diff --git a/modules/db/doc/db.rst b/modules/db/doc/db.rst
index 87dc0919e840133815ea56af101ca8d9096b2d11..a296c1ec6e5db939085a79dab3563841a38c5b39 100644
--- a/modules/db/doc/db.rst
+++ b/modules/db/doc/db.rst
@@ -309,14 +309,14 @@ Data Extraction
--------------------------------------------------------------------------------
Openstructure provides data extraction functionality for the following scenario:
-There is a SEQRES container and an ATOMSEQ container
-(both: :class:`LinearCharacterContainer`).
-Positions are stored in :class:`LinearPositionContainer`.
-The containers contain entries from the protein structure database
+There are three binary container. A position container to hold CA-positions
+(:class:`LinearPositionContainer`), a SEQRES container and
+an ATOMSEQ container (both: :class:`LinearCharacterContainer`).
+They contain entries from the protein structure database
and sequence/position data is relative to the SEQRES of those entries.
This means, if the SEQRES has more characters as there are resolved residues
-in the structure, the entry in the position container(s) still contains the exact
-number of SEQRES characters but some positions remain invalid. Thats where the
+in the structure, the entry in the position container still contains the exact
+number of SEQRES characters but some position remain invalid. Thats where the
ATOMSEQ container comes in. It only contains matching residues to the SEQRES but
marks non-resolved residues with '-'.
@@ -378,16 +378,13 @@ marks non-resolved residues with '-'.
: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`
+ :type position_container: :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`.
+ starts from one. Second Element: :class:`geom.Vec3List`
+ with the according positions.
:rtype: :class:`tuple`
:raises: :exc:`ost.Error` if requested data is not present in
diff --git a/modules/db/pymod/export_linear_db.cc b/modules/db/pymod/export_linear_db.cc
index 1cb623cb5b8644d6af0dbd939ca84fc8d44a31c0..597f4243e1f447d47d39f771b12a09a56e6c5e57 100644
--- a/modules/db/pymod/export_linear_db.cc
+++ b/modules/db/pymod/export_linear_db.cc
@@ -148,50 +148,24 @@ void WrapGetPositions(LinearPositionContainerPtr 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;
+tuple WrapExtractTemplateData(const String& entry_name, const String& chain_name,
+ const ost::seq::AlignmentHandle& aln,
+ LinearIndexer& indexer,
+ LinearCharacterContainer& seqres_container,
+ LinearCharacterContainer& atomseq_container,
+ LinearPositionContainer& position_container) {
- ost::db::ExtractTemplateData(entry_name, chain_name, aln, indexer,
- seqres_container, atomseq_container,
- position_containers, v_residue_numbers,
- position_vec);
-
- 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) {
-
- std::vector<LinearPositionContainerPtr> v_position_containers;
- ListToVec(position_containers, v_position_containers);
std::vector<int> v_residue_numbers;
- std::vector<geom::Vec3List> position_vec;
+ geom::Vec3List ca_positions;
ost::db::ExtractTemplateData(entry_name, chain_name, aln, indexer,
seqres_container, atomseq_container,
- v_position_containers, v_residue_numbers,
- position_vec);
+ position_container, v_residue_numbers,
+ ca_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);
+ return boost::python::make_tuple(residue_numbers, ca_positions);
}
}
@@ -252,20 +226,13 @@ void export_linear_db() {
arg("position_container"),
arg("seq"), arg("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")));
+ def("ExtractTemplateData", &WrapExtractTemplateData, (arg("entry_name"),
+ arg("chain_name"),
+ arg("aln"),
+ arg("linear_indexer"),
+ arg("seqres_container"),
+ arg("atomseq_container"),
+ arg("position_container")));
+
}
diff --git a/modules/db/src/extract_data_helper.cc b/modules/db/src/extract_data_helper.cc
index d8e18bc6978714693dd0ee9bd6a94601f5570215..f95ff73e3c1b5e20d026af755f2c36b76d3f389e 100644
--- a/modules/db/src/extract_data_helper.cc
+++ b/modules/db/src/extract_data_helper.cc
@@ -50,15 +50,15 @@ void ExtractValidPositions(const String& entry_name, const String& chain_name,
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,
+ LinearIndexer& indexer,
+ LinearCharacterContainer& seqres_container,
+ LinearCharacterContainer& atomseq_container,
+ LinearPositionContainer& position_container,
std::vector<int>& residue_numbers,
- std::vector<geom::Vec3List>& positions) {
+ geom::Vec3List& ca_positions) {
- std::pair<uint64_t, uint64_t> data_range = indexer->GetDataRange(entry_name,
- chain_name);
+ 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();
@@ -67,19 +67,16 @@ void ExtractTemplateData(const String& entry_name, const String& chain_name,
// 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);
+ 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);
- 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]);
- }
+ atomseq_container.GetCharacters(data_range, template_atomseq);
+ geom::Vec3List extracted_positions;
+ position_container.GetPositions(data_range, extracted_positions);
uint current_rnum = aln.GetSequence(0).GetOffset() + 1;
uint current_template_pos = 0;
@@ -88,21 +85,18 @@ void ExtractTemplateData(const String& entry_name, const String& chain_name,
// 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);
- }
+ ca_positions.clear();
residue_numbers.clear();
+ ca_positions.reserve(template_atomseq_size);
residue_numbers.reserve(template_atomseq_size);
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);
- for(int j = 0; j < n_pos_containers; ++j) {
- positions[j].push_back(extracted_positions[j][current_template_pos]);
- }
+ ca_positions.push_back(extracted_positions[current_template_pos]);
}
}
diff --git a/modules/db/src/extract_data_helper.hh b/modules/db/src/extract_data_helper.hh
index b83c9a3154c0fb0ce4f5865b21b9e0c755cee260..271d03b3d920bf7c5cd1670d99ceaf9496e13191 100644
--- a/modules/db/src/extract_data_helper.hh
+++ b/modules/db/src/extract_data_helper.hh
@@ -37,12 +37,12 @@ void ExtractValidPositions(const String& entry_name, const String& chain_name,
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,
+ LinearIndexer& indexer,
+ LinearCharacterContainer& seqres_container,
+ LinearCharacterContainer& atomseq_container,
+ LinearPositionContainer& position_container,
std::vector<int>& residue_numbers,
- std::vector<geom::Vec3List>& positions);
+ geom::Vec3List& ca_positions);
}} //ns