diff --git a/modelling/pymod/export_sidechain_reconstructor.cc b/modelling/pymod/export_sidechain_reconstructor.cc
index 81e75700c9393359e67a27238159166a5e58c3e0..5c8306f3becb3f13b9c99b3ac0e5906ebf7895a9 100644
--- a/modelling/pymod/export_sidechain_reconstructor.cc
+++ b/modelling/pymod/export_sidechain_reconstructor.cc
@@ -8,6 +8,20 @@ using namespace boost::python;
namespace {
+boost::python::list
+WrapGetLoopStartIndices(const SidechainReconstructionData& sc_rec_data) {
+ boost::python::list return_list;
+ core::AppendVectorToList(sc_rec_data.loop_start_indices, return_list);
+ return return_list;
+}
+
+boost::python::list
+WrapGetLoopLengths(const SidechainReconstructionData& sc_rec_data) {
+ boost::python::list return_list;
+ core::AppendVectorToList(sc_rec_data.loop_lengths, return_list);
+ return return_list;
+}
+
boost::python::list
WrapGetRotamerResIndices(const SidechainReconstructionData& sc_rec_data) {
boost::python::list return_list;
@@ -80,7 +94,8 @@ void export_SidechainReconstructor() {
class_<SidechainReconstructionData, SidechainReconstructionDataPtr>
("SidechainReconstructionData", init<>())
.def_readonly("env_pos", &SidechainReconstructionData::env_pos)
- .def_readonly("length", &SidechainReconstructionData::length)
+ .add_property("loop_start_indices", &WrapGetLoopStartIndices)
+ .add_property("loop_lengths", &WrapGetLoopLengths)
.add_property("rotamer_res_indices", &WrapGetRotamerResIndices)
.add_property("disulfid_bridges", &WrapGetDisulfidBridges)
.add_property("is_n_ter", &WrapGetIsNTer)
diff --git a/modelling/src/all_atom_relaxer.cc b/modelling/src/all_atom_relaxer.cc
index 6aa0c960b7b2bcd760c1e2e3edc551e078259256..3f99edbf13851294773042c9fc4d4b98c388efe5 100644
--- a/modelling/src/all_atom_relaxer.cc
+++ b/modelling/src/all_atom_relaxer.cc
@@ -19,11 +19,13 @@ AllAtomRelaxer::AllAtomRelaxer(ScRecDataPtr sc_data,
std::vector<uint>& res_indices = sc_data->env_pos->res_indices;
for (uint i = 0; i < res_indices.size(); ++i) {
const uint res_idx = res_indices[i];
- all_pos_->SetResidue(res_idx, *(sc_data_->env_pos->all_pos), i);
+ all_pos_->SetResidue(res_idx, *(sc_data->env_pos->all_pos), i);
}
// setup system
- mm_system_creator_->SetupSystem(*all_pos_, res_indices, sc_data_->length,
+ mm_system_creator_->SetupSystem(*all_pos_, res_indices,
+ sc_data->loop_start_indices,
+ sc_data->loop_lengths,
sc_data->is_n_ter, sc_data->is_c_ter,
sc_data->disulfid_bridges);
}
diff --git a/modelling/src/sidechain_reconstructor.cc b/modelling/src/sidechain_reconstructor.cc
index 81e503c2ca6f2e1f5c61d3c1b7c3c276dc37ea1d..02c47aacca66e71c3c0a6addbf936ca8d1cac11e 100644
--- a/modelling/src/sidechain_reconstructor.cc
+++ b/modelling/src/sidechain_reconstructor.cc
@@ -41,17 +41,20 @@ SidechainReconstructor::Reconstruct(uint start_resnum, uint num_residues,
}
// get loop indices
- std::vector<uint> indices = idx_handler_->ToIdxVector(start_resnum,
+ std::vector<uint> indices = idx_handler_->ToIdxVector(start_resnum,
num_residues,
chain_idx);
- return this->ReconstructFromIndices(indices);
+ std::vector<uint> loop_start_indices(1, 0);
+ std::vector<uint> loop_lengths(1, num_residues);
+ return ReconstructFromIndices(indices, loop_start_indices, loop_lengths);
}
SidechainReconstructionDataPtr
-SidechainReconstructor::Reconstruct(const std::vector<uint>& start_resnums,
- const std::vector<uint>& num_residues,
- const std::vector<uint>& chain_indices) const {
+SidechainReconstructor::Reconstruct(
+ const std::vector<uint>& start_resnums,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_indices) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SidechainReconstructor::Reconstruct", 2);
@@ -61,32 +64,20 @@ SidechainReconstructor::Reconstruct(const std::vector<uint>& start_resnums,
"attached!");
}
- if(start_resnums.size() != num_residues.size()){
- String err = "Size inconsistency of input data in SidechainReconstructor!";
- throw promod3::Error(err);
- }
-
- if(start_resnums.size() != chain_indices.size()){
- String err = "Size inconsistency of input data in SidechainReconstructor!";
- throw promod3::Error(err);
- }
-
- std::vector<uint> full_indices;
-
- for(uint i = 0; i < start_resnums.size(); ++i){
- // get loop indices
- std::vector<uint> indices = idx_handler_->ToIdxVector(start_resnums[i],
- num_residues[i],
- chain_indices[i]);
-
- full_indices.insert(full_indices.end(), indices.begin(), indices.end());
- }
-
- return this->ReconstructFromIndices(full_indices);
+ // get loop indices
+ std::vector<uint> loop_start_indices;
+ std::vector<uint> loop_lengths;
+ std::vector<uint> indices = idx_handler_->ToIdxVector(start_resnums,
+ num_residues,
+ chain_indices,
+ loop_start_indices,
+ loop_lengths, true);
+ return ReconstructFromIndices(indices, loop_start_indices, loop_lengths);
}
void SidechainReconstructor::AttachEnvironment(loop::AllAtomEnv& env,
- bool use_frm, bool use_bbdep_lib) {
+ bool use_frm,
+ bool use_bbdep_lib) {
loop::AllAtomEnvListenerPtr tst = env.GetListener("SidechainEnvListener");
if (tst) {
env_ = boost::dynamic_pointer_cast<SidechainEnvListener>(tst);
@@ -133,14 +124,18 @@ void SidechainReconstructor::AttachEnvironment(loop::AllAtomEnv& env,
}
SidechainReconstructionDataPtr
-SidechainReconstructor::ReconstructFromIndices(const std::vector<uint>& indices) const{
+SidechainReconstructor::ReconstructFromIndices(
+ const std::vector<uint>& indices,
+ const std::vector<uint>& loop_start_indices,
+ const std::vector<uint>& loop_lengths) const {
// prepare result
SidechainReconstructionDataPtr res(new SidechainReconstructionData());
res->env_pos.reset(new loop::AllAtomEnvPositions);
std::vector<uint>& res_indices = res->env_pos->res_indices;
res_indices = indices;
- res->length = indices.size();
+ res->loop_start_indices = loop_start_indices;
+ res->loop_lengths = loop_lengths;
res->all_pos = all_pos_;
std::set<uint> nb_frame_indices;
@@ -150,7 +145,7 @@ SidechainReconstructor::ReconstructFromIndices(const std::vector<uint>& indices)
std::set<uint> nb_indices;
ScCBetaSpatialOrganizer::WithinResult within_result;
std::pair<ScCBetaSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < res->length; ++i) {
+ for (uint i = 0; i < indices.size(); ++i) {
const uint res_idx = res_indices[i];
within_result = env_->FindWithin(GetCxPos_(*all_pos_, res_idx),
overall_cutoff);
@@ -162,27 +157,27 @@ SidechainReconstructor::ReconstructFromIndices(const std::vector<uint>& indices)
}
// remove the indices form nb_indices
- for(std::vector<uint>::iterator i = res_indices.begin();
- i != res_indices.end(); ++i){
+ for (std::vector<uint>::iterator i = res_indices.begin();
+ i != res_indices.end(); ++i) {
nb_indices.erase(*i);
}
// remove indices from nb_frame_indices
- for(std::vector<uint>::iterator i = res_indices.begin();
- i != res_indices.end(); ++i){
+ for (std::vector<uint>::iterator i = res_indices.begin();
+ i != res_indices.end(); ++i) {
nb_frame_indices.erase(*i);
}
// and also the nb_indices
- for(std::set<uint>::iterator i = nb_indices.begin();
- i != nb_indices.end(); ++i) {
+ for (std::set<uint>::iterator i = nb_indices.begin();
+ i != nb_indices.end(); ++i) {
nb_frame_indices.erase(*i);
}
// append unique surrounding residue indices (first loop part, then rest)
res_indices.insert(res_indices.end(), nb_indices.begin(), nb_indices.end());
// assign all frame residues close to the unique surrounding residues
- res->rigid_frame_indices.assign(nb_frame_indices.begin(),
+ res->rigid_frame_indices.assign(nb_frame_indices.begin(),
nb_frame_indices.end());
// add information on termini
diff --git a/modelling/src/sidechain_reconstructor.hh b/modelling/src/sidechain_reconstructor.hh
index 25292bb82d67b3f682c51d5bda1044ec288e8476..abe8be222f85787b027f554dfd73f591980a58df 100644
--- a/modelling/src/sidechain_reconstructor.hh
+++ b/modelling/src/sidechain_reconstructor.hh
@@ -17,9 +17,11 @@ class SidechainReconstructionData {
public:
// atoms and res. indices
loop::AllAtomEnvPositionsPtr env_pos;
- // first *length* residues of env_pos are the ones actually
- // being reconstructed
- uint length;
+ // loop residues of env_pos are the ones actually being reconstructed
+ // -> loop i_loop has res. indices "env_pos->res_indices[i]" for i in
+ // (loop_start_indices[i_loop] + [0, loop_lengths[i_loop] - 1])
+ std::vector<uint> loop_start_indices;
+ std::vector<uint> loop_lengths;
// indices (into env_pos) of residues where we added rotamer sidechains
std::vector<uint> rotamer_res_indices;
// pairs of indices (into env_pos) of residues where we added disulfid bridge
@@ -75,8 +77,13 @@ public:
private:
+ // indices = res. indices of loops to reconstruct
+ // -> loop i_loop has res. indices "indices[i]" for i in
+ // (loop_start_indices[i_loop] + [0, loop_lengths[i_loop] - 1])
SidechainReconstructionDataPtr
- ReconstructFromIndices(const std::vector<uint>& indices) const;
+ ReconstructFromIndices(const std::vector<uint>& indices,
+ const std::vector<uint>& loop_start_indices,
+ const std::vector<uint>& loop_lengths) const;
// HELPERS
void CheckEnvListener_(bool use_frm) const;
diff --git a/modelling/tests/test_sidechain_reconstructor.cc b/modelling/tests/test_sidechain_reconstructor.cc
index a1db8ba86c0dfdbdf8f58d009ade2d726687281f..f7be288b4192618537aeb5a9f4cbcc85ddd3d5e6 100644
--- a/modelling/tests/test_sidechain_reconstructor.cc
+++ b/modelling/tests/test_sidechain_reconstructor.cc
@@ -61,11 +61,14 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
sc_data->all_pos->GetAA(res_idx));
}
// check loop
- BOOST_CHECK_EQUAL(sc_data->length, loop_length);
- for (uint i = 0; i < sc_data->length; ++i) {
+ BOOST_CHECK_EQUAL(sc_data->loop_start_indices.size(), 1u);
+ BOOST_CHECK_EQUAL(sc_data->loop_lengths.size(), 1u);
+ BOOST_CHECK_EQUAL(sc_data->loop_lengths[0], loop_length);
+ for (uint i = 0; i < loop_length; ++i) {
// all loop res. assumed to be contiguous
- const uint res_idx = sc_data->env_pos->res_indices[i];
- BOOST_CHECK(res_idx == start_resnum+i-1);
+ const uint start_idx = sc_data->loop_start_indices[0];
+ const uint res_idx = sc_data->env_pos->res_indices[start_idx + i];
+ BOOST_CHECK(res_idx == start_resnum + i - 1);
}
// check N-ter / C-ter info
BOOST_CHECK_EQUAL(sc_data->env_pos->res_indices.size(),