diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index 302720245b63d534d88aceb2bba9c4d64bba0464..8704a4657d5a7f152f96d339164976fe5bbeb0ce 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -33,6 +33,7 @@ using namespace boost::python;
#include <ost/io/mol/entity_io_sdf_handler.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/mol/dcd_io.hh>
+#include <ost/io/stereochemical_params_reader.hh>
using namespace ost;
using namespace ost::io;
@@ -120,6 +121,15 @@ BOOST_PYTHON_MODULE(_ost_io)
def("LoadMAE", &LoadMAE);
def("LoadPQR", &LoadPQR);
+ class_<io::StereoChemicalParamsReader>("StereoChemicalParamsReader",
+ init<String>(arg("filename")))
+ .def(init<>())
+ .def("Read", &io::StereoChemicalParamsReader::Read, (arg("check")=false))
+ .def_readwrite("filename", &io::StereoChemicalParamsReader::filename)
+ .def_readwrite("bond_table", &io::StereoChemicalParamsReader::bond_table)
+ .def_readwrite("angle_table", &io::StereoChemicalParamsReader::angle_table)
+ .def_readwrite("nonbonded_table", &io::StereoChemicalParamsReader::nonbonded_table);
+
export_pdb_io();
export_mmcif_io();
#if OST_IMG_ENABLED
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 9f6c7f850fcaa869be30b337b1c94c654e5d2927..fd2b9eb2d8fc97c886f0be1f8e133c3f03c2a2f3 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -50,6 +50,7 @@ namespace {
std::pair<long int,long int> (*lddt_a)(const mol::EntityView&, const mol::alg::GlobalRDMap& , std::vector<Real>, int, const String&)=&mol::alg::LocalDistDiffTest;
Real (*lddt_c)(const mol::EntityView&, const mol::EntityView& , Real, Real, const String&)=&mol::alg::LocalDistDiffTest;
+// Real (*lddt_d)(const mol::EntityView&, std::vector<mol::EntityView>&, const mol::alg::GlobalRDMap&, mol::alg::lDDTSettings&)=&mol::alg::LocalDistDiffTest;
Real (*lddt_b)(const seq::AlignmentHandle&,Real, Real, int, int)=&mol::alg::LocalDistDiffTest;
std::pair<mol::EntityView,mol::alg::ClashingInfo> (*fc_a)(const mol::EntityView&, const mol::alg::ClashingDistances&,bool)=&mol::alg::FilterClashes;
std::pair<mol::EntityView,mol::alg::ClashingInfo> (*fc_b)(const mol::EntityHandle&, const mol::alg::ClashingDistances&, bool)=&mol::alg::FilterClashes;
@@ -58,6 +59,18 @@ std::pair<mol::EntityView,mol::alg::StereoChemistryInfo> (*csc_b)(const mol::Ent
mol::CoordGroupHandle (*superpose_frames1)(mol::CoordGroupHandle&, mol::EntityView&, int, int, int)=&mol::alg::SuperposeFrames;
mol::CoordGroupHandle (*superpose_frames2)(mol::CoordGroupHandle&, mol::EntityView&, mol::EntityView&, int, int)=&mol::alg::SuperposeFrames;
+
+Real local_dist_diff_test_wrapper(const mol::EntityView& v, list& ref_list, const mol::alg::GlobalRDMap& glob_dist_list, mol::alg::lDDTSettings& settings){
+ int ref_list_length = boost::python::extract<int>(ref_list.attr("__len__")());
+ std::vector<ost::mol::EntityView> ref_list_vector(ref_list_length);
+
+ for (int i=0; i<ref_list_length; i++) {
+ ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
+ }
+
+ return LocalDistDiffTest(v, ref_list_vector, glob_dist_list, settings);
+}
+
ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const String& header, const list& stereo_chemical_props_file)
{
int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
@@ -100,6 +113,126 @@ ost::mol::alg::GlobalRDMap create_distance_list_from_multiple_references(const l
return ost::mol::alg::CreateDistanceListFromMultipleReferences(ref_list_vector, cutoff_list_vector, sequence_separation, max_dist);
}
+object lDDTSettingsInitWrapper(tuple args, dict kwargs){
+
+ object self = args[0];
+ args = tuple(args.slice(1,_));
+
+ Real bond_tolerance = 12;
+ if(kwargs.contains("bond_tolerance")){
+ bond_tolerance = extract<bool>(kwargs["bond_tolerance"]);
+ kwargs["bond_tolerance"].del();
+ }
+
+ Real angle_tolerance = 12;
+ if(kwargs.contains("angle_tolerance")){
+ angle_tolerance = extract<bool>(kwargs["angle_tolerance"]);
+ kwargs["angle_tolerance"].del();
+ }
+
+ Real radius = 15;
+ if(kwargs.contains("radius")){
+ radius = extract<bool>(kwargs["radius"]);
+ kwargs["radius"].del();
+ }
+
+ int sequence_separation = 0;
+ if(kwargs.contains("sequence_separation")){
+ sequence_separation = extract<bool>(kwargs["sequence_separation"]);
+ kwargs["sequence_separation"].del();
+ }
+
+ String sel = "";
+ if(kwargs.contains("sel")){
+ sel = extract<bool>(kwargs["sel"]);
+ kwargs["sel"].del();
+ }
+
+ String parameter_file_path = "";
+ if(kwargs.contains("parameter_file_path")){
+ parameter_file_path = extract<bool>(kwargs["parameter_file_path"]);
+ kwargs["parameter_file_path"].del();
+ }
+
+ bool structural_checks = true;
+ if(kwargs.contains("structural_checks")){
+ structural_checks = extract<bool>(kwargs["structural_checks"]);
+ kwargs["structural_checks"].del();
+ }
+
+ bool consistency_checks = true;
+ if(kwargs.contains("consistency_checks")){
+ consistency_checks = extract<bool>(kwargs["consistency_checks"]);
+ kwargs["consistency_checks"].del();
+ }
+
+ std::vector<Real> cutoffs;
+ if(kwargs.contains("cutoffs")){
+ list cutoff_list = extract<list>(kwargs["cutoffs"]);
+ int cutoff_list_length = boost::python::extract<int>(cutoff_list.attr("__len__")());
+ for (int i=0; i<cutoff_list_length; i++) {
+ cutoffs.push_back(boost::python::extract<Real>(cutoff_list[i]));
+ }
+ kwargs["cutoffs"].del();
+ } else {
+ cutoffs.push_back(0.5);
+ cutoffs.push_back(1.0);
+ cutoffs.push_back(2.0);
+ cutoffs.push_back(4.0);
+ }
+
+ String label = "localldt";
+ if(kwargs.contains("label")){
+ label = extract<bool>(kwargs["label"]);
+ kwargs["label"].del();
+ }
+
+ if(len(kwargs) > 0){
+ std::stringstream ss;
+ ss << "Invalid keywords observed when setting up MolckSettings! ";
+ ss << "Or did you pass the same keyword twice? ";
+ ss << "Valid keywords are: bond_tolerance, angle_tolerance, radius, ";
+ ss << "sequence_separation, sel, parameter_file_path, structural_checks, ";
+ ss << "consistency_checks, cutoffs, label!";
+ throw std::invalid_argument(ss.str());
+ }
+
+ return self.attr("__init__")(bond_tolerance,
+ angle_tolerance,
+ radius,
+ sequence_separation,
+ sel,
+ parameter_file_path,
+ structural_checks,
+ consistency_checks,
+ cutoffs,
+ label);
+}
+
+
+void clean_lddt_references_wrapper(const list& ref_list)
+{
+ int ref_list_length = boost::python::extract<int>(ref_list.attr("__len__")());
+ std::vector<ost::mol::EntityView> ref_list_vector(ref_list_length);
+
+ for (int i=0; i<ref_list_length; i++) {
+ ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
+ }
+
+ return ost::mol::alg::CleanlDDTReferences(ref_list_vector);
+}
+
+ost::mol::alg::GlobalRDMap prepare_lddt_global_rdmap_wrapper(const list& ref_list, mol::alg::lDDTSettings settings)
+{
+ int ref_list_length = boost::python::extract<int>(ref_list.attr("__len__")());
+ std::vector<ost::mol::EntityView> ref_list_vector(ref_list_length);
+
+ for (int i=0; i<ref_list_length; i++) {
+ ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
+ }
+
+ return mol::alg::PreparelDDTGlobalRDMap(ref_list_vector, settings);
+}
}
@@ -120,6 +253,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("LocalDistDiffTest", lddt_a, (arg("sequence_separation")=0,arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_c, (arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_b, (arg("ref_index")=0, arg("mdl_index")=1));
+ def("LocalDistDiffTest", &local_dist_diff_test_wrapper, (arg("v"), arg("ref_list"), ("glob_dist_list"), arg("settings")));
def("FilterClashes", fc_a, (arg("ent"), arg("clashing_distances"), arg("always_remove_bb")=false));
def("FilterClashes", fc_b, (arg("ent"), arg("clashing_distances"), arg("always_remove_bb")=false));
def("CheckStereoChemistry", csc_a, (arg("ent"), arg("bonds"), arg("angles"), arg("bond_tolerance"), arg("angle_tolerance"), arg("always_remove_bb")=false));
@@ -161,13 +295,44 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
.def("GetResidueName",&mol::alg::UniqueAtomIdentifier::GetResidueName)
.def("GetAtomName",&mol::alg::UniqueAtomIdentifier::GetAtomName)
.def("GetQualifiedAtomName",&mol::alg::UniqueAtomIdentifier::GetQualifiedAtomName)
- ;
+ ;
+
+ class_<mol::alg::lDDTSettings>("lDDTSettings", no_init)
+ .def("__init__", raw_function(lDDTSettingsInitWrapper))
+ .def(init<Real, Real, Real, int, String, String, bool, bool, std::vector<Real>&, String>())
+ .def("ToString", &mol::alg::lDDTSettings::ToString)
+ .def("SetStereoChemicalParamsPath", &mol::alg::lDDTSettings::SetStereoChemicalParamsPath)
+ .def("PrintParameters", &mol::alg::lDDTSettings::PrintParameters)
+ .def("__repr__", &mol::alg::lDDTSettings::ToString)
+ .def("__str__", &mol::alg::lDDTSettings::ToString)
+ .def_readwrite("bond_tolerance", &mol::alg::lDDTSettings::bond_tolerance)
+ .def_readwrite("angle_tolerance", &mol::alg::lDDTSettings::angle_tolerance)
+ .def_readwrite("radius", &mol::alg::lDDTSettings::radius)
+ .def_readwrite("sequence_separation", &mol::alg::lDDTSettings::sequence_separation)
+ .def_readwrite("sel", &mol::alg::lDDTSettings::sel)
+ .def_readwrite("parameter_file_path", &mol::alg::lDDTSettings::parameter_file_path)
+ .def_readwrite("structural_checks", &mol::alg::lDDTSettings::structural_checks)
+ .def_readwrite("consistency_checks", &mol::alg::lDDTSettings::consistency_checks)
+ .def_readwrite("cutoffs", &mol::alg::lDDTSettings::cutoffs)
+ .def_readwrite("label", &mol::alg::lDDTSettings::label);
def("FillClashingDistances",&fill_clashing_distances_wrapper);
def("FillStereoChemicalParams",&fill_stereochemical_params_wrapper);
def("IsStandardResidue",&mol::alg::IsStandardResidue);
def("PrintGlobalRDMap",&mol::alg::PrintGlobalRDMap);
def("PrintResidueRDMap",&mol::alg::PrintResidueRDMap);
+ def("CleanlDDTReferences", &clean_lddt_references_wrapper);
+ def("PreparelDDTGlobalRDMap",
+ &prepare_lddt_global_rdmap_wrapper,
+ (arg("ref_list"), arg("settings")));
+ def("CheckStructure",
+ &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,
+ (arg("model"), arg("glob_dist_list"), arg("settings")));
+
class_<mol::alg::PDBize>("PDBize",
init<int>(arg("min_polymer_size")=10))
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 2cff1c815d12dc2f591b4d6a7005f6afdd62cfef..357e766906e7ad97151830c9ec7eb926b50199af 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -157,6 +157,7 @@ int main (int argc, char **argv)
// sets some default values for parameters
String version = OST_VERSION_STRING;
lDDTSettings settings;
+ settings.structural_checks=false;
// creates the required loading profile
IOProfile profile;
// parses options
@@ -278,7 +279,7 @@ int main (int argc, char **argv)
ref_list.push_back(ref.CreateFullView());
}
CleanlDDTReferences(ref_list);
- glob_dist_list = PreparelDDTGlobalRDMap(ref_list,settings.cutoffs,settings.sequence_separation,settings.radius);
+ glob_dist_list = PreparelDDTGlobalRDMap(ref_list, settings);
files.pop_back();
// prints out parameters used in the lddt calculation
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 79eb285a54de807ef8393302fac693c833d92efb..a019251b96492d54585a3c0fa81055d8fe15ac3b 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -5,12 +5,25 @@
#include <ost/platform.hh>
#include "local_dist_diff_test.hh"
#include <boost/concept_check.hpp>
+#include <boost/filesystem/convenience.hpp>
#include <ost/mol/alg/consistency_checks.hh>
namespace ost { namespace mol { namespace alg {
namespace {
+// helper_function
+String vector_to_string(std::vector<Real> vec) {
+ std::ostringstream str;
+ for (unsigned int i = 0; i < vec.size(); ++i) {
+ str << vec[i];
+ if (i+1 != vec.size()) {
+ str << ", ";
+ }
+ }
+ return str.str();
+}
+
// helper function
bool within_tolerance(Real mdl_dist, const std::pair<Real,Real>& values, Real tol)
{
@@ -382,22 +395,14 @@ lDDTSettings::lDDTSettings(): bond_tolerance(12.0),
radius(15.0),
sequence_separation(0),
sel(""),
- structural_checks(false),
+ structural_checks(true),
consistency_checks(true),
- print_stats(true),
label("localldt") {
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;
- // }
+ SetStereoChemicalParamsPath();
}
lDDTSettings::lDDTSettings(Real init_bond_tolerance,
@@ -409,18 +414,42 @@ lDDTSettings::lDDTSettings(Real init_bond_tolerance,
bool init_structural_checks,
bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
- bool init_print_stats,
String init_label):
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),
- print_stats(init_print_stats),
- label(init_label) {}
+ cutoffs(init_cutoffs),
+ label(init_label) {
+ SetStereoChemicalParamsPath(init_parameter_file_path);
+}
+
+void lDDTSettings::SetStereoChemicalParamsPath(const String& path) {
+ if (path == ""){
+ try {
+ std::cerr << "Setting default stereochemical parameters file path." << std::endl;
+ parameter_file_path = ost::GetSharedDataPath() + "/stereo_chemical_props.txt";
+ if (! structural_checks) {
+ std::cerr << "WARNING: Stereochemical parameters file is set but structural checks are disabled" << std::endl;
+ }
+ } catch (std::runtime_error& e) {
+ std::cerr << "WARNING: " << e.what() << std::endl;
+ std::cerr << "WARNING: Parameter file setting failed - structural check will be disabled" << std::endl;
+ structural_checks = false;
+ parameter_file_path = "";
+ }
+ } else if (! boost::filesystem::exists(path)) {
+ std::cerr << "WARNING: Parameter file does not exist - structural check will be disabled" << std::endl;
+ structural_checks = false;
+ parameter_file_path = "";
+ } else {
+ parameter_file_path = path;
+ structural_checks = true;
+ }
+}
std::string lDDTSettings::ToString() {
std::ostringstream rep;
@@ -429,9 +458,11 @@ std::string lDDTSettings::ToString() {
} else {
rep << "Stereo-chemical and steric clash checks: Off \n";
}
- rep << "Inclusion Radius: " << radius << "\n";
+ rep << "Inclusion Radius: " << radius << "\n";
rep << "Sequence separation: " << sequence_separation << "\n";
+ rep << "Cutoffs: " << vector_to_string(cutoffs) << "\n";
+
if (structural_checks) {
rep << "Parameter filename: " + parameter_file_path + "\n";
rep << "Tolerance in stddevs for bonds: " << bond_tolerance << "\n";
@@ -586,7 +617,6 @@ Real LocalDistDiffTest(const EntityView& v,
std::vector<EntityView>& ref_list,
const GlobalRDMap& glob_dist_list,
lDDTSettings& settings) {
-
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,settings.consistency_checks);
@@ -693,19 +723,17 @@ void CleanlDDTReferences(std::vector<EntityView>& ref_list){
}
GlobalRDMap PreparelDDTGlobalRDMap(const std::vector<EntityView>& ref_list,
- std::vector<Real>& cutoff_list,
- int sequence_separation,
- Real max_dist){
+ lDDTSettings& settings){
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);
+ glob_dist_list = CreateDistanceList(ref_list[0], settings.radius);
} else {
std::cout << "Multi-reference mode: On" << std::endl;
glob_dist_list = CreateDistanceListFromMultipleReferences(ref_list,
- cutoff_list,
- sequence_separation,
- max_dist);
+ settings.cutoffs,
+ settings.sequence_separation,
+ settings.radius);
}
return glob_dist_list;
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 7759447246922c98e777b72c4065049d2097edf5..f44d972a22fbc1398232926ed9ec6329b14c08b3 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -36,7 +36,6 @@ struct lDDTSettings {
bool structural_checks;
bool consistency_checks;
std::vector<Real> cutoffs;
- bool print_stats;
String label;
lDDTSettings();
@@ -49,8 +48,8 @@ struct lDDTSettings {
bool init_structural_checks,
bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
- bool init_print_stats,
String init_label);
+ void SetStereoChemicalParamsPath(const String& path="");
void PrintParameters();
std::string ToString();
};
@@ -180,9 +179,7 @@ void DLLEXPORT_OST_MOL_ALG CleanlDDTReferences(std::vector<EntityView>& ref_list
// Prepare GlobalRDMap from reference list
GlobalRDMap DLLEXPORT_OST_MOL_ALG PreparelDDTGlobalRDMap(
const std::vector<EntityView>& ref_list,
- std::vector<Real>& cutoff_list,
- int sequence_separation,
- Real max_dist);
+ lDDTSettings& settings);
void DLLEXPORT_OST_MOL_ALG CheckStructure(EntityView& ent,
StereoChemicalParams& bond_table,