SCHWED-1740: handle loops of length 0 in SidechainReconstructor

modelling/src/sidechain_reconstructor.cc

@@ -44,8 +44,12 @@ SidechainReconstructor::Reconstruct(uint start_resnum, uint num_residues,
   std::vector<uint> indices = idx_handler_->ToIdxVector(start_resnum,
                                                         num_residues,
                                                         chain_idx);
-  std::vector<uint> loop_start_indices(1, 0);
-  std::vector<uint> loop_lengths(1, num_residues);
+  std::vector<uint> loop_start_indices;
+  std::vector<uint> loop_lengths;
+  if (num_residues > 0) {
+    loop_start_indices.push_back(0);
+    loop_lengths.push_back(num_residues);
+  }
   return ReconstructFromIndices(indices, loop_start_indices, loop_lengths);
 
 }
@@ -399,6 +403,9 @@ void SidechainReconstructor::SolveSystem_(
   // prepare solution
   res->env_pos->all_pos = all_pos_->Extract(res_indices);
   loop::AllAtomPositions& out_pos = *(res->env_pos->all_pos);
+
+  // nothing to be done if empty
+  if (res_indices.empty()) return;
   
   // collect frame residues and cysteins (if needed)
   std::vector<sidechain::FrameResiduePtr> frame_residues;

modelling/tests/test_sidechain_reconstructor.cc

@@ -102,12 +102,32 @@ void CheckLoopRec(const SidechainReconstructorPtr sc_rec,
   }
 }
 
+void CheckEmptyLoop(const SidechainReconstructionDataPtr sc_data,
+                    uint num_residues) {
+  // must all be valid and empty
+  BOOST_CHECK_EQUAL(sc_data->env_pos->res_indices.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->env_pos->all_pos->GetNumResidues(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->loop_start_indices.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->loop_lengths.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->rotamer_res_indices.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->disulfid_bridges.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->is_n_ter.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->is_c_ter.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->rigid_frame_indices.size(), 0u);
+  BOOST_CHECK_EQUAL(sc_data->all_pos->GetNumResidues(), num_residues);
+}
+
 } // anon ns
 
 BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops) {
   // setup
   ost::mol::EntityHandle test_ent = LoadTestStructure("data/1eye_sc_test.pdb");
-  // NOTE: missing sidechains from res.idx. 4 to 67 and at 126 (total: 270 res.)
+  // -> missing at least 1 sidechain for each AA (total: 270 res., 30 sc cut)
+  // -> sc cut: ['PRO1', 'VAL2', 'GLN3', 'MET5', 'LEU8', 'ASN9', 'THR11',
+  //             'ASP12', 'SER14', 'PHE15', 'CYS20', 'TYR21', 'LYS29', 'HIS30',
+  //             'ILE41', 'GLU47', 'SER48', 'SER49', 'ARG50', 'PRO51', 'THR54',
+  //             'ARG55', 'VAL56', 'ASP57', 'PRO58', 'VAL60', 'GLU61', 'THR62',
+  //             'ARG64', 'TRP123']
   uint num_residues = test_ent.GetResidueCount();
   SidechainReconstructorPtr sc_rec = GetScRec(test_ent);
   
@@ -115,6 +135,16 @@ BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops) {
   CheckLoopRec(sc_rec, 1, 4, num_residues);
   CheckLoopRec(sc_rec, 100, 3, num_residues);
   CheckLoopRec(sc_rec, num_residues-4, 5, num_residues);
+
+  // try empty loop
+  SidechainReconstructionDataPtr sc_data = sc_rec->Reconstruct(2, 0);
+  CheckEmptyLoop(sc_data, num_residues);
+  // same with "multi-loop" signature
+  std::vector<uint> start_resnums(1, 2);
+  std::vector<uint> loop_lengths(1, 0);
+  std::vector<uint> chain_indices(1, 0);
+  sc_data = sc_rec->Reconstruct(start_resnums, loop_lengths, chain_indices);
+  CheckEmptyLoop(sc_data, num_residues);
 }
 
 BOOST_AUTO_TEST_CASE(test_sidechain_reconstructor_loops_crn) {