Reintroduced PDB conversion code

CMakeLists.txt

@@ -192,6 +192,10 @@ set(project_sources
 	${PROJECT_SOURCE_DIR}/src/symmetry.cpp
 
 	${PROJECT_SOURCE_DIR}/src/model.cpp
+
+	${PROJECT_SOURCE_DIR}/src/pdb/cif2pdb.cpp
+	${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif.cpp
+	${PROJECT_SOURCE_DIR}/src/pdb/pdb2cif_remark_3.cpp
 )
 
 set(project_headers
@@ -216,7 +220,12 @@ set(project_headers
 	${PROJECT_SOURCE_DIR}/include/cif++/symmetry.hpp
 
 	${PROJECT_SOURCE_DIR}/include/cif++/model.hpp
-)
+
+	${PROJECT_SOURCE_DIR}/include/cif++/pdb/cif2pdb.hpp
+	${PROJECT_SOURCE_DIR}/include/cif++/pdb/io.hpp
+	${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif.hpp
+	${PROJECT_SOURCE_DIR}/include/cif++/pdb/pdb2cif_remark_3.hpp
+	)
 
 add_library(cifpp ${project_sources} ${project_headers} ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
 add_library(cifpp::cifpp ALIAS cifpp)

include/cif++.hpp

@@ -35,4 +35,6 @@
 #include <cif++/point.hpp>
 #include <cif++/symmetry.hpp>
 
-#include <cif++/model.hpp>
\ No newline at end of file
+#include <cif++/model.hpp>
+
+#include <cif++/pdb/io.hpp>

include/cif++/pdb/TlsParser.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 <vector>
+#include <string>
+#include <tuple>
+
+#include <cif++.hpp>
+
+namespace cif
+{
+	
+extern const int
+	kResidueNrWildcard,
+	kNoSeqNum;
+
+struct TLSSelection;
+typedef std::unique_ptr<TLSSelection> TLSSelectionPtr;
+
+struct TLSResidue;
+
+struct TLSSelection
+{
+	virtual ~TLSSelection() {}
+	virtual void CollectResidues(cif::datablock& db, std::vector<TLSResidue>& residues, std::size_t indentLevel = 0) const = 0;
+	std::vector<std::tuple<std::string,int,int>> GetRanges(cif::datablock& db, bool pdbNamespace) const;
+};
+
+// Low level: get the selections
+TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::string& selection);
+
+}

include/cif++/pdb/cif2pdb.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++.hpp>
+
+namespace cif::pdb
+{
+
+/// \brief Just the HEADER, COMPND, SOURCE and AUTHOR lines
+void write_header_lines(std::ostream &os, const datablock &data);
+
+std::string get_HEADER_line(const datablock &data, std::string::size_type truncate_at = 127);
+std::string get_COMPND_line(const datablock &data, std::string::size_type truncate_at = 127);
+std::string get_SOURCE_line(const datablock &data, std::string::size_type truncate_at = 127);
+std::string get_AUTHOR_line(const datablock &data, std::string::size_type truncate_at = 127);
+
+} // namespace pdbx

include/cif++/pdb/io.hpp

+/*-
+ * SPDX-License-Identifier: BSD-2-Clause
+ * 
+ * Copyright (c) 2022 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++.hpp>
+
+namespace cif::pdb
+{
+
+file read(std::istream &is);
+
+void write(std::ostream &os, const datablock &db);
+
+inline void write(std::ostream &os, const file &f)
+{
+	write(os, f.front());
+}
+
+}
\ No newline at end of file

include/cif++/pdb/pdb2cif.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++.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);
+};
+
+// --------------------------------------------------------------------
+
+void ReadPDBFile(std::istream &pdbFile, file &cifFile);
+
+} // namespace pdbx
\ No newline at end of file

include/cif++/pdb/pdb2cif_remark_3.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++/pdb/pdb2cif.hpp>
+
+// --------------------------------------------------------------------
+
+namespace cif::pdb
+{
+
+struct TemplateLine;
+
+class Remark3Parser
+{
+  public:
+	virtual ~Remark3Parser() {}
+
+	static bool parse(const std::string &expMethod, PDBRecord *r, cif::datablock &db);
+
+	virtual std::string program();
+	virtual std::string version();
+
+  protected:
+	Remark3Parser(const std::string &name, const std::string &expMethod, PDBRecord *r, cif::datablock &db,
+		const TemplateLine templatelines[], uint32_t templateLineCount, std::regex programVersion);
+
+	virtual float parse();
+	std::string nextLine();
+
+	bool match(const char *expr, int nextState);
+	void storeCapture(const char *category, std::initializer_list<const char *> items, bool createNew = false);
+	void storeRefineLsRestr(const char *type, std::initializer_list<const char *> values);
+	void updateRefineLsRestr(const char *type, std::initializer_list<const char *> values);
+
+	virtual void fixup() {}
+
+	std::string mName;
+	std::string mExpMethod;
+	PDBRecord *mRec;
+	cif::datablock mDb;
+	std::string mLine;
+	std::smatch mM;
+	uint32_t mState;
+
+	const TemplateLine *mTemplate;
+	uint32_t mTemplateCount;
+	std::regex mProgramVersion;
+};
+
+} // namespace pdbx