diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 406647f479ad8324d9f3486e300edd72235ad38a..42072cdc5b8b782aed42e533f61efd8a0c698f8b 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -190,22 +190,15 @@ int main (int argc, char **argv)
{
// sets some default values for parameters
String version = OST_VERSION_STRING;
- Real bond_tolerance = 12.0;
- Real angle_tolerance = 12.0;
- Real radius=15.0;
- int sequence_separation = 0;
-
+ lDDTSettings settings;
// creates the required loading profile
IOProfile profile;
// parses options
- String sel;
String custom_path;
- bool structural_checks=false;
- bool consistency_checks=true;
po::options_description desc("Options");
desc.add_options()
("calpha,c", "consider only calpha atoms")
- ("sel,s", po::value<String>(&sel)->default_value(""), "selection performed on reference structure")
+ ("sel,s", po::value<String>(&settings.sel)->default_value(""), "selection performed on reference structure")
("tolerant,t", "fault tolerant mode")
("structural-checks,f", "perform stereo-chemical and clash checks")
("ignore-consistency-checks,x", "ignore residue name consistency checks")
@@ -254,18 +247,18 @@ int main (int argc, char **argv)
profile.calpha_only=true;
}
if (vm.count("structural-checks")) {
- structural_checks=true;
+ settings.structural_checks=true;
}
if (vm.count("ignore-consistency-checks")) {
- consistency_checks=false;
+ settings.consistency_checks=false;
}
if (vm.count("tolerant")) {
profile.fault_tolerant=true;
}
- String parameter_filename;
+
if (vm.count("parameter-file")) {
- parameter_filename=vm["parameter-file"].as<String>();
- } else if (structural_checks==true) {
+ settings.parameter_file_path=vm["parameter-file"].as<String>();
+ } else if (settings.structural_checks==true) {
std::cout << "Please specify a stereo-chemical parameter file" << std::endl;
exit(-1);
}
@@ -288,23 +281,17 @@ int main (int argc, char **argv)
Logger::Instance().PushVerbosityLevel(ost_verbosity_level);
if (vm.count("bond_tolerance")) {
- bond_tolerance=vm["bond_tolerance"].as<Real>();
+ settings.bond_tolerance=vm["bond_tolerance"].as<Real>();
}
if (vm.count("angle_tolerance")) {
- angle_tolerance=vm["angle_tolerance"].as<Real>();
+ settings.angle_tolerance=vm["angle_tolerance"].as<Real>();
}
if (vm.count("inclusion_radius")) {
- radius=vm["inclusion_radius"].as<Real>();
+ settings.radius=vm["inclusion_radius"].as<Real>();
}
if (vm.count("sequence_separation")) {
- sequence_separation=vm["sequence_separation"].as<int>();
+ settings.sequence_separation=vm["sequence_separation"].as<int>();
}
-
- std::vector<Real> cutoffs;
- cutoffs.push_back(0.5);
- cutoffs.push_back(1.0);
- cutoffs.push_back(2.0);
- cutoffs.push_back(4.0);
std::vector<EntityView> ref_list;
@@ -325,23 +312,23 @@ int main (int argc, char **argv)
ref_list.push_back(ref.CreateFullView());
}
CleanlDDTReferences(ref_list);
- glob_dist_list = PreparelDDTGlobalRDMap(ref_list,cutoffs,sequence_separation,radius);
+ glob_dist_list = PreparelDDTGlobalRDMap(ref_list,settings.cutoffs,settings.sequence_separation,settings.radius);
files.pop_back();
// prints out parameters used in the lddt calculation
std::cout << "Verbosity level: " << verbosity_level << std::endl;
- if (structural_checks) {
+ if (settings.structural_checks) {
std::cout << "Stereo-chemical and steric clash checks: On " << std::endl;
} else {
std::cout << "Stereo-chemical and steric clash checks: Off " << std::endl;
}
- std::cout << "Inclusion Radius: " << radius << std::endl;
+ std::cout << "Inclusion Radius: " << settings.radius << std::endl;
- std::cout << "Sequence separation: " << sequence_separation << std::endl;
- if (structural_checks) {
- std::cout << "Parameter filename: " << parameter_filename << std::endl;
- std::cout << "Tolerance in stddevs for bonds: " << bond_tolerance << std::endl;
- std::cout << "Tolerance in stddevs for angles: " << angle_tolerance << std::endl;
+ std::cout << "Sequence separation: " << settings.sequence_separation << std::endl;
+ if (settings.structural_checks) {
+ std::cout << "Parameter filename: " << settings.parameter_file_path << std::endl;
+ std::cout << "Tolerance in stddevs for bonds: " << settings.bond_tolerance << std::endl;
+ std::cout << "Tolerance in stddevs for angles: " << settings.angle_tolerance << std::endl;
LOG_INFO("Log entries format:");
LOG_INFO("BOND INFO FORMAT: Chain Residue ResNum Bond Min Max Observed Z-score Status");
LOG_INFO("ANGLE INFO FORMAT: Chain Residue ResNum Angle Min Max Observed Z-score Status");
@@ -368,9 +355,9 @@ int main (int argc, char **argv)
EntityView outv=model.GetChainList()[0].Select("peptide=true");
for (std::vector<EntityView>::const_iterator ref_list_it = ref_list.begin();
ref_list_it != ref_list.end(); ++ref_list_it) {
- bool cons_check = ResidueNamesMatch(v,*ref_list_it,consistency_checks);
+ bool cons_check = ResidueNamesMatch(v,*ref_list_it,settings.consistency_checks);
if (cons_check==false) {
- if (consistency_checks==true) {
+ if (settings.consistency_checks==true) {
LOG_ERROR("Residue names in model: " << files[i] << " and in reference structure(s) are inconsistent.");
exit(-1);
} else {
@@ -390,8 +377,8 @@ int main (int argc, char **argv)
std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
}
- if (structural_checks) {
- StereoChemicalParamsReader stereochemical_params(parameter_filename);
+ if (settings.structural_checks) {
+ StereoChemicalParamsReader stereochemical_params(settings.parameter_file_path);
try {
stereochemical_params.Read(true);
} catch (std::exception& e) {
@@ -404,8 +391,8 @@ int main (int argc, char **argv)
stereochemical_params.bond_table,
stereochemical_params.angle_table,
stereochemical_params.nonbonded_table,
- bond_tolerance,
- angle_tolerance);
+ settings.bond_tolerance,
+ settings.angle_tolerance);
} catch (std::exception& e) {
std::cout << e.what() << std::endl;
exit(-1);
@@ -419,14 +406,14 @@ int main (int argc, char **argv)
// computes the lddt score
String label="localldt";
- std::pair<int,int> total_ov=alg::LocalDistDiffTest(v, glob_dist_list, cutoffs, sequence_separation, label);
+ std::pair<int,int> total_ov=alg::LocalDistDiffTest(v, glob_dist_list, settings.cutoffs, settings.sequence_separation, 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 " << cutoffs.size() << " thresholds)" << std::endl;
+ << " checked, over " << settings.cutoffs.size() << " thresholds)" << std::endl;
// prints the residue-by-residue statistics
- if (structural_checks) {
+ 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;
@@ -434,10 +421,10 @@ int main (int argc, char **argv)
} else {
std::cout << "Local LDDT Scores:" << std::endl;
}
- if (structural_checks) {
- std::cout << "Chain\tResName\tResNum\tAsses.\tQ.Prob.\tScore\t(Conserved/Total, over " << cutoffs.size() << " thresholds)" << 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 " << cutoffs.size() << " thresholds)" << std::endl;
+ 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) {
@@ -486,7 +473,7 @@ int main (int argc, char **argv)
dist_string="(0/0)";
}
}
- if (structural_checks) {
+ 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;
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 3ad22db00bcea5b2d078e004e10fe909912d62b6..4f525571fd2dbe0742b52c61c143a8f0dc97d021 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -1,6 +1,7 @@
#include <iomanip>
#include <ost/log.hh>
#include <ost/mol/mol.hh>
+#include <ost/platform.hh>
#include "local_dist_diff_test.hh"
#include <boost/concept_check.hpp>
@@ -338,6 +339,45 @@ bool IsStandardResidue(String rn)
return false;
}
+lDDTSettings::lDDTSettings(): bond_tolerance(12.0),
+ angle_tolerance(12.0),
+ radius(15.0),
+ sequence_separation(0),
+ sel(""),
+ structural_checks(false),
+ consistency_checks(true) {
+ cutoffs.push_back(0.5);
+ cutoffs.push_back(1.0);
+ cutoffs.push_back(2.0);
+ cutoffs.push_back(4.0);
+ try {
+ parameter_file_path = ost::GetSharedDataPath() + "/stereo_chemical_props.txt";
+ } catch (std::runtime_error& e) {
+ std::cerr << "WARNING: " << e.what();
+ }
+ // if ((! boost::filesystem::exists(parameter_file_path)) || parameter_file_path == "") {
+ // std::cerr << "WARNING: Could not find stereo_chemical_props.txt at the provided location." << std::endl;
+ // }
+ }
+
+lDDTSettings::lDDTSettings(Real init_bond_tolerance,
+ Real init_angle_tolerance,
+ Real init_radius,
+ int init_sequence_separation,
+ String init_sel,
+ String init_parameter_file_path,
+ bool init_structural_checks,
+ bool init_consistency_checks,
+ std::vector<Real> init_cutoffs):
+ bond_tolerance(init_bond_tolerance),
+ angle_tolerance(init_angle_tolerance),
+ radius(init_radius),
+ sequence_separation(init_sequence_separation),
+ sel(init_sel),
+ parameter_file_path(init_parameter_file_path),
+ structural_checks(init_structural_checks),
+ consistency_checks(init_consistency_checks) {}
+
GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist)
{
@@ -539,7 +579,7 @@ Real LDDTHA(EntityView& v, const GlobalRDMap& global_dist_list, int sequence_sep
void CleanlDDTReferences(std::vector<EntityView>& ref_list){
- for (int i=0;i<ref_list.size();i++) {
+ for (unsigned int i=0;i<ref_list.size();i++) {
if (ref_list[0].GetChainList()[0].GetName()!=ref_list[i].GetChainList()[0].GetName()) {
std::cout << "ERROR: First chains in the reference structures have different names" << std::endl;
exit(-1);
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 05b9fd887c1631ef9e3c70123f6fb8667ead6757..8d29e79ac396903e5da5841703c2cba3284cf0f7 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -25,6 +25,30 @@
#include <ost/mol/alg/filter_clashes.hh>
namespace ost { namespace mol { namespace alg {
+
+
+struct lDDTSettings {
+ Real bond_tolerance;
+ Real angle_tolerance;
+ Real radius;
+ int sequence_separation;
+ String sel;
+ String parameter_file_path;
+ bool structural_checks;
+ bool consistency_checks;
+ std::vector<Real> cutoffs;
+
+ lDDTSettings();
+ lDDTSettings(Real init_bond_tolerance,
+ Real init_angle_tolerance,
+ Real init_radius,
+ int init_sequence_separation,
+ String init_sel,
+ String init_parameter_file_path,
+ bool init_structural_checks,
+ bool init_consistency_checks,
+ std::vector<Real> init_cutoffs);
+};
/// \brief Calculates number of distances conserved in a model, given a list of distances to check and a model
///
@@ -74,6 +98,12 @@ Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& mdl,
Real cutoff,
Real max_dist,
const String& local_ldt_property_string="");
+/// TODO document me
+Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& mdl,
+ const std::vector<EntityView>& targets,
+ const lDDTSettings& settings,
+ const String& local_ldt_property_string="");
+
/// \brief Calculates the Local Distance Difference Test score for a given model starting from an alignment between a reference structure and the model.
///
/// Calculates the Local Distance Difference Test score given an alignment between a model and a taget structure.