refactoring PDB interface

CMakeLists.txt

@@ -240,6 +240,8 @@ set(project_sources
 
 
 	${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
 	${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
 	${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/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/tls.cpp
 	${PROJECT_SOURCE_DIR}/src/pdb/tls.cpp
 )
 )
@@ -269,7 +271,6 @@ set(project_headers
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
-	${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif_remark_3.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/tls.hpp
 	${PROJECT_SOURCE_DIR}/include/cif++/pdb/tls.hpp
 )
 )
 
 

include/cif++/pdb/cif2pdb.hpp

@@ -28,6 +28,8 @@
 
 
 #include "cif++/datablock.hpp"
 #include "cif++/datablock.hpp"
 
 
+/// \file cif2pdb.hpp
+
 namespace cif::pdb
 namespace cif::pdb
 {
 {
 
 

include/cif++/pdb/io.hpp

@@ -28,6 +28,8 @@
 
 
 #include "cif++/datablock.hpp"
 #include "cif++/datablock.hpp"
 
 
+/// \file io.hpp
+
 namespace cif::pdb
 namespace cif::pdb
 {
 {
 
 

include/cif++/pdb/pdb2cif.hpp

@@ -27,38 +27,12 @@
 #pragma once
 #pragma once
 
 
 #include "cif++/file.hpp"
 #include "cif++/file.hpp"
-namespace cif::pdb
-{
 
 
-// --------------------------------------------------------------------
+/// \file pdb2cif.hpp
 
 
-struct PDBRecord
+namespace cif::pdb
 {
 {
-	PDBRecord *mNext;
-	uint32_t mLineNr;
-	char mName[11];
-	size_t mVlen;
-	char mValue[1];
-
-	PDBRecord(uint32_t lineNr, const std::string &name, const std::string &value);
-	~PDBRecord();
-
-	void *operator new(size_t);
-	void *operator new(size_t size, size_t vLen);
-
-	void operator delete(void *p);
-	void operator delete(void *p, size_t vLen);
-
-	bool is(const char *name) const;
-
-	char vC(size_t column);
-	std::string vS(size_t columnFirst, size_t columnLast = std::numeric_limits<size_t>::max());
-	int vI(int columnFirst, int columnLast);
-	std::string vF(size_t columnFirst, size_t columnLast);
-};
-
-// --------------------------------------------------------------------
 
 
 void ReadPDBFile(std::istream &pdbFile, file &cifFile);
 void ReadPDBFile(std::istream &pdbFile, file &cifFile);
 
 
-} // namespace pdbx
+} // namespace cif::pdb
\ No newline at end of file

include/cif++/pdb/tls.hpp

@@ -32,6 +32,8 @@
 #include <tuple>
 #include <tuple>
 #include <vector>
 #include <vector>
 
 
+/// \file tls.hpp
+
 namespace cif
 namespace cif
 {
 {
 
 

src/pdb/pdb2cif.cpp

@@ -24,9 +24,10 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
  */
 
 
+#include "pdb2cif_remark_3.hpp"
+
 #include <cif++.hpp>
 #include <cif++.hpp>
 #include <cif++/pdb/pdb2cif.hpp>
 #include <cif++/pdb/pdb2cif.hpp>
-#include <cif++/pdb/pdb2cif_remark_3.hpp>
 #include <cif++/gzio.hpp>
 #include <cif++/gzio.hpp>
 
 
 #include <iomanip>
 #include <iomanip>

src/pdb/pdb2cif_remark_3.cpp

@@ -24,8 +24,9 @@
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
  */
 
 
-#include "cif++.hpp"
-#include "cif++/pdb/pdb2cif_remark_3.hpp"
+#include "pdb2cif_remark_3.hpp"
+
+#include <cif++.hpp>
 
 
 #include <map>
 #include <map>
 #include <set>
 #include <set>

include/cif++/pdb/pdb2cif_remark_3.hpp → src/pdb/pdb2cif_remark_3.hpp

@@ -26,7 +26,7 @@
 
 
 #pragma once
 #pragma once
 
 
-#include "pdb2cif.hpp"
+#include "pdb_record.hpp"
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 
 

src/pdb/pdb_record.hpp

+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ *
+ * Copyright (c) 2020 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.
+ */
+
+#pragma once
+
+#include "cif++/file.hpp"
+
+/// \file pdb_record.hpp
+
+namespace cif::pdb
+{
+
+// --------------------------------------------------------------------
+
+struct PDBRecord
+{
+	PDBRecord *mNext;
+	uint32_t mLineNr;
+	char mName[11];
+	size_t mVlen;
+	char mValue[1];
+
+	PDBRecord(uint32_t lineNr, const std::string &name, const std::string &value);
+	~PDBRecord();
+
+	void *operator new(size_t);
+	void *operator new(size_t size, size_t vLen);
+
+	void operator delete(void *p);
+	void operator delete(void *p, size_t vLen);
+
+	bool is(const char *name) const;
+
+	char vC(size_t column);
+	std::string vS(size_t columnFirst, size_t columnLast = std::numeric_limits<size_t>::max());
+	int vI(int columnFirst, int columnLast);
+	std::string vF(size_t columnFirst, size_t columnLast);
+};
+
+} // namespace pdbx
\ No newline at end of file