refactored mmcif::File

changelog

+Version 3.0.5
+- mmcif::Structure redesign. It is now a wrapper around a cif::Datablock.
+
 Version 3.0.4
 - Fix in mmCIF parser, now correctly handles the unquoted
   string ??

include/cif++/Cif++.hpp

@@ -2169,17 +2169,21 @@ class File
 	File();
 	File(std::istream &is, bool validate = false);
 	File(const std::filesystem::path &path, bool validate = false);
+	File(const char *data, size_t length); // good luck trying to find out what it is...
+
 	File(File &&rhs);
 	File(const File &rhs) = delete;
 	File &operator=(const File &rhs) = delete;
 
-	~File();
+	virtual ~File();
+
+	virtual void load(const std::filesystem::path &p);
+	virtual void save(const std::filesystem::path &p);
 
-	void load(const std::filesystem::path &p);
-	void save(const std::filesystem::path &p);
+	virtual void load(std::istream &is);
+	virtual void save(std::ostream &os);
 
-	void load(std::istream &is);
-	void save(std::ostream &os);
+	virtual void load(const char *data, std::size_t length);
 
 	/// \brief Load only the data block \a datablock from the mmCIF file
 	void load(std::istream &is, const std::string &datablock);
@@ -2211,6 +2215,12 @@ class File
 
 	void append(Datablock *e);
 
+	Datablock &emplace(std::string_view name)
+	{
+		append(new Datablock(name));
+		return back();
+	}
+	
 	Datablock *get(std::string_view name) const;
 	Datablock &operator[](std::string_view name);
 
@@ -2248,6 +2258,9 @@ class File
 	iterator begin() const;
 	iterator end() const;
 
+	Datablock &front();
+	Datablock &back();
+
 	bool empty() const { return mHead == nullptr; }
 
 	const Validator &getValidator() const;

include/cif++/Point.hpp

@@ -221,7 +221,7 @@ struct PointF
 
 	FType length() const
 	{
-		return sqrt(mX * mX + mY * mY + mZ * mZ);
+		return std::sqrt(mX * mX + mY * mY + mZ * mZ);
 	}
 };
 
@@ -285,7 +285,7 @@ inline double DistanceSquared(const PointF<F> &a, const PointF<F> &b)
 template <typename F>
 inline double Distance(const PointF<F> &a, const PointF<F> &b)
 {
-	return sqrt(
+	return std::sqrt(
 		(a.mX - b.mX) * (a.mX - b.mX) +
 		(a.mY - b.mY) * (a.mY - b.mY) +
 		(a.mZ - b.mZ) * (a.mZ - b.mZ));
@@ -332,10 +332,10 @@ double DihedralAngle(const PointF<F> &p1, const PointF<F> &p2, const PointF<F> &
 	double result = 360;
 	if (u > 0 and v > 0)
 	{
-		u = DotProduct(p, x) / sqrt(u);
-		v = DotProduct(p, y) / sqrt(v);
+		u = DotProduct(p, x) / std::sqrt(u);
+		v = DotProduct(p, y) / std::sqrt(v);
 		if (u != 0 or v != 0)
-			result = atan2(v, u) * 180 / kPI;
+			result = std::atan2(v, u) * 180 / kPI;
 	}
 
 	return result;
@@ -351,7 +351,7 @@ double CosinusAngle(const PointF<F> &p1, const PointF<F> &p2, const PointF<F> &p
 
 	double x = DotProduct(v12, v12) * DotProduct(v34, v34);
 	if (x > 0)
-		result = DotProduct(v12, v34) / sqrt(x);
+		result = DotProduct(v12, v34) / std::sqrt(x);
 
 	return result;
 }
@@ -436,9 +436,9 @@ class SphericalDots
 			double lat = std::asin((2.0 * i) / P);
 			double lon = std::fmod(i, kGoldenRatio) * 2 * kPI / kGoldenRatio;
 
-			p->mX = sin(lon) * cos(lat);
-			p->mY = cos(lon) * cos(lat);
-			p->mZ = sin(lat);
+			p->mX = std::sin(lon) * std::cos(lat);
+			p->mY = std::cos(lon) * std::cos(lat);
+			p->mZ = std::sin(lat);
 
 			++p;
 		}

include/cif++/Structure.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
@@ -34,16 +34,16 @@
 #include "cif++/Point.hpp"
 
 /*
-	To modify a structure, you will have to use actions.
-	
-	The currently supported actions are:
-	
+    To modify a structure, you will have to use actions.
+
+    The currently supported actions are:
+
 //	- Move atom to new location
-	- Remove atom
+    - Remove atom
 //	- Add new atom that was formerly missing
 //	- Add alternate Residue
-	- 
-	
+    -
+
 */
 
 namespace mmcif
@@ -61,7 +61,6 @@ class File;
 class Atom
 {
   private:
-
 	struct AtomImpl : public std::enable_shared_from_this<AtomImpl>
 	{
 		AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row);
@@ -99,7 +98,7 @@ class Atom
 		int mRefcount;
 		cif::Row mRow;
 
-		mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
+		mutable std::vector<std::tuple<std::string, cif::detail::ItemReference>> mCachedRefs;
 
 		mutable const Compound *mCompound = nullptr;
 
@@ -110,14 +109,17 @@ class Atom
 	};
 
   public:
-
 	Atom() {}
 
 	Atom(std::shared_ptr<AtomImpl> impl)
-		: mImpl(impl) {}
+		: mImpl(impl)
+	{
+	}
 
 	Atom(const Atom &rhs)
-		: mImpl(rhs.mImpl) {}
+		: mImpl(rhs.mImpl)
+	{
+	}
 
 	Atom(cif::Datablock &db, cif::Row &row);
 
@@ -152,10 +154,10 @@ class Atom
 		set_property(name, std::to_string(value));
 	}
 
-	const std::string &id() const			{ return impl().mID; }
-	AtomType type() const					{ return impl().mType; }
+	const std::string &id() const { return impl().mID; }
+	AtomType type() const { return impl().mType; }
 
-	Point location() const					{ return impl().mLocation; }
+	Point location() const { return impl().mLocation; }
 	void location(Point p)
 	{
 		if (not mImpl)
@@ -176,33 +178,33 @@ class Atom
 	void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
 
 	// for direct access to underlying data, be careful!
-	const cif::Row getRow() const			{ return impl().mRow; }
+	const cif::Row getRow() const { return impl().mRow; }
 	const cif::Row getRowAniso() const;
 
-	bool isSymmetryCopy() const				{ return impl().mSymmetryCopy; }
-	std::string symmetry() const			{ return impl().mSymmetryOperator; }
+	bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
+	std::string symmetry() const { return impl().mSymmetryOperator; }
 
-	const Compound &comp() const			{ return impl().comp(); }
-	bool isWater() const					{ return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
+	const Compound &comp() const { return impl().comp(); }
+	bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
 	int charge() const;
 
 	float uIso() const;
-	bool getAnisoU(float anisou[6]) const	{ return impl().getAnisoU(anisou); }
+	bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
 	float occupancy() const;
 
 	// specifications
-	const std::string& labelAtomID() const		{ return impl().mAtomID; }
-	const std::string& labelCompID() const		{ return impl().mCompID; }
-	const std::string& labelAsymID() const		{ return impl().mAsymID; }
+	const std::string &labelAtomID() const { return impl().mAtomID; }
+	const std::string &labelCompID() const { return impl().mCompID; }
+	const std::string &labelAsymID() const { return impl().mAsymID; }
 	std::string labelEntityID() const;
-	int labelSeqID() const						{ return impl().mSeqID; }
-	const std::string& labelAltID() const		{ return impl().mAltID; }
-	bool isAlternate() const					{ return not impl().mAltID.empty(); }
+	int labelSeqID() const { return impl().mSeqID; }
+	const std::string &labelAltID() const { return impl().mAltID; }
+	bool isAlternate() const { return not impl().mAltID.empty(); }
 
 	std::string authAtomID() const;
 	std::string authCompID() const;
 	std::string authAsymID() const;
-	const std::string& authSeqID() const		{ return impl().mAuthSeqID; }
+	const std::string &authSeqID() const { return impl().mAuthSeqID; }
 	std::string pdbxAuthInsCode() const;
 	std::string pdbxAuthAltID() const;
 
@@ -225,7 +227,7 @@ class Atom
 		std::swap(mImpl, b.mImpl);
 	}
 
-	int compare(const Atom &b) const		{ return impl().compare(*b.mImpl); }
+	int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
 
 	bool operator<(const Atom &rhs) const
 	{
@@ -487,31 +489,33 @@ class Polymer : public std::vector<Monomer>
 // file is a reference to the data stored in e.g. the cif file.
 // This object is not copyable.
 
-class File : public std::enable_shared_from_this<File>
+class File : public cif::File
 {
   public:
-	File();
-	File(const std::filesystem::path &path);
-	File(const char *data, size_t length); // good luck trying to find out what it is...
-	~File();
+	File() {}
 
-	File(const File &) = delete;
-	File &operator=(const File &) = delete;
-
-	cif::Datablock& createDatablock(const std::string_view name);
+	File(const std::filesystem::path &path)
+	{
+		load(path);
+	}
 
-	void load(const std::filesystem::path &path);
-	void save(const std::filesystem::path &path);
+	File(const char *data, size_t length)
+	{
+		load(data, length);
+	}
 
-	Structure *model(size_t nr = 1);
+	File(const File &) = delete;
+	File &operator=(const File &) = delete;
 
-	struct FileImpl &impl() const { return *mImpl; }
+	void load(const std::filesystem::path &p) override;
+	void save(const std::filesystem::path &p) override;
 
-	cif::Datablock &data();
-	cif::File &file();
+	void load(std::istream &is) override;
+	
+	using cif::File::save;
+	using cif::File::load;
 
-  private:
-	struct FileImpl *mImpl;
+	cif::Datablock &data() { return front(); }
 };
 
 // --------------------------------------------------------------------
@@ -531,14 +535,18 @@ inline bool operator&(StructureOpenOptions a, StructureOpenOptions b)
 class Structure
 {
   public:
-	Structure(File &p, size_t modelNr = 1, StructureOpenOptions options = {});
-	Structure &operator=(const Structure &) = delete;
-	~Structure();
+	Structure(File &p, size_t modelNr = 1, StructureOpenOptions options = {})
+		: Structure(p.firstDatablock(), modelNr, options)
+	{
+	}
+
+	Structure(cif::Datablock &db, size_t modelNr = 1, StructureOpenOptions options = {});
 
 	// Create a read-only clone of the current structure (for multithreaded calculations that move atoms)
 	Structure(const Structure &);
 
-	File &getFile() const;
+	Structure &operator=(const Structure &) = delete;
+	~Structure();
 
 	const AtomView &atoms() const { return mAtoms; }
 	AtomView waters() const;
@@ -655,8 +663,15 @@ class Structure
 	void cleanupEmptyCategories();
 
 	/// \brief Direct access to underlying data
-	cif::Category &category(std::string_view name) const;
-	cif::Datablock &datablock() const;
+	cif::Category &category(std::string_view name) const
+	{
+		return mDb[name];
+	}
+
+	cif::Datablock &datablock() const
+	{
+		return mDb;
+	}
 
   private:
 	friend Polymer;
@@ -671,7 +686,7 @@ class Structure
 
 	void loadAtomsForModel(StructureOpenOptions options);
 
-	File &mFile;
+	cif::Datablock &mDb;
 	size_t mModelNr;
 	AtomView mAtoms;
 	std::vector<size_t> mAtomIndex;

src/BondMap.cpp

@@ -233,7 +233,7 @@ BondMap::BondMap(const Structure &p)
 		link[b].insert(a);
 	};
 
-	cif::Datablock &db = p.getFile().data();
+	cif::Datablock &db = p.datablock();
 
 	// collect all compounds first
 	std::set<std::string> compounds;

src/Cif++.cpp

@@ -2408,7 +2408,7 @@ namespace detail
 
 	size_t writeValue(std::ostream &os, std::string value, size_t offset, size_t width)
 	{
-		if (value.find('\n') != std::string::npos or width == 0 or value.length() >= 132) // write as text field
+		if (value.find('\n') != std::string::npos or width == 0 or value.length() > 132) // write as text field
 		{
 			ba::replace_all(value, "\n;", "\n\\;");
 
@@ -2511,7 +2511,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
 					if (not isUnquotedString(v->mText))
 						l += 2;
 
-					if (l >= 132)
+					if (l > 132)
 						continue;
 
 					if (columnWidths[v->mColumnIndex] < l + 1)
@@ -2547,7 +2547,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
 				if (l < w)
 					l = w;
 
-				if (offset + l >= 132 and offset > 0)
+				if (offset + l > 132 and offset > 0)
 				{
 					os << std::endl;
 					offset = 0;
@@ -2555,7 +2555,7 @@ void Category::write(std::ostream &os, const std::vector<size_t> &order, bool in
 
 				offset = detail::writeValue(os, s, offset, w);
 
-				if (offset >= 132)
+				if (offset > 132)
 				{
 					os << std::endl;
 					offset = 0;
@@ -3367,6 +3367,11 @@ File::File(const std::filesystem::path &path, bool validate)
 	}
 }
 
+File::File(const char *data, std::size_t length)
+{
+	load(data, length);
+}
+
 File::File(File &&rhs)
 	: mHead(nullptr)
 	, mValidator(nullptr)
@@ -3483,6 +3488,25 @@ void File::load(std::istream &is, const std::string &datablock)
 	}
 }
 
+void File::load(const char *data, std::size_t length)
+{
+	bool gzipped = length > 2 and data[0] == static_cast<char>(0x1f) and data[1] == static_cast<char>(0x8b);
+
+	struct membuf : public std::streambuf
+	{
+		membuf(char *data, size_t length) { this->setg(data, data, data + length); }
+	} buffer(const_cast<char *>(data), length);
+
+	std::istream is(&buffer);
+
+	io::filtering_stream<io::input> in;
+	if (gzipped)
+		in.push(io::gzip_decompressor());
+	in.push(is);
+
+	load(is);
+}
+
 void File::save(std::ostream &os)
 {
 	Datablock *e = mHead;
@@ -3523,6 +3547,21 @@ Datablock &File::operator[](std::string_view name)
 	return *result;
 }
 
+Datablock &File::front()
+{
+	assert(mHead);
+	return *mHead;
+}
+
+Datablock &File::back()
+{
+	assert(mHead);
+	auto *block = mHead;
+	while (block->mNext != nullptr)
+		block = block->mNext;
+	return *block;
+}
+
 bool File::isValid()
 {
 	if (mValidator == nullptr)

src/Point.cpp

@@ -301,7 +301,7 @@ std::tuple<double,Point> QuaternionToAngleAxis(Quaternion q)
 		q = Normalize(q);
 
 	// angle:
-	double angle = 2 * acos(q.R_component_1());
+	double angle = 2 * std::acos(q.R_component_1());
 	angle = angle * 180 / kPI;
 
 	// axis:

src/Secondary.cpp

@@ -535,7 +535,7 @@ double CalculateHBondEnergy(Res &inDonor, Res &inAcceptor)
 			result = kCouplingConstant / distanceHO - kCouplingConstant / distanceHC + kCouplingConstant / distanceNC - kCouplingConstant / distanceNO;
 
 		// DSSP compatibility mode:
-		result = round(result * 1000) / 1000;
+		result = std::round(result * 1000) / 1000;
 
 		if (result < kMinHBondEnergy)
 			result = kMinHBondEnergy;
@@ -1230,7 +1230,7 @@ DSSPImpl::DSSPImpl(const Structure &s, int min_poly_proline_stretch_length)
 
 void DSSPImpl::calculateSecondaryStructure()
 {
-	auto &db = mStructure.getFile().data();
+	auto &db = mStructure.datablock();
 	for (auto r : db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
 	{
 		std::string asym1, asym2;

test/rename-compound-test.cpp

@@ -37,7 +37,7 @@ int main(int argc, char* argv[])
 
 		structure.cleanupEmptyCategories();
 
-		f.file().save(std::cout);
+		f.save(std::cout);
 	}
 	catch (const std::exception& e)
 	{

test/structure-test.cpp

@@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE(create_nonpoly_1)
     cif::VERBOSE = 1;
 
 	mmcif::File file;
-	file.file().loadDictionary("mmcif_pdbx_v50.dic");
-	file.createDatablock("TEST");	// create a datablock
+	file.loadDictionary("mmcif_pdbx_v50.dic");
+	file.emplace("TEST");	// create a datablock
 	
 	mmcif::Structure structure(file);
 
@@ -171,12 +171,12 @@ _struct_asym.details                       ?
 
 	expected.loadDictionary("mmcif_pdbx_v50.dic");
 
-	if (not (expected.firstDatablock() == structure.getFile().data()))
+	if (not (expected.firstDatablock() == structure.datablock()))
 	{
 		BOOST_TEST(false);
 		std::cout << expected.firstDatablock() << std::endl
 				<< std::endl
-				<< structure.getFile().data() << std::endl;
+				<< structure.datablock() << std::endl;
 	}
 }
 

test/unit-test.cpp

@@ -1626,7 +1626,7 @@ PRO OXT HXT SING N N 17
 	mmcif::File file(example.string());
 	mmcif::Structure structure(file);
 
-	(void)file.file().isValid();
+	(void)file.isValid();
 
 	mmcif::BondMap bm(structure);