Merge branch 'trunk' into develop

changelog

 Version 4.1.0
 Version 4.1.0
 - Some interface changes for mmcif::Atom
 - Some interface changes for mmcif::Atom
 
 
+Version 4.0.1
+- Added a bunch of const methods to Datablock and Category.
+- Changed PDB writing interface to accept Datablock instead of File.
+
 Version 4.0.0
 Version 4.0.0
 - getResidue in mmcif::Structure now requires both a
 - getResidue in mmcif::Structure now requires both a
   sequence ID and an auth sequence ID. As a result the code was cleaned
   sequence ID and an auth sequence ID. As a result the code was cleaned

include/cif++/Cif++.hpp

@@ -254,8 +254,15 @@ class Datablock
 	const_iterator begin() const { return mCategories.begin(); }
 	const_iterator begin() const { return mCategories.begin(); }
 	const_iterator end() const { return mCategories.end(); }
 	const_iterator end() const { return mCategories.end(); }
 
 
+	/// \brief Access to the category with name \a name, will create it if it doesn't exist.
 	Category &operator[](std::string_view name);
 	Category &operator[](std::string_view name);
 
 
+	// /// \brief Access to the category with name \a name, will throw if it doesn't exist.
+	// const Category &operator[](std::string_view name) const;
+
+	/// \brief Access to the category with name \a name, will return an empty category if is doesn't exist.
+	const Category &operator[](std::string_view name) const;
+
 	std::tuple<iterator, bool> emplace(std::string_view name);
 	std::tuple<iterator, bool> emplace(std::string_view name);
 
 
 	bool isValid();
 	bool isValid();
@@ -285,6 +292,9 @@ class Datablock
 	std::string mName;
 	std::string mName;
 	const Validator *mValidator;
 	const Validator *mValidator;
 	Datablock *mNext;
 	Datablock *mNext;
+
+	// for returning empty categories in the const operator[]
+	mutable std::unique_ptr<Category> mNullCategory;
 };
 };
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
@@ -1863,6 +1873,9 @@ class Category
 	Row front() { return Row(mHead); }
 	Row front() { return Row(mHead); }
 	Row back() { return Row(mTail); }
 	Row back() { return Row(mTail); }
 
 
+	const Row front() const { return Row(mHead); }
+	const Row back() const { return Row(mTail); }
+
 	Row operator[](Condition &&cond);
 	Row operator[](Condition &&cond);
 	const Row operator[](Condition &&cond) const;
 	const Row operator[](Condition &&cond) const;
 
 

include/cif++/Cif2PDB.hpp

 /*-
 /*-
  * SPDX-License-Identifier: BSD-2-Clause
  * SPDX-License-Identifier: BSD-2-Clause
- * 
+ *
  * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
  * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
- * 
+ *
  * Redistribution and use in source and binary forms, with or without
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice, this
  * 1. Redistributions of source code must retain the above copyright notice, this
  *    list of conditions and the following disclaimer
  *    list of conditions and the following disclaimer
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  * 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
  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
@@ -28,12 +28,12 @@
 
 
 #include "cif++/Cif++.hpp"
 #include "cif++/Cif++.hpp"
 
 
-void WritePDBFile(std::ostream& pdbFile, cif::File& cifFile);
+void WritePDBFile(std::ostream &os, const cif::Datablock &data);
 
 
 /// \brief Just the HEADER, COMPND, SOURCE and AUTHOR lines
 /// \brief Just the HEADER, COMPND, SOURCE and AUTHOR lines
-void WritePDBHeaderLines(std::ostream& os, cif::File& cifFile);
+void WritePDBHeaderLines(std::ostream &os, const cif::Datablock &data);
 
 
-std::string GetPDBHEADERLine(cif::File& cifFile, std::string::size_type truncate_at = 127);
-std::string GetPDBCOMPNDLine(cif::File& cifFile, std::string::size_type truncate_at = 127);
-std::string GetPDBSOURCELine(cif::File& cifFile, std::string::size_type truncate_at = 127);
-std::string GetPDBAUTHORLine(cif::File& cifFile, std::string::size_type truncate_at = 127);
+std::string GetPDBHEADERLine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
+std::string GetPDBCOMPNDLine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
+std::string GetPDBSOURCELine(const cif::Datablock &data, std::string::size_type truncate_at = 127);
+std::string GetPDBAUTHORLine(const cif::Datablock &data, std::string::size_type truncate_at = 127);

src/Cif++.cpp

@@ -409,6 +409,22 @@ Category &Datablock::operator[](std::string_view name)
 	return *i;
 	return *i;
 }
 }
 
 
+const Category &Datablock::operator[](std::string_view name) const
+{
+	using namespace std::literals;
+
+	auto result = get(name);
+	if (result == nullptr)
+		// throw std::out_of_range("The category with name " + std::string(name) + " does not exist");
+	{
+		std::unique_lock lock(mLock);
+		if (not mNullCategory)
+			mNullCategory.reset(new Category(const_cast<Datablock&>(*this), "<null>", nullptr));
+		result = mNullCategory.get();
+	}
+	return *result;
+}
+
 Category *Datablock::get(std::string_view name)
 Category *Datablock::get(std::string_view name)
 {
 {
 	std::shared_lock lock(mLock);
 	std::shared_lock lock(mLock);
@@ -1525,6 +1541,11 @@ void Category::drop(const std::string &field)
 	}
 	}
 }
 }
 
 
+const Row Category::operator[](Condition &&cond) const
+{
+	return const_cast<Category*>(this)->operator[](std::forward<Condition>(cond));
+}
+
 Row Category::operator[](Condition &&cond)
 Row Category::operator[](Condition &&cond)
 {
 {
 	Row result;
 	Row result;

src/Structure.cpp

@@ -1373,7 +1373,7 @@ void File::save(const std::filesystem::path &path)
 	out.push(outFile);
 	out.push(outFile);
 
 
 	if (file.extension() == ".pdb")
 	if (file.extension() == ".pdb")
-		WritePDBFile(out, *this);
+		WritePDBFile(out, data());
 	else
 	else
 		cif::File::save(out);
 		cif::File::save(out);
 }
 }