diff --git a/modules/db/doc/db.rst b/modules/db/doc/db.rst
index 73f885dae77fbed5a89709ba219514349c10aaa9..87dc0919e840133815ea56af101ca8d9096b2d11 100644
--- a/modules/db/doc/db.rst
+++ b/modules/db/doc/db.rst
@@ -351,164 +351,45 @@ marks non-resolved residues with '-'.
:raises: :exc:`ost.Error` if requested data is not present
-.. class:: DisCoDataContainers(indexer_path, \
- seqres_container_path, \
- atomseq_container_path, \
- position_container_path)
+.. method:: ExtractTemplateData(entry_name, chain_name, aln, indexer, \
+ seqres_container, atomseq_container, \
+ position_container)
- Thin wrapper to organize the data containers required in
- :meth:`ExtractTemplateDataDisCo`. All containers are loaded
- from disk and are expected to be consistent.
-
- :param indexer_path: Path to indexer file to access the data containers
- (:class:`LinearIndexer`)
- :param seqres_container_path: Path to container with SEQRES data
- (:class:`LinearCharacterContainer`)
- :param atomseq_container_path: Path to container with ATOMSEQ data
- (:class:`LinearCharacterContainer`)
- :param position_container_path: Path to container with CA position data
- (:class:`LinearPositionContainer`)
-
- :type indexer_path: :class:`str`
- :type seqres_container_path: :class:`str`
- :type atomseq_container_path: :class:`str`
- :type position_container_path: :class:`str`
-
- .. attribute:: indexer
-
- .. attribute:: seqres_container
-
- .. attribute:: atomseq_container
-
- .. attribute:: position_container
-
-.. method:: ExtractTemplateDataDisCo(entry_name, chain_name, aln, \
- data_containers, residue_numbers, \
- positions)
-
- Data extraction helper for the specific use of extracting data required
- to generate DisCoContainers in the QMEAN scoring function.
Let's say we have a target-template alignment in *aln* (first seq: target,
second seq: template). This function extracts all valid template positions
- and their residue numbers given the entry specified by *entry_name* and
- *chain_name*. The template sequence in *aln* must match the sequence in
- *seqres_container*. Again, the *atomseq_container* is used to identify valid
- positions.
-
- :param entry_name: Name of assembly you want the data from
- :param chain_name: Name of chain you want the data from
- :param aln: Target-template sequence alignment
- :param data_containers: Contains all required data containers
- :param residue_numbers: Residue numbers of extracted positions will be stored
- in here
- :param positions: Extracted positions will be stored in here
- :type entry_name: :class:`str`
- :type chain_name: :class:`str`
- :type aln: :ost.seq.SequenceHandle:
- :type data_containers: :class:`DisCoDataContainers`
- :type residue_numbers: :class:`list` of :class:`int`
- :type positions: :class:`geom::Vec3List`
-
- :raises: :exc:`ost.Error` if requested data is not present in
- the containers or if the template sequence in *aln*
- doesn't match with the sequence in *seqres_container*
-
-
-
-
-.. class:: GMQEDataContainers(indexer_path, \
- seqres_container_path, \
- atomseq_container_path, \
- dssp_container_path, \
- n_position_container_path, \
- ca_position_container_path, \
- c_position_container_path, \
- cb_position_container_path, \)
-
- Thin wrapper to organize the data containers required in
- :meth:`ExtractTemplateDataGMQE`. All containers are loaded
- from disk and are expected to be consistent.
-
- :param indexer_path: Path to indexer file to access the data containers
- (:class:`LinearIndexer`)
- :param seqres_container_path: Path to container with SEQRES data
- (:class:`LinearCharacterContainer`)
- :param atomseq_container_path: Path to container with ATOMSEQ data
- (:class:`LinearCharacterContainer`)
- :param dssp_container_path: Path to container containing dssp states
- (:class:`LinearCharacterContainer`)
- :param n_position_container_path: Path to container with N position data
- (:class:`LinearPositionContainer`)
- :param ca_position_container_path: Path to container with CA position data
- (:class:`LinearPositionContainer`)
- :param c_position_container_path: Path to container with C position data
- (:class:`LinearPositionContainer`)
- :param cb_position_container_path: Path to container with CB position data
- (:class:`LinearPositionContainer`)
-
- :type indexer_path: :class:`str`
- :type seqres_container_path: :class:`str`
- :type atomseq_container_path: :class:`str`
- :type dssp_container_path: :class:`str`
- :type n_position_container_path: :class:`str`
- :type ca_position_container_path: :class:`str`
- :type c_position_container_path: :class:`str`
- :type cb_position_container_path: :class:`str`
-
- .. attribute:: indexer
-
- .. attribute:: seqres_container
-
- .. attribute:: atomseq_container
-
- .. attribute:: dssp_container
-
- .. attribute:: n_position_container
-
- .. attribute:: ca_position_container
-
- .. attribute:: c_position_container
-
- .. attribute:: cb_position_container
-
-
-.. method:: ExtractTemplateDataGMQE(entry_name, chain_name, aln, \
- data_containers, residue_numbers, \
- dssp, n_positions, ca_positions, \
- c_positions, cb_positions)
-
- Data extraction helper for the specific use of extracting data required
- to estimate GMQE as available in the QMEAN software package.
- Let's say we have a target-template alignment in *aln* (first seq: target,
- second seq: template). This function extracts all valid template positions,
- their dssp states and their residue numbers given the entry specified by
- *entry_name* and *chain_name*. The template sequence in *aln* must match the
- sequence in *seqres_container*. Again, the *atomseq_container* is used to
- identify valid positions.
+ given the entry specified by *entry_name* and *chain_name*. The template
+ sequence in *aln* must match the sequence in *seqres_container*. Again,
+ the *atomseq_container* is used to identify valid positions. The according
+ residue numbers relative to the target sequence in *aln* are also returned.
:param entry_name: Name of assembly you want the data from
:param chain_name: Name of chain you want the data from
:param aln: Target-template sequence alignment
- :param data_containers: Contains all required data containers
- :param residue_numbers: Residue numbers of extracted positions will be stored
- in here
- :param dssp: Extracted DSSP states will be stored in here
- :param n_positions: Extracted n_positions will be stored in here
- :param ca_positions: Extracted ca_positions will be stored in here
- :param c_positions: Extracted c_positions will be stored in here
- :param cb_positions: Extracted cb_positions will be stored in here
+ :param indexer: Used to access *atomseq_container*, *seqres_container*
+ and *position_container*
+ :param seqres_container: Container containing the full sequence data
+ :param atomseq_container: Container that marks locations with invalid position
+ data with '-'
+ :param position_container: Container containing position data
:type entry_name: :class:`str`
:type chain_name: :class:`str`
:type aln: :ost.seq.SequenceHandle:
- :type data_containers: :class:`GMQEDataContainers`
- :type residue_numbers: :class:`list` of :class:`int`
- :type dssp: :class:`str`
- :type n_positions: :class:`geom::Vec3List`
- :type ca_positions: :class:`geom::Vec3List`
- :type c_positions: :class:`geom::Vec3List`
- :type cb_positions: :class:`geom::Vec3List`
+ :type indexer: :class:`LinearIndexer`
+ :type seqres_container: :class:`LinearCharacterContainer`
+ :type atomseq_container: :class:`LinearCharacterContainer`
+ :type position_container: :class:`LinearPositionContainer` or
+ :class:`list` of :class:`LinearPositionContainer`
+
+ :returns: First element: :class:`list` of residue numbers that
+ relate each entry in the second element to the target
+ sequence specified in *aln*. The numbering scheme
+ starts from one. Second Element: the according positions.
+ :class:`ost.geom.Vec3List` if *position_container* was a
+ :class:`LinearPositionContainer`, a list of
+ :class:`ost.geom.Vec3List` if it was a :class:`list`.
+ :rtype: :class:`tuple`
:raises: :exc:`ost.Error` if requested data is not present in
- the containers or if the template sequence in *aln*
+ the container or if the template sequence in *aln*
doesn't match with the sequence in *seqres_container*
diff --git a/modules/db/pymod/export_linear_db.cc b/modules/db/pymod/export_linear_db.cc
index 6ee2d2f0191be3b4a78a3652d0edf3da2ca33483..1cb623cb5b8644d6af0dbd939ca84fc8d44a31c0 100644
--- a/modules/db/pymod/export_linear_db.cc
+++ b/modules/db/pymod/export_linear_db.cc
@@ -147,102 +147,52 @@ void WrapGetPositions(LinearPositionContainerPtr container,
container->GetPositions(p_range, positions);
}
-// helper struct to reduce number of input parameters
-struct DisCoDataContainers {
-
- DisCoDataContainers(const String& indexer_path,
- const String& seqres_container_path,
- const String& atomseq_container_path,
- const String& position_container_path) {
- indexer = LinearIndexer::Load(indexer_path);
- seqres_container = LinearCharacterContainer::Load(seqres_container_path);
- atomseq_container = LinearCharacterContainer::Load(atomseq_container_path);
- position_container = LinearPositionContainer::Load(position_container_path);
- }
- LinearIndexerPtr indexer;
- LinearCharacterContainerPtr seqres_container;
- LinearCharacterContainerPtr atomseq_container;
- LinearPositionContainerPtr position_container;
-};
+tuple WrapExtractTemplateDataSingle(const String& entry_name, const String& chain_name,
+ const ost::seq::AlignmentHandle& aln,
+ LinearIndexerPtr indexer,
+ LinearCharacterContainerPtr seqres_container,
+ LinearCharacterContainerPtr atomseq_container,
+ LinearPositionContainerPtr position_container) {
+ std::vector<LinearPositionContainerPtr> position_containers;
+ position_containers.push_back(position_container);
+ std::vector<int> v_residue_numbers;
+ std::vector<geom::Vec3List> position_vec;
-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) {
+ ost::db::ExtractTemplateData(entry_name, chain_name, aln, indexer,
+ seqres_container, atomseq_container,
+ position_containers, v_residue_numbers,
+ position_vec);
- 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,
- v_residue_numbers,
- positions);
- residue_numbers = boost::python::list();
+ list residue_numbers;
VecToList(v_residue_numbers, residue_numbers);
+ return boost::python::make_tuple(residue_numbers, position_vec[0]);
}
+tuple WrapExtractTemplateDataList(const String& entry_name, const String& chain_name,
+ const ost::seq::AlignmentHandle& aln,
+ LinearIndexerPtr indexer,
+ LinearCharacterContainerPtr seqres_container,
+ LinearCharacterContainerPtr atomseq_container,
+ boost::python::list& position_containers) {
-// helper struct to reduce number of input parameters
-struct GMQEDataContainers {
-
- GMQEDataContainers(const String& indexer_path,
- const String& seqres_container_path,
- const String& atomseq_container_path,
- const String& dssp_container_path,
- const String& n_position_container_path,
- const String& ca_position_container_path,
- const String& c_position_container_path,
- const String& cb_position_container_path) {
- indexer = LinearIndexer::Load(indexer_path);
- seqres_container = LinearCharacterContainer::Load(seqres_container_path);
- atomseq_container = LinearCharacterContainer::Load(atomseq_container_path);
- dssp_container = LinearCharacterContainer::Load(dssp_container_path);
- n_position_container = LinearPositionContainer::Load(n_position_container_path);
- ca_position_container = LinearPositionContainer::Load(ca_position_container_path);
- c_position_container = LinearPositionContainer::Load(c_position_container_path);
- cb_position_container = LinearPositionContainer::Load(cb_position_container_path);
- }
+ std::vector<LinearPositionContainerPtr> v_position_containers;
+ ListToVec(position_containers, v_position_containers);
+ std::vector<int> v_residue_numbers;
+ std::vector<geom::Vec3List> position_vec;
- LinearIndexerPtr indexer;
- LinearCharacterContainerPtr seqres_container;
- LinearCharacterContainerPtr atomseq_container;
- LinearCharacterContainerPtr dssp_container;
- LinearPositionContainerPtr n_position_container;
- LinearPositionContainerPtr ca_position_container;
- LinearPositionContainerPtr c_position_container;
- LinearPositionContainerPtr cb_position_container;
-};
-
-
-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) {
+ ost::db::ExtractTemplateData(entry_name, chain_name, aln, indexer,
+ seqres_container, atomseq_container,
+ v_position_containers, v_residue_numbers,
+ position_vec);
- std::vector<int> v_residue_numbers;
- ost::db::ExtractTemplateDataGMQE(entry_name, chain_name, aln,
- data_containers.indexer,
- data_containers.seqres_container,
- data_containers.atomseq_container,
- data_containers.dssp_container,
- data_containers.n_position_container,
- data_containers.ca_position_container,
- data_containers.c_position_container,
- data_containers.cb_position_container,
- v_residue_numbers, dssp, n_positions,
- ca_positions, c_positions, cb_positions);
+ list residue_numbers;
+ list position_list;
VecToList(v_residue_numbers, residue_numbers);
-}
+ VecToList(position_vec, position_list);
+ return boost::python::make_tuple(residue_numbers, position_list);
+}
}
@@ -302,51 +252,20 @@ void export_linear_db() {
arg("position_container"),
arg("seq"), arg("positions")));
- class_<DisCoDataContainers>("DisCoDataContainers", init<const String&,
- const String&,
- const String&,
- const String&>())
- .def_readonly("indexer", &DisCoDataContainers::indexer)
- .def_readonly("seqres_container", &DisCoDataContainers::seqres_container)
- .def_readonly("atomseq_container", &DisCoDataContainers::atomseq_container)
- .def_readonly("position_container", &DisCoDataContainers::position_container)
- ;
-
- def("ExtractTemplateDataDisCo", &WrapExtractTemplateDataDisCo, (arg("entry_name"),
- arg("chain_name"),
- arg("aln"),
- arg("data_containers"),
- arg("residue_numbers"),
- arg("positions")));
-
- class_<GMQEDataContainers>("GMQEDataContainers", init<const String&,
- const String&,
- const String&,
- const String&,
- const String&,
- const String&,
- const String&,
- const String&>())
- .def_readonly("indexer", &GMQEDataContainers::indexer)
- .def_readonly("seqres_container", &GMQEDataContainers::seqres_container)
- .def_readonly("atomseq_container", &GMQEDataContainers::atomseq_container)
- .def_readonly("dssp_container", &GMQEDataContainers::dssp_container)
- .def_readonly("n_position_container", &GMQEDataContainers::n_position_container)
- .def_readonly("ca_position_container", &GMQEDataContainers::ca_position_container)
- .def_readonly("c_position_container", &GMQEDataContainers::c_position_container)
- .def_readonly("cb_position_container", &GMQEDataContainers::cb_position_container)
- ;
-
- def("ExtractTemplateDataGMQE", &WrapExtractTemplateDataGMQE, (arg("entry_name"),
- arg("chain_name"),
- arg("aln"),
- arg("data_containers"),
- arg("residue_numbers"),
- arg("dssp"),
- arg("n_positions"),
- arg("ca_positions"),
- arg("c_positions"),
- arg("cb_positions")));
-
+ def("ExtractTemplateData", &WrapExtractTemplateDataSingle, (arg("entry_name"),
+ arg("chain_name"),
+ arg("aln"),
+ arg("linear_indexer"),
+ arg("seqres_container"),
+ arg("atomseq_container"),
+ arg("position_container")));
+
+ def("ExtractTemplateData", &WrapExtractTemplateDataList, (arg("entry_name"),
+ arg("chain_name"),
+ arg("aln"),
+ arg("linear_indexer"),
+ arg("seqres_container"),
+ arg("atomseq_container"),
+ arg("position_containers")));
}
diff --git a/modules/db/src/extract_data_helper.cc b/modules/db/src/extract_data_helper.cc
index 519c6945feae7c6122c59ddf38f779b0a6c2aaaa..d8e18bc6978714693dd0ee9bd6a94601f5570215 100644
--- a/modules/db/src/extract_data_helper.cc
+++ b/modules/db/src/extract_data_helper.cc
@@ -48,14 +48,14 @@ void ExtractValidPositions(const String& entry_name, const String& chain_name,
valid_seq.end()));
}
-void ExtractTemplateDataDisCo(const String& entry_name, const String& chain_name,
- const ost::seq::AlignmentHandle& aln,
- LinearIndexerPtr indexer,
- LinearCharacterContainerPtr seqres_container,
- LinearCharacterContainerPtr atomseq_container,
- LinearPositionContainerPtr& position_container,
- std::vector<int>& residue_numbers,
- geom::Vec3List& positions) {
+void ExtractTemplateData(const String& entry_name, const String& chain_name,
+ const ost::seq::AlignmentHandle& aln,
+ LinearIndexerPtr indexer,
+ LinearCharacterContainerPtr seqres_container,
+ LinearCharacterContainerPtr atomseq_container,
+ std::vector<LinearPositionContainerPtr>& position_containers,
+ std::vector<int>& residue_numbers,
+ std::vector<geom::Vec3List>& positions) {
std::pair<uint64_t, uint64_t> data_range = indexer->GetDataRange(entry_name,
chain_name);
@@ -75,119 +75,34 @@ void ExtractTemplateDataDisCo(const String& entry_name, const String& chain_name
String template_atomseq;
atomseq_container->GetCharacters(data_range, template_atomseq);
- geom::Vec3List extracted_positions;
- position_container->GetPositions(data_range, extracted_positions);
-
- // prepare output
- uint template_atomseq_size = template_atomseq.size();
- residue_numbers.clear();
- residue_numbers.reserve(template_atomseq_size);
- positions.clear();
- positions.reserve(template_atomseq_size);
+ int n_pos_containers = position_containers.size();
+ std::vector<geom::Vec3List> extracted_positions(n_pos_containers);
+ for(int i = 0; i < n_pos_containers; ++i) {
+ position_containers[i]->GetPositions(data_range, extracted_positions[i]);
+ }
- // extract
uint current_rnum = aln.GetSequence(0).GetOffset() + 1;
uint current_template_pos = 0;
String seqres_seq = aln.GetSequence(0).GetString();
String template_seq = aln.GetSequence(1).GetString();
- for(int i = 0; i < aln.GetLength(); ++i) {
- if(seqres_seq[i] != '-' && template_seq[i] != '-') {
- if(template_atomseq[current_template_pos] != '-') {
- // it is aligned and we have a valid position!
- residue_numbers.push_back(current_rnum);
- positions.push_back(extracted_positions[current_template_pos]);
- }
- }
-
- if(seqres_seq[i] != '-') {
- ++current_rnum;
- }
-
- if(template_seq[i] != '-') {
- ++current_template_pos;
- }
- }
-}
-
-void ExtractTemplateDataGMQE(const String& entry_name, const String& chain_name,
- const ost::seq::AlignmentHandle& aln,
- LinearIndexerPtr indexer,
- LinearCharacterContainerPtr seqres_container,
- LinearCharacterContainerPtr atomseq_container,
- LinearCharacterContainerPtr dssp_container,
- LinearPositionContainerPtr& n_position_container,
- LinearPositionContainerPtr& ca_position_container,
- LinearPositionContainerPtr& c_position_container,
- LinearPositionContainerPtr& cb_position_container,
- std::vector<int>& residue_numbers,
- String& dssp,
- geom::Vec3List& n_positions,
- geom::Vec3List& ca_positions,
- geom::Vec3List& c_positions,
- geom::Vec3List& cb_positions) {
-
- std::pair<uint64_t, uint64_t> data_range = indexer->GetDataRange(entry_name,
- chain_name);
-
- String template_seqres = aln.GetSequence(1).GetGaplessString();
- data_range.first += aln.GetSequence(1).GetOffset();
- data_range.second = data_range.first + template_seqres.size();
-
- // check, whether the the template seqres is consistent with what
- // we find in seqres_container
- String expected_template_seqres;
- seqres_container->GetCharacters(data_range, expected_template_seqres);
- if(expected_template_seqres != template_seqres) {
- throw std::runtime_error("Template sequence in input alignment is "
- "inconsistent with sequence in SEQRES container!");
- }
-
- String template_atomseq;
- atomseq_container->GetCharacters(data_range, template_atomseq);
- String extracted_dssp;
- dssp_container->GetCharacters(data_range, extracted_dssp);
- geom::Vec3List extracted_n_positions;
- n_position_container->GetPositions(data_range, extracted_n_positions);
- geom::Vec3List extracted_ca_positions;
- ca_position_container->GetPositions(data_range, extracted_ca_positions);
- geom::Vec3List extracted_c_positions;
- c_position_container->GetPositions(data_range, extracted_c_positions);
- geom::Vec3List extracted_cb_positions;
- cb_position_container->GetPositions(data_range, extracted_cb_positions);
-
// prepare output
uint template_atomseq_size = template_atomseq.size();
+ positions.assign(n_pos_containers, geom::Vec3List());
+ for(int i = 0; i < n_pos_containers; ++i) {
+ positions[i].reserve(template_atomseq_size);
+ }
residue_numbers.clear();
residue_numbers.reserve(template_atomseq_size);
- dssp.clear();
- dssp.reserve(template_atomseq_size);
- n_positions.clear();
- n_positions.reserve(template_atomseq_size);
- ca_positions.clear();
- ca_positions.reserve(template_atomseq_size);
- c_positions.clear();
- c_positions.reserve(template_atomseq_size);
- cb_positions.clear();
- cb_positions.reserve(template_atomseq_size);
-
-
- // extract
- uint current_rnum = aln.GetSequence(0).GetOffset() + 1;
- uint current_template_pos = 0;
- String seqres_seq = aln.GetSequence(0).GetString();
- String template_seq = aln.GetSequence(1).GetString();
for(int i = 0; i < aln.GetLength(); ++i) {
if(seqres_seq[i] != '-' && template_seq[i] != '-') {
if(template_atomseq[current_template_pos] != '-') {
// it is aligned and we have a valid position!
residue_numbers.push_back(current_rnum);
- dssp.push_back(extracted_dssp[current_template_pos]);
- n_positions.push_back(extracted_n_positions[current_template_pos]);
- ca_positions.push_back(extracted_ca_positions[current_template_pos]);
- c_positions.push_back(extracted_c_positions[current_template_pos]);
- cb_positions.push_back(extracted_cb_positions[current_template_pos]);
+ for(int j = 0; j < n_pos_containers; ++j) {
+ positions[j].push_back(extracted_positions[j][current_template_pos]);
+ }
}
}
diff --git a/modules/db/src/extract_data_helper.hh b/modules/db/src/extract_data_helper.hh
index dbcf7a214d526ea5c8d2919eff0f7dc5a0edb241..b83c9a3154c0fb0ce4f5865b21b9e0c755cee260 100644
--- a/modules/db/src/extract_data_helper.hh
+++ b/modules/db/src/extract_data_helper.hh
@@ -35,31 +35,15 @@ void ExtractValidPositions(const String& entry_name, const String& chain_name,
ost::seq::SequenceHandle& seq,
geom::Vec3List& positions);
-void ExtractTemplateDataDisCo(const String& entry_name, const String& chain_name,
- const ost::seq::AlignmentHandle& aln,
- LinearIndexerPtr indexer,
- LinearCharacterContainerPtr seqres_container,
- LinearCharacterContainerPtr atomseq_container,
- LinearPositionContainerPtr& position_container,
- std::vector<int>& residue_numbers,
- geom::Vec3List& positions);
+void ExtractTemplateData(const String& entry_name, const String& chain_name,
+ const ost::seq::AlignmentHandle& aln,
+ LinearIndexerPtr indexer,
+ LinearCharacterContainerPtr seqres_container,
+ LinearCharacterContainerPtr atomseq_container,
+ std::vector<LinearPositionContainerPtr>& position_container,
+ std::vector<int>& residue_numbers,
+ std::vector<geom::Vec3List>& positions);
-void ExtractTemplateDataGMQE(const String& entry_name, const String& chain_name,
- const ost::seq::AlignmentHandle& aln,
- LinearIndexerPtr indexer,
- LinearCharacterContainerPtr seqres_container,
- LinearCharacterContainerPtr atomseq_container,
- LinearCharacterContainerPtr dssp_container,
- LinearPositionContainerPtr& n_position_container,
- LinearPositionContainerPtr& ca_position_container,
- LinearPositionContainerPtr& c_position_container,
- LinearPositionContainerPtr& cb_position_container,
- std::vector<int>& residue_numbers,
- String& dssp,
- geom::Vec3List& n_positions,
- geom::Vec3List& ca_positions,
- geom::Vec3List& c_positions,
- geom::Vec3List& cb_positions);
}} //ns
#endif