Merge

CMakeLists.txt

@@ -298,7 +298,9 @@ set(project_sources
     ${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
     ${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
     ${PROJECT_SOURCE_DIR}/src/pdb/pdb_record.hpp
     ${PROJECT_SOURCE_DIR}/src/pdb/pdb_record.hpp
     ${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.hpp
     ${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.hpp
-    ${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp)
+    ${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
+	${PROJECT_SOURCE_DIR}/src/pdb/reconstruct.cpp
+	)
 
 
 set(project_headers
 set(project_headers
     ${PROJECT_SOURCE_DIR}/include/cif++.hpp
     ${PROJECT_SOURCE_DIR}/include/cif++.hpp

include/cif++/model.hpp

@@ -1115,11 +1115,4 @@ class structure
 	std::vector<residue> m_non_polymers;
 	std::vector<residue> m_non_polymers;
 };
 };
 
 
-// --------------------------------------------------------------------
-
-/// \brief Reconstruct all missing categories for an assumed PDBx file.
-/// Some people believe that simply dumping some atom records is enough.
-/// \param db The cif::datablock that hopefully contains some valid data
-void reconstruct_pdbx(datablock &db);
-
 } // namespace cif::mm
 } // namespace cif::mm

include/cif++/pdb.hpp

@@ -100,6 +100,17 @@ inline void write(const std::filesystem::path &p, const file &f)
 }
 }
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
+
+/** \brief Reconstruct all missing categories for an assumed PDBx file.
+ * 
+ * Some people believe that simply dumping some atom records is enough.
+ * 
+ * \param db The cif::datablock that hopefully contains some valid data
+ */
+
+void reconstruct_pdbx(datablock &db);
+
+// --------------------------------------------------------------------
 // Other I/O related routines
 // Other I/O related routines
 
 
 /** @brief Return the HEADER line for the data in @a data
 /** @brief Return the HEADER line for the data in @a data

src/model.cpp

@@ -2836,15 +2836,4 @@ void structure::validate_atoms() const
 	assert(atoms.empty());
 	assert(atoms.empty());
 }
 }
 
 
-// --------------------------------------------------------------------
-
-void reconstruct_pdbx(datablock &db)
-{
-	if (db.get("atom_site") == nullptr)
-		throw std::runtime_error("Cannot reconstruct PDBx file, atom data missing");
-	
-	assert(false);
-	throw std::runtime_error("not implemented yet");
-}
-
 } // namespace pdbx
 } // namespace pdbx

src/pdb/reconstruct.cpp

+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ *
+ * Copyright (c) 2024 NKI/AVL, Netherlands Cancer Institute
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include "cif++/pdb.hpp"
+
+// --------------------------------------------------------------------
+
+namespace cif::pdb
+{
+
+void reconstruct_pdbx(datablock &db)
+{
+	if (db.get("atom_site") == nullptr)
+		throw std::runtime_error("Cannot reconstruct PDBx file, atom data missing");
+
+
+
+}
+
+} // namespace cif::pdb