errstr;
+ errstr << "Structure check failed: " << e.what();
+ throw std::runtime_error(errstr.str());
+ }
}
+}
Real lDDTScorer::GetGlobalScore(){
if (!_score_calculated) {
@@ -630,7 +605,7 @@ void lDDTScorer::PrintPerResidueStats(){
settings.cutoffs.size());
}
-void lDDTScorer::_PrepareReferences(){
+void lDDTScorer::_PrepareReferences(std::vector<EntityHandle>& references){
for (unsigned int i = 0; i < references.size(); i++) {
if (settings.sel != ""){
std::cout << "Performing \"" << settings.sel << "\" selection on reference " << references[i].GetName() << std::endl;
@@ -646,8 +621,6 @@ void lDDTScorer::_PrepareReferences(){
references_view.push_back(references[i].CreateFullView());
}
}
-
- CleanlDDTReferences(references_view);
}
void lDDTScorer::_PrepareGlobalRDMap(){
@@ -708,7 +681,7 @@ void lDDTScorer::_GetLocallDDT(){
if (!_score_calculated){
_ComputelDDT();
}
- _local_scores = GetlDDTPerResidueStats(model,
+ _local_scores = GetlDDTPerResidueStats(model_view,
glob_dist_list,
settings.structural_checks,
settings.label);
@@ -1022,12 +995,12 @@ void CheckStructure(EntityView& ent,
std::cout << "Distances shorter than tolerance are on average shorter by: " << std::fixed << std::setprecision(5) << clash_info.GetAverageOffset() << std::endl;
}
-std::vector<lDDTLocalScore> GetlDDTPerResidueStats(EntityHandle& model,
+std::vector<lDDTLocalScore> GetlDDTPerResidueStats(EntityView& model,
GlobalRDMap& glob_dist_list,
bool structural_checks,
String label){
std::vector<lDDTLocalScore> scores;
- EntityView outv = model.GetChainList()[0].Select("peptide=true");
+ EntityView outv = model;
for (ChainViewList::const_iterator ci = outv.GetChainList().begin(),
ce = outv.GetChainList().end(); ci != ce; ++ci) {
for (ResidueViewList::const_iterator rit = ci->GetResidueList().begin(),
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index cf77b6c495e9afab94dc4c3bcecd044663bedeba..e155f749cacad95353d7362164b71c5b245b3317 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -96,18 +96,16 @@ class lDDTScorer
{
public:
lDDTSettings settings;
- ost::mol::EntityHandle model;
- std::vector<EntityHandle> references;
EntityView model_view;
std::vector<EntityView> references_view;
GlobalRDMap glob_dist_list;
StereoChemicalProps stereochemical_params;
- lDDTScorer(std::vector<EntityHandle>& init_references,
- ost::mol::EntityHandle& init_model,
+ lDDTScorer(std::vector<EntityView>& init_references,
+ ost::mol::EntityView& init_model,
lDDTSettings& init_settings);
- lDDTScorer(std::vector<EntityHandle>& init_references,
- ost::mol::EntityHandle& init_model,
+ lDDTScorer(std::vector<EntityView>& init_references,
+ ost::mol::EntityView& init_model,
lDDTSettings& init_settings,
StereoChemicalProps& init_stereochemical_params);
Real GetGlobalScore();
@@ -127,10 +125,11 @@ class lDDTScorer
int _num_tot_con;
Real _global_score;
std::vector<lDDTLocalScore> _local_scores;
+ void _Init();
void _ComputelDDT();
void _GetLocallDDT();
void _CheckConsistency();
- void _PrepareReferences();
+ void _PrepareReferences(std::vector<EntityHandle>& references);
void _PrepareGlobalRDMap();
};
@@ -270,7 +269,7 @@ void DLLEXPORT_OST_MOL_ALG CheckStructure(EntityView& ent,
Real bond_tolerance,
Real angle_tolerance);
-std::vector<lDDTLocalScore> DLLEXPORT_OST_MOL_ALG GetlDDTPerResidueStats(EntityHandle& model,
+std::vector<lDDTLocalScore> DLLEXPORT_OST_MOL_ALG GetlDDTPerResidueStats(EntityView& model,
GlobalRDMap& glob_dist_list,
bool structural_checks,
String label);