diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index fd2b9eb2d8fc97c886f0be1f8e133c3f03c2a2f3..0f5ac5190a7c23fb73d2cc234450322dacb86995 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -234,6 +234,28 @@ ost::mol::alg::GlobalRDMap prepare_lddt_global_rdmap_wrapper(const list& ref_lis
return mol::alg::PreparelDDTGlobalRDMap(ref_list_vector, settings);
}
+list get_lddt_per_residue_stats_wrapper(mol::EntityHandle& model,
+ ost::mol::alg::GlobalRDMap& glob_dist_list,
+ ost::mol::alg::lDDTSettings& settings) {
+ std::vector<mol::alg::lDDTLocalScore> scores = GetlDDTPerResidueStats(model, glob_dist_list, settings);
+ list local_scores_list;
+ for (std::vector<mol::alg::lDDTLocalScore>::const_iterator sit = scores.begin(); sit != scores.end(); ++sit) {
+ local_scores_list.append(*sit);
+ }
+ return local_scores_list;
+}
+
+void print_lddt_per_residue_stats_wrapper(list& scores, mol::alg::lDDTSettings settings){
+ int scores_length = boost::python::extract<int>(scores.attr("__len__")());
+ std::vector<mol::alg::lDDTLocalScore> scores_vector(scores_length);
+
+ for (int i=0; i<scores_length; i++) {
+ scores_vector[i] = boost::python::extract<mol::alg::lDDTLocalScore>(scores[i]);
+ }
+
+ return mol::alg::PrintlDDTPerResidueStats(scores_vector, settings);
+}
+
}
@@ -315,6 +337,18 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
.def_readwrite("consistency_checks", &mol::alg::lDDTSettings::consistency_checks)
.def_readwrite("cutoffs", &mol::alg::lDDTSettings::cutoffs)
.def_readwrite("label", &mol::alg::lDDTSettings::label);
+
+ class_<mol::alg::lDDTLocalScore>("lDDTLocalScore", init<String, String, int, String, String, Real, int, int>())
+ .def("ToString", &mol::alg::lDDTLocalScore::ToString)
+ .def("GetHeader", &mol::alg::lDDTLocalScore::GetHeader)
+ .def_readwrite("cname", &mol::alg::lDDTLocalScore::cname)
+ .def_readwrite("rname", &mol::alg::lDDTLocalScore::rname)
+ .def_readwrite("rnum", &mol::alg::lDDTLocalScore::rnum)
+ .def_readwrite("is_assessed", &mol::alg::lDDTLocalScore::is_assessed)
+ .def_readwrite("quality_problems", &mol::alg::lDDTLocalScore::quality_problems)
+ .def_readwrite("local_lddt", &mol::alg::lDDTLocalScore::local_lddt)
+ .def_readwrite("conserved_dist", &mol::alg::lDDTLocalScore::conserved_dist)
+ .def_readwrite("total_dist", &mol::alg::lDDTLocalScore::total_dist);
def("FillClashingDistances",&fill_clashing_distances_wrapper);
def("FillStereoChemicalParams",&fill_stereochemical_params_wrapper);
@@ -329,9 +363,12 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
&mol::alg::CheckStructure,
(arg("ent"), arg("bond_table"), arg("angle_table"), arg("nonbonded_table"),
arg("bond_tolerance"), arg("angle_tolerance")));
- def("PrintlDDTPerResidueStats",
- &mol::alg::PrintlDDTPerResidueStats,
+ def("GetlDDTPerResidueStats",
+ &get_lddt_per_residue_stats_wrapper,
(arg("model"), arg("glob_dist_list"), arg("settings")));
+ def("PrintlDDTPerResidueStats",
+ &print_lddt_per_residue_stats_wrapper,
+ (arg("scores"), arg("settings")));
class_<mol::alg::PDBize>("PDBize",
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 357e766906e7ad97151830c9ec7eb926b50199af..7c8079d567b23a587426950c5bc27991e78e18a6 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -340,7 +340,9 @@ int main (int argc, char **argv)
Real lddt = LocalDistDiffTest(model_view, ref_list, glob_dist_list, settings);
// prints the residue-by-residue statistics
- PrintlDDTPerResidueStats(model, glob_dist_list, settings);
+ std::vector<lDDTLocalScore> local_scores;
+ local_scores = GetlDDTPerResidueStats(model, glob_dist_list, settings);
+ PrintlDDTPerResidueStats(local_scores, settings);
}
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 a019251b96492d54585a3c0fa81055d8fe15ac3b..9c988d1005c1ca2614a48fbf74e7258a07caf135 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -477,6 +477,55 @@ void lDDTSettings::PrintParameters() {
std::cout << ToString();
}
+// Default constructor is neccessary for boost exposure
+lDDTLocalScore::lDDTLocalScore(): cname(""),
+ rname(""),
+ rnum(-1),
+ is_assessed(""),
+ quality_problems(""),
+ local_lddt(-1.0),
+ conserved_dist(-1),
+ total_dist(-1) {}
+
+lDDTLocalScore::lDDTLocalScore(String init_cname,
+ String init_rname,
+ int init_rnum,
+ String init_is_assessed,
+ String init_quality_problems,
+ Real init_local_lddt,
+ int init_conserved_dist,
+ int init_total_dist):
+ cname(init_cname),
+ rname(init_rname),
+ rnum(init_rnum),
+ is_assessed(init_is_assessed),
+ quality_problems(init_quality_problems),
+ local_lddt(init_local_lddt),
+ conserved_dist(init_conserved_dist),
+ total_dist(init_total_dist) {}
+
+String lDDTLocalScore::ToString(bool structural_checks) const {
+ std::stringstream stkeylddt;
+ std::stringstream outstr;
+ stkeylddt << "(" << conserved_dist << "/" << total_dist << ")";
+ String dist_string = stkeylddt.str();
+ if (structural_checks) {
+ outstr << cname << "\t" << rname << "\t" << rnum << '\t' << is_assessed << '\t' << quality_problems << '\t' << local_lddt << "\t" << dist_string;
+ } else {
+ outstr << cname << "\t" << rname << "\t" << rnum << '\t' << is_assessed << '\t' << local_lddt << "\t" << dist_string;
+ }
+ return outstr.str();
+}
+
+String lDDTLocalScore::GetHeader(bool structural_checks, int cutoffs_length) {
+ std::stringstream outstr;
+ if (structural_checks) {
+ outstr << "Chain\tResName\tResNum\tAsses.\tQ.Prob.\tScore\t(Conserved/Total, over " << cutoffs_length << " thresholds)";
+ } else {
+ outstr << "Chain\tResName\tResNum\tAsses.\tScore\t(Conserved/Total, over " << cutoffs_length << " thresholds)";
+ }
+ return outstr.str();
+}
GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist)
{
@@ -782,36 +831,28 @@ 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;
}
-void PrintlDDTPerResidueStats(EntityHandle& model, GlobalRDMap& glob_dist_list, lDDTSettings& settings){
+std::vector<lDDTLocalScore> GetlDDTPerResidueStats(EntityHandle& model, GlobalRDMap& glob_dist_list, lDDTSettings& settings){
+ std::vector<lDDTLocalScore> scores;
EntityView outv = model.GetChainList()[0].Select("peptide=true");
- if (settings.structural_checks) {
- std::cout << "Local LDDT Scores:" << std::endl;
- std::cout << "(A 'Yes' in the 'Quality Problems' column stands for problems" << std::endl;
- std::cout << "in the side-chain of a residue, while a 'Yes+' for problems" << std::endl;
- std::cout << "in the backbone)" << std::endl;
- } else {
- std::cout << "Local LDDT Scores:" << std::endl;
- }
- if (settings.structural_checks) {
- std::cout << "Chain\tResName\tResNum\tAsses.\tQ.Prob.\tScore\t(Conserved/Total, over " << settings.cutoffs.size() << " thresholds)" << std::endl;
- } else {
- std::cout << "Chain\tResName\tResNum\tAsses.\tScore\t(Conserved/Total, over " << settings.cutoffs.size() << " thresholds)" << std::endl;
- }
for (ChainViewList::const_iterator ci = outv.GetChainList().begin(),
ce = outv.GetChainList().end(); ci != ce; ++ci) {
for (ResidueViewList::const_iterator rit = ci->GetResidueList().begin(),
re = ci->GetResidueList().end(); rit != re; ++rit) {
-
+
ResidueView ritv=*rit;
ResNum rnum = ritv.GetNumber();
bool assessed = false;
String assessed_string="No";
- String quality_problems_string="No";
+ String quality_problems_string;
+ if (settings.structural_checks) {
+ quality_problems_string="No";
+ } else {
+ quality_problems_string="NA";
+ }
Real lddt_local = -1;
String lddt_local_string="-";
int conserved_dist = -1;
int total_dist = -1;
- String dist_string = "-";
if (IsResnumInGlobalRDMap(rnum,glob_dist_list)) {
assessed = true;
assessed_string="Yes";
@@ -833,25 +874,43 @@ void PrintlDDTPerResidueStats(EntityHandle& model, GlobalRDMap& glob_dist_list,
lddt_local_string=stkeylddt.str();
conserved_dist=ritv.GetIntProp(settings.label+"_conserved");
total_dist=ritv.GetIntProp(settings.label+"_total");
- std::stringstream stkeydist;
- stkeydist << "("<< conserved_dist << "/" << total_dist << ")";
- dist_string=stkeydist.str();
} else {
std::cout << settings.label << std::endl;
lddt_local = 0;
lddt_local_string="0.0000";
conserved_dist = 0;
total_dist = 0;
- dist_string="(0/0)";
}
}
- if (settings.structural_checks) {
- std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << assessed_string << '\t' << quality_problems_string << '\t' << lddt_local_string << "\t" << dist_string << std::endl;
- } else {
- std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << assessed_string << '\t' << lddt_local_string << "\t" << dist_string << std::endl;
- }
+ // std::tuple<String, String, int, String, String, Real, int, int>
+ lDDTLocalScore row(ritv.GetChain().GetName(),
+ ritv.GetName(),
+ ritv.GetNumber().GetNum(),
+ assessed_string,
+ quality_problems_string,
+ lddt_local,
+ conserved_dist,
+ total_dist);
+ scores.push_back(row);
}
}
+
+ return scores;
+}
+
+void PrintlDDTPerResidueStats(std::vector<lDDTLocalScore>& scores, lDDTSettings& settings){
+ if (settings.structural_checks) {
+ std::cout << "Local LDDT Scores:" << std::endl;
+ std::cout << "(A 'Yes' in the 'Quality Problems' column stands for problems" << std::endl;
+ std::cout << "in the side-chain of a residue, while a 'Yes+' for problems" << std::endl;
+ std::cout << "in the backbone)" << std::endl;
+ } else {
+ std::cout << "Local LDDT Scores:" << std::endl;
+ }
+ std::cout << lDDTLocalScore::GetHeader(settings.structural_checks, settings.cutoffs.size()) << std::endl;
+ for (std::vector<lDDTLocalScore>::const_iterator sit = scores.begin(); sit != scores.end(); ++sit) {
+ std::cout << sit->ToString(settings.structural_checks) << std::endl;
+ }
std::cout << std::endl;
}
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index f44d972a22fbc1398232926ed9ec6329b14c08b3..21aee5a1d7a035ae21450b05c84212bc103a1b9d 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -54,6 +54,32 @@ struct lDDTSettings {
std::string ToString();
};
+struct lDDTLocalScore {
+ String cname;
+ String rname;
+ int rnum;
+ String is_assessed;
+ String quality_problems;
+ Real local_lddt;
+ int conserved_dist;
+ int total_dist;
+
+ lDDTLocalScore();
+
+ lDDTLocalScore(String init_cname,
+ String init_rname,
+ int init_rnum,
+ String init_is_assessed,
+ String init_quality_problems,
+ Real init_local_lddt,
+ int init_conserved_dist,
+ int init_total_dist);
+
+ String ToString(bool structural_checks) const;
+
+ static String GetHeader(bool structural_checks, int cutoffs_length);
+};
+
std::pair<int,int> DLLEXPORT_OST_MOL_ALG ComputeCoverage(const EntityView& v,const GlobalRDMap& glob_dist_list);
bool DLLEXPORT_OST_MOL_ALG IsResnumInGlobalRDMap(const ResNum& resnum, const GlobalRDMap& glob_dist_list);
@@ -188,9 +214,12 @@ void DLLEXPORT_OST_MOL_ALG CheckStructure(EntityView& ent,
Real bond_tolerance,
Real angle_tolerance);
-void PrintlDDTPerResidueStats(EntityHandle& model,
- GlobalRDMap& glob_dist_list,
- lDDTSettings& settings);
+std::vector<lDDTLocalScore> DLLEXPORT_OST_MOL_ALG GetlDDTPerResidueStats(EntityHandle& model,
+ GlobalRDMap& glob_dist_list,
+ lDDTSettings& settings);
+
+void DLLEXPORT_OST_MOL_ALG PrintlDDTPerResidueStats(std::vector<lDDTLocalScore>& scores,
+ lDDTSettings& settings);
}}}