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Commit f377869e authored by Rafal Gumienny's avatar Rafal Gumienny
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fix: SCHWED-3127 Extract correct variables

parent 39e5f504
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modules/mol/alg/pymod/wrap_mol_alg.cc
+ 40
− 40
View file @ f377869e
......@@ -60,15 +60,15 @@ mol::CoordGroupHandle (*superpose_frames1)(mol::CoordGroupHandle&, mol::EntityVi
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);
Real lddt_d(const mol::EntityView& model, list& reference_list, const mol::alg::GlobalRDMap& distance_list, mol::alg::lDDTSettings& settings){
int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
for (int i=0; i<ref_list_length; i++) {
ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
for (int i=0; i<reference_list_length; i++) {
reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
}
return LocalDistDiffTest(v, ref_list_vector, glob_dist_list, settings);
return LocalDistDiffTest(model, reference_list_vector, distance_list, settings);
}
ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const String& header, const list& stereo_chemical_props_file)
......@@ -95,13 +95,13 @@ ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& st
return ost::mol::alg::FillClashingDistances(stereo_chemical_props_file_vector);
}
ost::mol::alg::GlobalRDMap create_distance_list_from_multiple_references(const list& ref_list, const list& cutoff_list, int sequence_separation, Real max_dist)
ost::mol::alg::GlobalRDMap create_distance_list_from_multiple_references(const list& reference_list, const list& cutoff_list, int sequence_separation, Real max_dist)
{
int ref_list_length = boost::python::extract<int>(ref_list.attr("__len__")());
std::vector<ost::mol::EntityView> ref_list_vector(ref_list_length);
int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
for (int i=0; i<ref_list_length; i++) {
ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
for (int i=0; i<reference_list_length; i++) {
reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
}
int cutoff_list_length = boost::python::extract<int>(cutoff_list.attr("__len__")());
......@@ -110,7 +110,7 @@ ost::mol::alg::GlobalRDMap create_distance_list_from_multiple_references(const l
for (int i=0; i<cutoff_list_length; i++) {
cutoff_list_vector[i] = boost::python::extract<Real>(cutoff_list[i]);
}
return ost::mol::alg::CreateDistanceListFromMultipleReferences(ref_list_vector, cutoff_list_vector, sequence_separation, max_dist);
return ost::mol::alg::CreateDistanceListFromMultipleReferences(reference_list_vector, cutoff_list_vector, sequence_separation, max_dist);
}
object lDDTSettingsInitWrapper(tuple args, dict kwargs){
......@@ -118,39 +118,39 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
object self = args[0];
args = tuple(args.slice(1,_));
Real bond_tolerance = 12;
Real bond_tolerance = 12.0;
if(kwargs.contains("bond_tolerance")){
bond_tolerance = extract<bool>(kwargs["bond_tolerance"]);
bond_tolerance = extract<Real>(kwargs["bond_tolerance"]);
kwargs["bond_tolerance"].del();
}
Real angle_tolerance = 12;
Real angle_tolerance = 12.0;
if(kwargs.contains("angle_tolerance")){
angle_tolerance = extract<bool>(kwargs["angle_tolerance"]);
angle_tolerance = extract<Real>(kwargs["angle_tolerance"]);
kwargs["angle_tolerance"].del();
}
Real radius = 15;
Real radius = 15.0;
if(kwargs.contains("radius")){
radius = extract<bool>(kwargs["radius"]);
radius = extract<Real>(kwargs["radius"]);
kwargs["radius"].del();
}
int sequence_separation = 0;
if(kwargs.contains("sequence_separation")){
sequence_separation = extract<bool>(kwargs["sequence_separation"]);
sequence_separation = extract<int>(kwargs["sequence_separation"]);
kwargs["sequence_separation"].del();
}
String sel = "";
if(kwargs.contains("sel")){
sel = extract<bool>(kwargs["sel"]);
sel = extract<String>(kwargs["sel"]);
kwargs["sel"].del();
}
String parameter_file_path = "";
if(kwargs.contains("parameter_file_path")){
parameter_file_path = extract<bool>(kwargs["parameter_file_path"]);
parameter_file_path = extract<String>(kwargs["parameter_file_path"]);
kwargs["parameter_file_path"].del();
}
......@@ -181,9 +181,9 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
cutoffs.push_back(4.0);
}
String label = "localldt";
String label = "locallddt";
if(kwargs.contains("label")){
label = extract<bool>(kwargs["label"]);
label = extract<String>(kwargs["label"]);
kwargs["label"].del();
}
......@@ -210,34 +210,34 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
}
void clean_lddt_references_wrapper(const list& ref_list)
void clean_lddt_references_wrapper(const list& reference_list)
{
int ref_list_length = boost::python::extract<int>(ref_list.attr("__len__")());
std::vector<ost::mol::EntityView> ref_list_vector(ref_list_length);
int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
for (int i=0; i<ref_list_length; i++) {
ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
for (int i=0; i<reference_list_length; i++) {
reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
}
return ost::mol::alg::CleanlDDTReferences(ref_list_vector);
return ost::mol::alg::CleanlDDTReferences(reference_list_vector);
}
ost::mol::alg::GlobalRDMap prepare_lddt_global_rdmap_wrapper(const list& ref_list, mol::alg::lDDTSettings settings)
ost::mol::alg::GlobalRDMap prepare_lddt_global_rdmap_wrapper(const list& reference_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);
int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
for (int i=0; i<ref_list_length; i++) {
ref_list_vector[i] = boost::python::extract<ost::mol::EntityView>(ref_list[i]);
for (int i=0; i<reference_list_length; i++) {
reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
}
return mol::alg::PreparelDDTGlobalRDMap(ref_list_vector, settings);
return mol::alg::PreparelDDTGlobalRDMap(reference_list_vector, settings);
}
list get_lddt_per_residue_stats_wrapper(mol::EntityHandle& model,
ost::mol::alg::GlobalRDMap& glob_dist_list,
ost::mol::alg::GlobalRDMap& distance_list,
ost::mol::alg::lDDTSettings& settings) {
std::vector<mol::alg::lDDTLocalScore> scores = GetlDDTPerResidueStats(model, glob_dist_list, settings);
std::vector<mol::alg::lDDTLocalScore> scores = GetlDDTPerResidueStats(model, distance_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);
......@@ -275,7 +275,7 @@ 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("LocalDistDiffTest", &lddt_d, (arg("model"), arg("reference_list"), ("distance_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));
......@@ -358,14 +358,14 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("CleanlDDTReferences", &clean_lddt_references_wrapper);
def("PreparelDDTGlobalRDMap",
&prepare_lddt_global_rdmap_wrapper,
(arg("ref_list"), arg("settings")));
(arg("reference_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("GetlDDTPerResidueStats",
&get_lddt_per_residue_stats_wrapper,
(arg("model"), arg("glob_dist_list"), arg("settings")));
(arg("model"), arg("distance_list"), arg("settings")));
def("PrintlDDTPerResidueStats",
&print_lddt_per_residue_stats_wrapper,
(arg("scores"), arg("settings")));
......
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