Merge branch 'trunk' into develop

PDB-REDO · Jan 14, 2025 · d1ca35e · d1ca35e
2 parents f3c89bb + 44226bd
commit d1ca35e
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Showing 4 changed files with 19 additions and 8 deletions.
diff --git a/.github/workflows/cmake-multi-platform.yml b/.github/workflows/cmake-multi-platform.yml
@@ -24,7 +24,7 @@ jobs:
             cpp_compiler: clang++
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set reusable strings
       id: strings

diff --git a/src/alphafill.cpp b/src/alphafill.cpp
@@ -48,7 +48,7 @@ using json = zeep::json::element;
 // --------------------------------------------------------------------
 
 // The regex to check and/or read FastA files
-const std::regex kIDRx(R"(^>pdb-entity\|(\w{4,})\|(\w+)\|([^ |]+)( .*)?)");
+const std::regex kIDRx(R"(^>pdb-entity\|(\w{4,})\|(\w+)\|([^ |]+)?( .*)?)");
 
 // --------------------------------------------------------------------
 
@@ -579,7 +579,7 @@ zeep::json::element alphafill(cif::datablock &db, const std::string &source,
 					throw std::runtime_error("Invalid sequence");
 
 				seq.erase(i, j - i + 1);
-				i = seq.find('(', i + 1);
+				i = seq.find('(', i);
 			}
 		}
 
@@ -1086,8 +1086,17 @@ zeep::json::element alphafill(cif::datablock &db, const std::string &source,
 
 								// validation info?
 								if (hsp.identity() == 1)
-									hsp_t["validation"] = calculateValidationScores(db, pdb_res, af_ix_trimmed, pdb_ix_trimmed,
-										af_structure.get_residue(asym_id), res, config.get<float>("max-ligand-to-polymer-atom-distance"), ligand);
+								{
+									try
+									{
+										hsp_t["validation"] = calculateValidationScores(db, af_asym_id, pdb_res, af_ix_trimmed, pdb_ix_trimmed,
+											af_structure.get_residue(asym_id), res, config.get<float>("max-ligand-to-polymer-atom-distance"), ligand);
+									}
+									catch (const std::exception &e)
+									{
+										std::cerr << e.what() << '\n';
+									}
+								}
 
 								if (cif::VERBOSE > 0)
 									std::cerr << "Created asym " << asym_id << " for " << res << '\n';

diff --git a/src/validate.cpp b/src/validate.cpp
@@ -521,13 +521,14 @@ zeep::json::element calculatePAEScore(const std::vector<cif::mm::residue *> &af_
 // --------------------------------------------------------------------
 
 zeep::json::element calculateValidationScores(
-	cif::datablock af_db, const std::vector<cif::mm::residue *> &pdb_res,
+	cif::datablock af_db, const std::string &asym_id,
+	const std::vector<cif::mm::residue *> &pdb_res,
 	const std::vector<size_t> &af_ix, const std::vector<size_t> &pdb_ix,
 	const cif::mm::residue &af_ligand, const cif::mm::residue &pdb_ligand,
 	float maxDistance, const Ligand &ligand)
 {
 	cif::mm::structure af_structure(af_db);
-	auto &poly = af_structure.get_polymer_by_asym_id("A");
+	auto &poly = af_structure.get_polymer_by_asym_id(asym_id);
 
 	std::vector<cif::mm::monomer *> af_res_selected, pdb_res_selected;
 

diff --git a/src/validate.hpp b/src/validate.hpp
@@ -69,7 +69,8 @@ float ClashScore(cif::datablock &db, float maxDistance = 4);
 // --------------------------------------------------------------------
 
 zeep::json::element calculateValidationScores(
-	cif::datablock af_db, const std::vector<cif::mm::residue *> &pdb_res,
+	cif::datablock af_db, const std::string &asym_id,
+	const std::vector<cif::mm::residue *> &pdb_res,
 	const std::vector<size_t> &af_ix, const std::vector<size_t> &pdb_ix,
 	const cif::mm::residue &af_ligand, const cif::mm::residue &pdb_ligand,
 	float maxDistance, const Ligand &ligand);