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Commit ad2fa114 authored by Studer Gabriel's avatar Studer Gabriel
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Revert "wrap data extracted from linear dbs in single objects" 

This reverts commit 55cd0493.
parent 0d675bb9
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modules/db/pymod/export_linear_db.cc
+ 37
− 60
View file @ ad2fa114
......@@ -166,32 +166,23 @@ struct DisCoDataContainers {
LinearPositionContainerPtr position_container;
};
// helper struct to wrap output
struct ExtractedDisCoData{
std::vector<int> residue_numbers;
geom::Vec3List ca_positions;
};
typedef boost::shared_ptr<ExtractedDisCoData> ExtractedDisCoDataPtr;
list WrapExtractedDisCoDataGetResNums(ExtractedDisCoDataPtr ptr) {
list residue_numbers;
VecToList(ptr->residue_numbers, residue_numbers);
return residue_numbers;
}
void WrapExtractTemplateDataDisCo(const String& entry_name, const String& chain_name,
const ost::seq::AlignmentHandle& aln,
DisCoDataContainers& data_containers,
boost::python::list& residue_numbers,
geom::Vec3List& positions) {
ExtractedDisCoDataPtr WrapExtractTemplateDataDisCo(const String& entry_name,
const String& chain_name,
const ost::seq::AlignmentHandle& aln,
DisCoDataContainers& data_containers) {
ExtractedDisCoDataPtr ptr(new ExtractedDisCoData);
std::vector<int> v_residue_numbers;
ost::db::ExtractTemplateDataDisCo(entry_name, chain_name, aln,
data_containers.indexer,
data_containers.seqres_container,
data_containers.atomseq_container,
data_containers.position_container,
ptr->residue_numbers,
ptr->ca_positions);
return ptr;
v_residue_numbers,
positions);
residue_numbers = boost::python::list();
VecToList(v_residue_numbers, residue_numbers);
}
......@@ -226,27 +217,19 @@ struct GMQEDataContainers {
LinearPositionContainerPtr cb_position_container;
};
// helper struct to wrap output
struct ExtractedGMQEData{
std::vector<int> residue_numbers;
String dssp;
geom::Vec3List n_positions;
geom::Vec3List ca_positions;
geom::Vec3List c_positions;
geom::Vec3List cb_positions;
};
typedef boost::shared_ptr<ExtractedGMQEData> ExtractedGMQEDataPtr;
list WrapExtractedGMQEDataGetResNums(ExtractedGMQEDataPtr ptr) {
list residue_numbers;
VecToList(ptr->residue_numbers, residue_numbers);
return residue_numbers;
}
ExtractedGMQEDataPtr WrapExtractTemplateDataGMQE(const String& entry_name,
const String& chain_name,
const ost::seq::AlignmentHandle& aln,
GMQEDataContainers& data_containers) {
ExtractedGMQEDataPtr ptr(new ExtractedGMQEData);
void WrapExtractTemplateDataGMQE(const String& entry_name,
const String& chain_name,
const ost::seq::AlignmentHandle& aln,
GMQEDataContainers& data_containers,
boost::python::list& residue_numbers,
String& dssp,
geom::Vec3List& n_positions,
geom::Vec3List& ca_positions,
geom::Vec3List& c_positions,
geom::Vec3List& cb_positions) {
std::vector<int> v_residue_numbers;
ost::db::ExtractTemplateDataGMQE(entry_name, chain_name, aln,
data_containers.indexer,
data_containers.seqres_container,
......@@ -256,10 +239,9 @@ ExtractedGMQEDataPtr WrapExtractTemplateDataGMQE(const String& entry_name,
data_containers.ca_position_container,
data_containers.c_position_container,
data_containers.cb_position_container,
ptr->residue_numbers, ptr->dssp,
ptr->n_positions, ptr->ca_positions,
ptr->c_positions, ptr->cb_positions);
return ptr;
v_residue_numbers, dssp, n_positions,
ca_positions, c_positions, cb_positions);
VecToList(v_residue_numbers, residue_numbers);
}
}
......@@ -327,18 +309,15 @@ void export_linear_db() {
.def_readonly("indexer", &DisCoDataContainers::indexer)
.def_readonly("seqres_container", &DisCoDataContainers::seqres_container)
.def_readonly("atomseq_container", &DisCoDataContainers::atomseq_container)
.def_readonly("ca_position_container", &DisCoDataContainers::position_container)
;
class_<ExtractedDisCoData, ExtractedDisCoDataPtr>("ExtractedDisCoData", no_init)
.add_property("residue_numbers", &WrapExtractedDisCoDataGetResNums)
.def_readonly("ca_positions", &ExtractedDisCoData::ca_positions)
.def_readonly("position_container", &DisCoDataContainers::position_container)
;
def("ExtractTemplateDataDisCo", &WrapExtractTemplateDataDisCo, (arg("entry_name"),
arg("chain_name"),
arg("aln"),
arg("data_containers")));
arg("data_containers"),
arg("residue_numbers"),
arg("positions")));
class_<GMQEDataContainers>("GMQEDataContainers", init<const String&,
const String&,
......@@ -358,18 +337,16 @@ void export_linear_db() {
.def_readonly("cb_position_container", &GMQEDataContainers::cb_position_container)
;
class_<ExtractedGMQEData, ExtractedGMQEDataPtr>("ExtractedGMQEData", no_init)
.add_property("residue_numbers", &WrapExtractedGMQEDataGetResNums)
.def_readonly("dssp", &ExtractedGMQEData::dssp)
.def_readonly("n_positions", &ExtractedGMQEData::n_positions)
.def_readonly("ca_positions", &ExtractedGMQEData::ca_positions)
.def_readonly("c_positions", &ExtractedGMQEData::c_positions)
.def_readonly("cb_positions", &ExtractedGMQEData::cb_positions)
;
def("ExtractTemplateDataGMQE", &WrapExtractTemplateDataGMQE, (arg("entry_name"),
arg("chain_name"),
arg("aln"),
arg("data_containers")));
arg("data_containers"),
arg("residue_numbers"),
arg("dssp"),
arg("n_positions"),
arg("ca_positions"),
arg("c_positions"),
arg("cb_positions")));
}
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