Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

f3c2e591 · Maarten L. Hekkelman · 24ab660e · 4732004b · f3c2e591 · f3c2e591
Commit f3c2e591 authored Jan 18, 2022 by Maarten L. Hekkelman
19 changed files
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,7 @@
 cmake_minimum_required(VERSION 3.16)
 # set the project name
-project(cifpp VERSION 3.0.1 LANGUAGES CXX)
+project(cifpp VERSION 3.0.2 LANGUAGES CXX)
 list(PREPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
@@ -133,8 +133,6 @@ if(MSVC)
 		message(FATAL_ERROR "Unsupported or unknown processor type ${CMAKE_SYSTEM_PROCESSOR}")
 	endif()	
-	set(COFF_SPEC "--coff=${COFF_TYPE}")
 	# for mrc, just in case
 	list(APPEND CMAKE_PREFIX_PATH "$ENV{LOCALAPPDATA}/mrc")
 endif()
@@ -150,12 +148,12 @@ endif()
 if(WIN32 AND BUILD_SHARED_LIBS)
 	message("Not using resources when building shared libraries for Windows")
 else()
-	find_program(MRC mrc)
+	find_package(Mrc)
-	if(MRC)
+	if(MRC_FOUND)
-		option(CIFPP_USE_RSRC "Use mrc to create resources" ON)
+		option(USE_RSRC "Use mrc to create resources" ON)
 	else()
-		message("Using resources not possible since mrc was not found")
+		message(WARNING "Not using resources since mrc was not found")
 	endif()
 	if(CIFPP_USE_RSRC STREQUAL "ON")
@@ -176,9 +174,7 @@ find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_opt
 if(NOT MSVC AND Boost_USE_STATIC_LIBS)
 	find_package(ZLIB REQUIRED)
-	find_package(BZip2 REQUIRED)
+	list(APPEND CIFPP_REQUIRED_LIBRARIES ${ZLIB_LIBRARIES})
-	list(APPEND CIFPP_REQUIRED_LIBRARIES ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
 endif()
 include(FindFilesystem)
@@ -341,6 +337,13 @@ install(TARGETS cifpp
 	RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 	INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+if(MSVC)
+	install(
+		FILES $<TARGET_PDB_FILE:${PROJECT_NAME}>
+		DESTINATION ${CMAKE_INSTALL_LIBDIR}
+		OPTIONAL)
+endif()
 install(EXPORT cifppTargets
 	FILE "cifppTargets.cmake"
 	NAMESPACE cifpp::
@@ -414,13 +417,6 @@ option(CIFPP_BUILD_TESTS "Build test exectuables" OFF)
 if(CIFPP_BUILD_TESTS)
-	if(CIFPP_USE_RSRC)
-		add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj
-			COMMAND ${MRC} -o ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic ${COFF_SPEC}
-		)
-		set(CIFPP_TEST_RESOURCE ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj)
-	endif()
 	list(APPEND CIFPP_tests
 		# pdb2cif
 		rename-compound
@@ -431,7 +427,7 @@ if(CIFPP_BUILD_TESTS)
 		set(CIFPP_TEST "${CIFPP_TEST}-test")
 		set(CIFPP_TEST_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}/test/${CIFPP_TEST}.cpp")
-		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE} ${CIFPP_TEST_RESOURCE})
+		add_executable(${CIFPP_TEST} ${CIFPP_TEST_SOURCE})
 		target_include_directories(${CIFPP_TEST} PRIVATE
 			${CMAKE_CURRENT_SOURCE_DIR}/include
@@ -439,7 +435,11 @@ if(CIFPP_BUILD_TESTS)
 		)
 		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp ${Boost_LIBRARIES} ${CIFPP_REQUIRED_LIBRARIES})
+		if(CIFPP_USE_RSRC)
+			mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic)
+		endif()
 		if(MSVC)
 			# Specify unwind semantics so that MSVC knowns how to handle exceptions
 			target_compile_options(${CIFPP_TEST} PRIVATE /EHsc)

--- a/Config.cmake.in
+++ b/Config.cmake.in
@@ -4,7 +4,6 @@ include(CMakeFindDependencyMacro)
 find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_options)
 if(NOT WIN32)
 find_dependency(ZLIB)
-find_dependency(BZip2)
 endif()
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")

--- a/changelog
+++ b/changelog
+Version 3.0.2
+- refactored mmcif::Atom for performance reasons
+Version 3.0.1
+- Fixed processing of proline restraints file from CCP4, proline
+  is a peptide, really.
+- Added code to facilitate DSSP
 Version 3.0.0
 - Replaced many strings in the API with string_view for
  performance reasons.

--- a/include/cif++/Cif++.hpp
+++ b/include/cif++/Cif++.hpp
@@ -792,7 +792,7 @@ class Row
 	}
 	void assign(const std::vector<Item> &values);
-	void assign(std::string_view name, const std::string &value, bool updateLinked);
+	void assign(std::string_view name, const std::string &value, bool updateLinked, bool validate = true);
 	bool operator==(const Row &rhs) const
 	{
@@ -814,7 +814,7 @@ class Row
 	friend std::ostream &operator<<(std::ostream &os, const Row &row);
  private:
-	void assign(size_t column, const std::string &value, bool updateLinked);
+	void assign(size_t column, const std::string &value, bool updateLinked, bool validate = true);
 	void assign(const Item &i, bool updateLinked);
 	static void swap(size_t column, ItemRow *a, ItemRow *b);
@@ -2152,6 +2152,7 @@ class Category
 	std::vector<ItemColumn> mColumns;
 	ItemRow *mHead;
 	ItemRow *mTail;
+	size_t mLastUniqueNr = 0;
 	class CatIndex *mIndex;
 	std::vector<Linked> mParentLinks, mChildLinks;

--- a/include/cif++/Secondary.hpp
+++ b/include/cif++/Secondary.hpp
@@ -184,6 +184,15 @@ class DSSP
 		std::tuple<ResidueInfo,double> acceptor(int i) const;
 		std::tuple<ResidueInfo,double> donor(int i) const;
+		/// \brief Simple compare equals
+		bool operator==(const ResidueInfo &rhs) const
+		{
+			return mImpl == rhs.mImpl;
+		}
+		/// \brief Returns \result true if there is a bond between two residues
+		friend bool TestBond(ResidueInfo const &a, ResidueInfo const &b);
 	  private:
 		ResidueInfo(Res* res) : mImpl(res) {}
@@ -193,7 +202,7 @@ class DSSP
 	class iterator
 	{
 	  public:
-		using iterator_category = std::input_iterator_tag;
+		using iterator_category = std::bidirectional_iterator_tag;
 		using value_type = ResidueInfo;
 		using difference_type = std::ptrdiff_t;
 		using pointer = value_type*;
@@ -214,6 +223,14 @@ class DSSP
 			return tmp;
 		}
+		iterator& operator--();
+		iterator operator--(int)
+		{
+			auto tmp(*this);
+			this->operator--();
+			return tmp;
+		}
 		bool operator==(const iterator& rhs) const		{ return mCurrent.mImpl == rhs.mCurrent.mImpl; }
 		bool operator!=(const iterator& rhs) const		{ return mCurrent.mImpl != rhs.mCurrent.mImpl; }

--- a/include/cif++/Structure.hpp
+++ b/include/cif++/Structure.hpp
@@ -60,30 +60,101 @@ 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);
+		// constructor for a symmetry copy of an atom
+		AtomImpl(const AtomImpl &impl, const Point &loc, const std::string &sym_op);
+		AtomImpl(const AtomImpl &i) = default;
+		void prefetch();
+		int compare(const AtomImpl &b) const;
+		bool getAnisoU(float anisou[6]) const;
+		void moveTo(const Point &p);
+		const Compound &comp() const;
+		const std::string get_property(const std::string_view name) const;
+		void set_property(const std::string_view name, const std::string &value);
+		const cif::Datablock &mDb;
+		std::string mID;
+		AtomType mType;
+		std::string mAtomID;
+		std::string mCompID;
+		std::string mAsymID;
+		int mSeqID;
+		std::string mAltID;
+		std::string mAuthSeqID;
+		Point mLocation;
+		int mRefcount;
+		cif::Row mRow;
+		mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
+		mutable const Compound *mCompound = nullptr;
+		bool mSymmetryCopy = false;
+		bool mClone = false;
+		std::string mSymmetryOperator = "1_555";
+	};
  public:
-	Atom();
-	Atom(struct AtomImpl *impl);
+	Atom() {}
-	Atom(const Atom &rhs);
+	Atom(std::shared_ptr<AtomImpl> impl)
+		: mImpl(impl) {}
+	Atom(const Atom &rhs)
+		: mImpl(rhs.mImpl) {}
 	Atom(cif::Datablock &db, cif::Row &row);
 	// a special constructor to create symmetry copies
 	Atom(const Atom &rhs, const Point &symmmetry_location, const std::string &symmetry_operation);
-	~Atom();
+	explicit operator bool() const { return (bool)mImpl; }
-	explicit operator bool() const { return mImpl_ != nullptr; }
 	// return a copy of this atom, with data copied instead of referenced
-	Atom clone() const;
+	Atom clone() const
+	{
+		auto copy = std::make_shared<AtomImpl>(*mImpl);
+		copy->mClone = true;
+		return Atom(copy);
+	}
+	Atom &operator=(const Atom &rhs) = default;
+	template <typename T>
+	T get_property(const std::string_view name) const;
-	Atom &operator=(const Atom &rhs);
+	void set_property(const std::string_view name, const std::string &value)
+	{
+		mImpl->set_property(name, value);
+	}
-	const std::string &id() const;
+	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
-	AtomType type() const;
+	void property(const std::string_view name, const T &value)
+	{
+		set_property(name, std::to_string(value));
+	}
-	Point location() const;
+	const std::string &id() const			{ return mImpl->mID; }
-	void location(Point p);
+	AtomType type() const					{ return mImpl->mType; }
+	Point location() const					{ return mImpl->mLocation; }
+	void location(Point p)					{ mImpl->moveTo(p); }
 	/// \brief Translate the position of this atom by \a t
 	void translate(Point t);
@@ -91,47 +162,40 @@ class Atom
 	/// \brief Rotate the position of this atom by \a q
 	void rotate(Quaternion q);
+	/// \brief Translate and rotate the position of this atom by \a t and \a q
+	void translateAndRotate(Point t, Quaternion q);
+	/// \brief Translate, rotate and translate again the coordinates this atom by \a t1 , \a q and \a t2
+	void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
 	// for direct access to underlying data, be careful!
-	const cif::Row getRow() const;
+	const cif::Row getRow() const			{ return mImpl->mRow; }
 	const cif::Row getRowAniso() const;
-	// Atom symmetryCopy(const Point& d, const clipper::RTop_orth& rt);
+	bool isSymmetryCopy() const				{ return mImpl->mSymmetryCopy; }
-	bool isSymmetryCopy() const;
+	std::string symmetry() const			{ return mImpl->mSymmetryOperator; }
-	std::string symmetry() const;
-	// const clipper::RTop_orth& symop() const;
-	const Compound &comp() const;
+	const Compound &comp() const			{ return mImpl->comp(); }
-	bool isWater() const;
+	bool isWater() const					{ return mImpl->mCompID == "HOH" or mImpl->mCompID == "H2O" or mImpl->mCompID == "WAT"; }
 	int charge() const;
 	float uIso() const;
-	bool getAnisoU(float anisou[6]) const;
+	bool getAnisoU(float anisou[6]) const	{ return mImpl->getAnisoU(anisou); }
 	float occupancy() const;
-	template <typename T>
-	T property(const std::string_view name) const;
-	void property(const std::string_view name, const std::string &value);
-	template <typename T, std::enable_if_t<std::is_arithmetic_v<T>, int> = 0>
-	void property(const std::string_view name, const T &value)
-	{
-		property(name, std::to_string(value));
-	}
 	// specifications
-	std::string labelAtomID() const;
+	const std::string& labelAtomID() const		{ return mImpl->mAtomID; }
-	std::string labelCompID() const;
+	const std::string& labelCompID() const		{ return mImpl->mCompID; }
-	std::string labelAsymID() const;
+	const std::string& labelAsymID() const		{ return mImpl->mAsymID; }
 	std::string labelEntityID() const;
-	int labelSeqID() const;
+	int labelSeqID() const						{ return mImpl->mSeqID; }
-	std::string labelAltID() const;
+	const std::string& labelAltID() const		{ return mImpl->mAltID; }
-	bool isAlternate() const;
+	bool isAlternate() const					{ return not mImpl->mAltID.empty(); }
 	std::string authAtomID() const;
 	std::string authCompID() const;
 	std::string authAsymID() const;
-	std::string authSeqID() const;
+	const std::string& authSeqID() const		{ return mImpl->mAuthSeqID; }
 	std::string pdbxAuthInsCode() const;
 	std::string pdbxAuthAltID() const;
@@ -140,13 +204,6 @@ class Atom
 	bool operator==(const Atom &rhs) const;
-	// // get clipper format Atom
-	// clipper::Atom toClipper() const;
-	// Radius calculation based on integrating the density until perc of electrons is found
-	void calculateRadius(float resHigh, float resLow, float perc);
-	float radius() const;
 	// access data in compound for this atom
 	// convenience routine
@@ -158,10 +215,10 @@ class Atom
 	void swap(Atom &b)
 	{
-		std::swap(mImpl_, b.mImpl_);
+		std::swap(mImpl, b.mImpl);
 	}
-	int compare(const Atom &b) const;
+	int compare(const Atom &b) const		{ return mImpl->compare(*b.mImpl); }
 	bool operator<(const Atom &rhs) const
 	{
@@ -172,14 +229,31 @@ class Atom
  private:
 	friend class Structure;
-	void setID(int id);
-	AtomImpl *impl();
+	void setID(int id);
-	const AtomImpl *impl() const;
-	struct AtomImpl *mImpl_;
+	std::shared_ptr<AtomImpl> mImpl;
 };
+template <>
+inline std::string Atom::get_property<std::string>(const std::string_view name) const
+{
+	return mImpl->get_property(name);
+}
+template <>
+inline int Atom::get_property<int>(const std::string_view name) const
+{
+	auto v = mImpl->get_property(name);
+	return v.empty() ? 0 : stoi(v);
+}
+template <>
+inline float Atom::get_property<float>(const std::string_view name) const
+{
+	return stof(mImpl->get_property(name));
+}
 inline void swap(mmcif::Atom &a, mmcif::Atom &b)
 {
 	a.swap(b);
@@ -202,19 +276,16 @@ typedef std::vector<Atom> AtomView;
 class Residue
 {
  public:
-	// constructors should be private, but that's not possible for now (needed in emplace)
+	// constructor
-	// constructor for waters
-	Residue(const Structure &structure, const std::string &compoundID,
-		const std::string &asymID, const std::string &authSeqID);
-	// constructor for a residue without a sequence number
-	Residue(const Structure &structure, const std::string &compoundID,
-		const std::string &asymID);
-	// constructor for a residue with a sequence number
 	Residue(const Structure &structure, const std::string &compoundID,
-		const std::string &asymID, int seqID, const std::string &authSeqID);
+		const std::string &asymID, int seqID = 0, const std::string &authSeqID = {})
+		: mStructure(&structure)
+		, mCompoundID(compoundID)
+		, mAsymID(asymID)
+		, mSeqID(seqID)
+		, mAuthSeqID(authSeqID)
+	{
+	}
 	Residue(const Residue &rhs) = delete;
 	Residue &operator=(const Residue &rhs) = delete;
@@ -227,6 +298,11 @@ class Residue
 	const Compound &compound() const;
 	const AtomView &atoms() const;
+	void addAtom(const Atom &atom)
+	{
+		mAtoms.push_back(atom);
+	}
 	/// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id.
 	AtomView unique_atoms() const;
@@ -277,6 +353,8 @@ class Residue
 	friend std::ostream &operator<<(std::ostream &os, const Residue &res);
+	friend Structure;
  protected:
 	Residue() {}
@@ -537,6 +615,12 @@ class Structure
 	/// \brief Rotate the coordinates of all atoms in the structure by \a q
 	void rotate(Quaternion t);
+	/// \brief Translate and rotate the coordinates of all atoms in the structure by \a t and \a q
+	void translateAndRotate(Point t, Quaternion q);
+	/// \brief Translate, rotate and translate again the coordinates of all atoms in the structure by \a t1 , \a q and \a t2
+	void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
 	const std::vector<Residue> &getNonPolymers() const { return mNonPolymers; }
 	const std::vector<Residue> &getBranchResidues() const { return mBranchResidues; }

--- a/src/BondMap.cpp
+++ b/src/BondMap.cpp
@@ -180,7 +180,10 @@ bool CompoundBondMap::bonded(const std::string &compoundID, const std::string &a
 	auto compound = mmcif::CompoundFactory::instance().create(compoundID);
 	if (not compound)
-		std::cerr << "Missing compound bond info for " << compoundID << std::endl;
+	{
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Missing compound bond info for " << compoundID << std::endl;
+	}
 	else
 	{
 		for (auto &atom : compound->bonds())
@@ -308,7 +311,7 @@ BondMap::BondMap(const Structure &p)
 	{
 		if (c == "HOH" or c == "H2O" or c == "WAT")
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "skipping water in bond map calculation" << std::endl;
 			continue;
 		}

--- a/src/Cif++.cpp
+++ b/src/Cif++.cpp
 /*-
 * 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
@@ -30,10 +30,10 @@
 #include <numeric>
 #include <regex>
 #include <set>
+#include <shared_mutex>
 #include <stack>
 #include <tuple>
 #include <unordered_map>
-#include <shared_mutex>
 #include <filesystem>
@@ -570,36 +570,6 @@ void Datablock::write(std::ostream &os, const std::vector<std::string> &order)
 		cat.write(os);
 	}
-	//	// mmcif support, sort of. First write the 'entry' Category
-	//	// and if it exists, _AND_ we have a Validator, write out the
-	//	// auditConform record.
-	//
-	//	for (auto& cat: mCategories)
-	//	{
-	//		if (cat.name() == "entry")
-	//		{
-	//			cat.write(os);
-	//
-	//			if (mValidator != nullptr)
-	//			{
-	//				Category auditConform(*this, "audit_conform", nullptr);
-	//				auditConform.emplace({
-	//					{ "dict_name", mValidator->dictName() },
-	//					{ "dict_version", mValidator->dictVersion() }
-	//				});
-	//				auditConform.write(os);
-	//			}
-	//
-	//			break;
-	//		}
-	//	}
-	//
-	//	for (auto& cat: mCategories)
-	//	{
-	//		if (cat.name() != "entry" and cat.name() != "audit_conform")
-	//			cat.write(os);
-	//	}
 }
 bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
@@ -636,15 +606,15 @@ bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
 	{
 		std::string nA = *catA_i;
 		ba::to_lower(nA);
 		std::string nB = *catB_i;
 		ba::to_lower(nB);
 		int d = nA.compare(nB);
 		if (d > 0)
 		{
 			auto cat = dbB.get(*catB_i);
 			if (cat == nullptr)
 				missingA.push_back(*catB_i);
@@ -653,7 +623,7 @@ bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
 		else if (d < 0)
 		{
 			auto cat = dbA.get(*catA_i);
 			if (cat == nullptr)
 				missingB.push_back(*catA_i);
@@ -662,25 +632,25 @@ bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
 		else
 			++catA_i, ++catB_i;
 	}
 	while (catA_i != catA.end())
 		missingB.push_back(*catA_i++);
 	while (catB_i != catB.end())
 		missingA.push_back(*catB_i++);
-	if (not (missingA.empty() and missingB.empty()))
+	if (not(missingA.empty() and missingB.empty()))
 	{
 		if (cif::VERBOSE > 1)
 		{
 			std::cerr << "compare of datablocks failed" << std::endl;
 			if (not missingA.empty())
 				std::cerr << "Categories missing in A: " << ba::join(missingA, ", ") << std::endl
-					<< std::endl;
+						  << std::endl;
 			if (not missingB.empty())
 				std::cerr << "Categories missing in B: " << ba::join(missingB, ", ") << std::endl
-					<< std::endl;
+						  << std::endl;
 			result = false;
 		}
@@ -706,7 +676,7 @@ bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
 			++catA_i;
 		else
 		{
-			if (not (*dbA.get(*catA_i) == *dbB.get(*catB_i)))
+			if (not(*dbA.get(*catA_i) == *dbB.get(*catB_i)))
 			{
 				if (cif::VERBOSE > 1)
 				{
@@ -724,10 +694,10 @@ bool operator==(const cif::Datablock &dbA, const cif::Datablock &dbB)
 	return result;
 }
-std::ostream& operator<<(std::ostream &os, const Datablock &data)
+std::ostream &operator<<(std::ostream &os, const Datablock &data)
 {
 	// whoohoo... this sucks!
-	const_cast<Datablock&>(data).write(os);
+	const_cast<Datablock &>(data).write(os);
 	return os;
 }
@@ -1162,7 +1132,7 @@ void CatIndex::reconstruct()
 		insert(r.mData);
 	// maybe reconstruction can be done quicker by using the following commented code.
-	// however, I've not had the time to think of a way to std::set the red/black flag correctly in that case.
+	// however, I've not had the time to think of a way to set the red/black flag correctly in that case.
 	//	std::vector<ItemRow*> rows;
 	//	transform(mCat.begin(), mCat.end(), backInserter(rows),
@@ -1254,82 +1224,15 @@ size_t CatIndex::size() const
 	return result;
 }
-//bool CatIndex::isValid() const
-//{
-//	bool result = true;
-//
-//	if (mRoot != nullptr)
-//	{
-//		uint32_t minBlack = numeric_limits<uint32_t>::max();
-//		uint32_t maxBlack = 0;
-//
-//		assert(not mRoot->mRed);
-//
-//		result = isValid(mRoot, false, 0, minBlack, maxBlack);
-//		assert(minBlack == maxBlack);
-//	}
-//
-//	return result;
-//}
-//
-//bool CatIndex::validate(entry* h, bool isParentRed, uint32_t blackDepth, uint32_t& minBlack, uint32_t& maxBlack) const
-//{
-//	bool result = true;
-//
-//	if (h->mRed)
-//		assert(not isParentRed);
-//	else
-//		++blackDepth;
-//
-//	if (isParentRed)
-//		assert(not h->mRed);
-//
-//	if (h->mLeft != nullptr and h->mRight != nullptr)
-//	{
-//		if (isRed(h->mLeft))
-//			assert(not isRed(h->mRight));
-//		if (isRed(h->mRight))
-//			assert(not isRed(h->mLeft));
-//	}
-//
-//	if (h->mLeft != nullptr)
-//	{
-//		assert(mComp(h->mLeft->mRow, h->mRow) < 0);
-//		validate(h->mLeft, h->mRed, blackDepth, minBlack, maxBlack);
-//	}
-//	else
-//	{
-//		if (minBlack > blackDepth)
-//			minBlack = blackDepth;
-//		if (maxBlack < blackDepth)
-//			maxBlack = blackDepth;
-//	}
-//
-//	if (h->mRight != nullptr)
-//	{
-//		assert(mComp(h->mRight->mRow, h->mRow) > 0);
-//		validate(h->mRight, h->mRight, blackDepth, minBlack, maxBlack);
-//	}
-//	else
-//	{
-//		if (minBlack > blackDepth)
-//			minBlack = blackDepth;
-//		if (maxBlack < blackDepth)
-//			maxBlack = blackDepth;
-//	}
-//}
 // --------------------------------------------------------------------
 RowSet::RowSet(Category &cat)
 	: mCat(&cat)
-// , mCond(nullptr)
 {
 }
 RowSet::RowSet(Category &cat, Condition &&cond)
 	: mCat(&cat)
-// , mCond(new Condition(std::forward<Condition>(cond)))
 {
 	cond.prepare(cat);
@@ -1343,21 +1246,17 @@ RowSet::RowSet(Category &cat, Condition &&cond)
 RowSet::RowSet(const RowSet &rhs)
 	: mCat(rhs.mCat)
 	, mItems(rhs.mItems)
-// , mCond(nullptr)
 {
 }
 RowSet::RowSet(RowSet &&rhs)
 	: mCat(rhs.mCat)
 	, mItems(std::move(rhs.mItems))
-// , mCond(rhs.mCond)
 {
-	// rhs.mCond = nullptr;
 }
 RowSet::~RowSet()
 {
-	// delete mCond;
 }
 RowSet &RowSet::operator=(const RowSet &rhs)
@@ -1469,7 +1368,7 @@ void Category::updateLinks()
 			auto childCat = mDb.get(link->mChildCategory);
 			if (childCat == nullptr)
 				continue;
-			mChildLinks.push_back({ childCat, link });
+			mChildLinks.push_back({childCat, link});
 		}
 		for (auto link : mValidator->getLinksForChild(mName))
@@ -1477,7 +1376,7 @@ void Category::updateLinks()
 			auto parentCat = mDb.get(link->mParentCategory);
 			if (parentCat == nullptr)
 				continue;
-			mParentLinks.push_back({ parentCat, link });
+			mParentLinks.push_back({parentCat, link});
 		}
 	}
 }
@@ -1497,7 +1396,7 @@ size_t Category::getColumnIndex(std::string_view name) const
 			break;
 	}
-	if (VERBOSE and result == mColumns.size() and mCatValidator != nullptr) // validate the name, if it is known at all (since it was not found)
+	if (VERBOSE > 0 and result == mColumns.size() and mCatValidator != nullptr) // validate the name, if it is known at all (since it was not found)
 	{
 		auto iv = mCatValidator->getValidatorForItem(name);
 		if (iv == nullptr)
@@ -1543,21 +1442,6 @@ size_t Category::addColumn(std::string_view name)
 	return result;
 }
-// RowSet Category::find(Condition&& cond)
-// {
-// 	RowSet result(*this);
-// 	cond.prepare(*this);
-// 	for (auto r: *this)
-// 	{
-// 		if (cond(*this, r))
-// 			result.push_back(r);
-// 	}
-// 	return result;
-// }
 void Category::reorderByIndex()
 {
 	if (mIndex != nullptr)
@@ -1601,11 +1485,13 @@ std::string Category::getUniqueID(std::function<std::string(int)> generator)
 	if (mCatValidator != nullptr and mCatValidator->mKeys.size() == 1)
 		key = mCatValidator->mKeys.front();
-	size_t nr = size();
+	// calling size() often is a waste of resources
+	if (mLastUniqueNr == 0)
+		mLastUniqueNr = size();
 	for (;;)
 	{
-		std::string result = generator(int(nr++));
+		std::string result = generator(static_cast<int>(mLastUniqueNr++));
 		if (exists(Key(key) == result))
 			continue;
@@ -1665,21 +1551,6 @@ Row Category::operator[](Condition &&cond)
 	return result;
 }
-// RowSet Category::find(Condition&& cond)
-// {
-// 	// return RowSet(*this, std::forward<Condition>(cond));
-// 	RowSet result(*this);
-// 	cond.prepare(*this);
-// 	for (auto r: *this)
-// 	{
-// 		if (cond(*this, r))
-// 			result.insert(result.end(), r);
-// 	}
-// 	return result;
-// }
 bool Category::exists(Condition &&cond) const
 {
 	bool result = false;
@@ -2340,7 +2211,7 @@ void Category::validateLinks() const
 			if (not hasParent(r, *parentCat, *link))
 				++missing;
-		if (missing)
+		if (missing and VERBOSE >= 0)
 		{
 			std::cerr << "Links for " << link->mLinkGroupLabel << " are incomplete" << std::endl
 					  << "  There are " << missing << " items in " << mName << " that don't have matching parent items in " << parentCat->mName << std::endl;
@@ -2408,26 +2279,26 @@ std::set<size_t> Category::keyFieldsByIndex() const
 bool operator==(const Category &a, const Category &b)
 {
-	using namespace std::placeholders; 
+	using namespace std::placeholders;
 	bool result = true;
-//	set<std::string> tagsA(a.fields()), tagsB(b.fields());
+	//	set<std::string> tagsA(a.fields()), tagsB(b.fields());
-//	
+	//
-//	if (tagsA != tagsB)
+	//	if (tagsA != tagsB)
-//		std::cout << "Unequal number of fields" << std::endl;
+	//		std::cout << "Unequal number of fields" << std::endl;
-	auto& validator = a.getValidator();
+	auto &validator = a.getValidator();
 	auto catValidator = validator.getValidatorForCategory(a.name());
 	if (catValidator == nullptr)
 		throw std::runtime_error("missing cat validator");
-	typedef std::function<int(const char*,const char*)> compType;
+	typedef std::function<int(const char *, const char *)> compType;
-	std::vector<std::tuple<std::string,compType>> tags;
+	std::vector<std::tuple<std::string, compType>> tags;
 	auto keys = catValidator->mKeys;
 	std::vector<size_t> keyIx;
-	for (auto& tag: a.fields())
+	for (auto &tag : a.fields())
 	{
 		auto iv = catValidator->getValidatorForItem(tag);
 		if (iv == nullptr)
@@ -2436,24 +2307,25 @@ bool operator==(const Category &a, const Category &b)
 		if (tv == nullptr)
 			throw std::runtime_error("missing type validator");
 		tags.push_back(std::make_tuple(tag, std::bind(&cif::ValidateType::compare, tv, std::placeholders::_1, std::placeholders::_2)));
-		auto pred = [tag](const std::string& s) -> bool { return cif::iequals(tag, s) == 0; };
+		auto pred = [tag](const std::string &s) -> bool
+		{ return cif::iequals(tag, s) == 0; };
 		if (find_if(keys.begin(), keys.end(), pred) == keys.end())
 			keyIx.push_back(tags.size() - 1);
 	}
 	// a.reorderByIndex();
 	// b.reorderByIndex();
-	auto rowEqual = [&](const cif::Row& ra, const cif::Row& rb)
+	auto rowEqual = [&](const cif::Row &ra, const cif::Row &rb)
 	{
 		int d = 0;
-		for (auto kix: keyIx)
+		for (auto kix : keyIx)
 		{
 			std::string tag;
 			compType compare;
 			std::tie(tag, compare) = tags[kix];
 			d = compare(ra[tag].c_str(), rb[tag].c_str());
@@ -2465,7 +2337,7 @@ bool operator==(const Category &a, const Category &b)
 				break;
 			}
 		}
 		return d == 0;
 	};
@@ -2483,9 +2355,9 @@ bool operator==(const Category &a, const Category &b)
 			else
 				return false;
 		}
 		cif::Row ra = *ai, rb = *bi;
 		if (not rowEqual(ra, rb))
 		{
 			if (cif::VERBOSE > 1)
@@ -2493,21 +2365,25 @@ bool operator==(const Category &a, const Category &b)
 			else
 				return false;
 		}
 		std::vector<std::string> missingA, missingB, different;
-		for (auto& tt: tags)
+		for (auto &tt : tags)
 		{
 			std::string tag;
 			compType compare;
 			std::tie(tag, compare) = tt;
 			// make it an option to compare unapplicable to empty or something
-			const char* ta = ra[tag].c_str();	if (strcmp(ta, ".") == 0 or strcmp(ta, "?") == 0) ta = "";
+			const char *ta = ra[tag].c_str();
-			const char* tb = rb[tag].c_str();	if (strcmp(tb, ".") == 0 or strcmp(tb, "?") == 0) tb = "";
+			if (strcmp(ta, ".") == 0 or strcmp(ta, "?") == 0)
+				ta = "";
+			const char *tb = rb[tag].c_str();
+			if (strcmp(tb, ".") == 0 or strcmp(tb, "?") == 0)
+				tb = "";
 			if (compare(ta, tb) != 0)
 			{
 				if (cif::VERBOSE > 1)
@@ -2519,7 +2395,7 @@ bool operator==(const Category &a, const Category &b)
 					return false;
 			}
 		}
 		++ai;
 		++bi;
 	}
@@ -2527,18 +2403,6 @@ bool operator==(const Category &a, const Category &b)
 	return result;
 }
-// auto Category::iterator::operator++() -> iterator&
-// {
-// 	mCurrent = Row(mCurrent.data()->mNext);
-// 	return *this;
-// }
-// auto Category::const_iterator::operator++() -> const_iterator&
-// {
-// 	mCurrent = Row(mCurrent.data()->mNext);
-// 	return *this;
-// }
 namespace detail
 {
@@ -2900,7 +2764,7 @@ void Category::update_value(RowSet &&rows, const std::string &tag, const std::st
 				}
 				// cannot update this...
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Cannot update child " << childCat->mName << "." << childTag << " with value " << value << std::endl;
 			}
@@ -3009,21 +2873,22 @@ void Row::assign(const Item &value, bool skipUpdateLinked)
 	assign(value.name(), value.value(), skipUpdateLinked);
 }
-void Row::assign(std::string_view name, const std::string &value, bool skipUpdateLinked)
+void Row::assign(std::string_view name, const std::string &value, bool skipUpdateLinked, bool validate)
 {
 	try
 	{
 		auto cat = mData->mCategory;
-		assign(cat->addColumn(name), value, skipUpdateLinked);
+		assign(cat->addColumn(name), value, skipUpdateLinked, validate);
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Could not assign value '" << value << "' to column _" << mData->mCategory->name() << '.' << name << std::endl;
 		throw;
 	}
 }
-void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked)
+void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked, bool validate)
 {
 	if (mData == nullptr)
 		throw std::logic_error("invalid Row, no data assigning value '" + value + "' to column with index " + std::to_string(column));
@@ -3049,7 +2914,7 @@ void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked)
 	std::string oldStrValue = oldValue ? oldValue : "";
 	// check the value
-	if (col.mValidator)
+	if (col.mValidator and validate)
 		(*col.mValidator)(value);
 	// If the field is part of the Key for this Category, remove it from the index
@@ -3181,7 +3046,7 @@ void Row::assign(size_t column, const std::string &value, bool skipUpdateLinked)
 			auto rows_n = childCat->find(std::move(cond_n));
 			if (not rows_n.empty())
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Will not rename in child category since there are already rows that link to the parent" << std::endl;
 				continue;
@@ -3387,7 +3252,7 @@ void Row::swap(size_t cix, ItemRow *a, ItemRow *b)
 					}
 					else
 					{
-						if (VERBOSE)
+						if (VERBOSE > 0)
 							std::cerr << "In " << childCat->mName << " changing " << linkChildColName << ": " << r[linkChildColName].as<std::string>() << " => " << (i ? i->mText : "") << std::endl;
 						r[linkChildColName] = i ? i->mText : "";
 					}
@@ -3496,7 +3361,8 @@ File::File(const std::filesystem::path &path, bool validate)
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Error while loading file " << path << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error while loading file " << path << std::endl;
 		throw;
 	}
 }
@@ -3564,7 +3430,8 @@ void File::load(const std::filesystem::path &p)
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Error loading file " << path << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error loading file " << path << std::endl;
 		throw;
 	}
 }
@@ -3660,7 +3527,7 @@ bool File::isValid()
 {
 	if (mValidator == nullptr)
 	{
-		if (VERBOSE)
+		if (VERBOSE > 0)
 			std::cerr << "No dictionary loaded explicitly, loading default" << std::endl;
 		loadDictionary();

--- a/src/Cif2PDB.cpp
+++ b/src/Cif2PDB.cpp
@@ -753,7 +753,8 @@ class Ff : public FBase
            }
            catch (const std::exception& ex)
            {
-                std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
+				if (cif::VERBOSE >= 0)
+	                std::cerr << "Failed to write '" << s << "' as a double, this indicates an error in the code for writing PDB files" << std::endl;
                os << s;
            }
        }
@@ -2329,7 +2330,8 @@ void WriteRemark200(std::ostream& pdbFile, Datablock& db)
 	}
 	catch (const std::exception& ex)
 	{
-		std::cerr << ex.what() << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << ex.what() << std::endl;
 	}
 }
@@ -2390,7 +2392,8 @@ void WriteRemark280(std::ostream& pdbFile, Datablock& db)
 	}
 	catch (const std::exception& ex)
 	{
-		std::cerr << ex.what() << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << ex.what() << std::endl;
 	}
 }

--- a/src/CifParser.cpp
+++ b/src/CifParser.cpp
@@ -288,7 +288,7 @@ SacParser::CIFToken SacParser::getNextToken()
 					mState = eStateTextField + 1;
 				else if (ch == kEOF)
 					error("unterminated textfield");
-				else if (not isAnyPrint(ch))
+				else if (not isAnyPrint(ch) and cif::VERBOSE >= 0)
 					//					error("invalid character in text field '" + string({ static_cast<char>(ch) }) + "' (" + to_string((int)ch) + ")");
 					std::cerr << "invalid character in text field '" << std::string({static_cast<char>(ch)}) << "' (" << ch << ") line: " << mLineNr << std::endl;
 				break;
@@ -1220,7 +1220,7 @@ void DictParser::linkItems()
 	{
 		for (auto &iv : cv.mItemValidators)
 		{
-			if (iv.mType == nullptr)
+			if (iv.mType == nullptr and cif::VERBOSE >= 0)
 				std::cerr << "Missing item_type for " << iv.mTag << std::endl;
 		}
 	}
@@ -1255,7 +1255,8 @@ void DictParser::loadDictionary()
 	}
 	catch (const std::exception &)
 	{
-		std::cerr << "Error parsing dictionary" << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error parsing dictionary" << std::endl;
 		throw;
 	}

--- a/src/CifUtils.cpp
+++ b/src/CifUtils.cpp
@@ -1237,7 +1237,7 @@ std::filesystem::path gDataDir;
 void addDataDirectory(std::filesystem::path dataDir)
 {
-	if (VERBOSE and not fs::exists(dataDir))
+	if (VERBOSE > 0 and not fs::exists(dataDir))
 		std::cerr << "The specified data directory " << dataDir << " does not exist" << std::endl;
 	gDataDir = dataDir;
 }

--- a/src/CifValidator.cpp
+++ b/src/CifValidator.cpp
@@ -354,7 +354,7 @@ void Validator::reportError(const std::string &msg, bool fatal) const
 {
 	if (mStrict or fatal)
 		throw ValidationError(msg);
-	else if (VERBOSE)
+	else if (VERBOSE > 0)
 		std::cerr << msg << std::endl;
 }

--- a/src/Compound.cpp
+++ b/src/Compound.cpp
@@ -193,7 +193,7 @@ Compound::Compound(cif::Datablock &db, const std::string &id, const std::string 
 			bond.type = BondType::delo;
 		else
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Unimplemented chem_comp_bond.type " << btype << " in " << id << std::endl;
 			bond.type = BondType::sing;
 		}
@@ -403,7 +403,7 @@ CompoundFactoryImpl::CompoundFactoryImpl(const std::filesystem::path &file, std:
 			if (cif::iequals(id, "gly"))
 				type = "peptide linking";
-			else if (cif::iequals(group, "l-peptide") or cif::iequals(group, "L-peptide linking") or cif::iequals(group, "peptide"))
+			else if (cif::iequals(group, "l-peptide") or cif::iequals(group, "L-peptide linking") or cif::iequals(group, "peptide") or cif::iequals(group, "p-peptide"))
 				type = "L-peptide linking";
 			else if (cif::iequals(group, "DNA"))
 				type = "DNA linking";
@@ -520,7 +520,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
 		}
 	}
-	if (result == nullptr and cif::VERBOSE)
+	if (result == nullptr and cif::VERBOSE > 0)
 		std::cerr << "Could not locate compound " << id << " in the CCD components file" << std::endl;
 	return result;
@@ -611,7 +611,7 @@ Compound *CCP4CompoundFactoryImpl::create(const std::string &id)
 			if (cif::iequals(id, "gly"))
 				type = "peptide linking";
-			else if (cif::iequals(group, "l-peptide") or cif::iequals(group, "L-peptide linking") or cif::iequals(group, "peptide"))
+			else if (cif::iequals(group, "l-peptide") or cif::iequals(group, "L-peptide linking") or cif::iequals(group, "peptide") or cif::iequals(group, "p-peptide"))
 				type = "L-peptide linking";
 			else if (cif::iequals(group, "DNA"))
 				type = "DNA linking";
@@ -645,13 +645,13 @@ CompoundFactory::CompoundFactory()
 	auto ccd = cif::loadResource("components.cif");
 	if (ccd)
 		mImpl.reset(new CCDCompoundFactoryImpl(mImpl));
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "CCD components.cif file was not found" << std::endl;
 	const char *clibd_mon = getenv("CLIBD_MON");
 	if (clibd_mon != nullptr and fs::is_directory(clibd_mon))
 		mImpl.reset(new CCP4CompoundFactoryImpl(clibd_mon));
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "CCP4 monomers library not found, CLIBD_MON is not defined" << std::endl;
 }
@@ -695,7 +695,8 @@ void CompoundFactory::setDefaultDictionary(const std::filesystem::path &inDictFi
 	}
 	catch (const std::exception &)
 	{
-		std::cerr << "Error loading dictionary " << inDictFile << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error loading dictionary " << inDictFile << std::endl;
 		throw;
 	}
 }
@@ -715,7 +716,8 @@ void CompoundFactory::pushDictionary(const std::filesystem::path &inDictFile)
 	}
 	catch (const std::exception &)
 	{
-		std::cerr << "Error loading dictionary " << inDictFile << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error loading dictionary " << inDictFile << std::endl;
 		throw;
 	}
 }

--- a/src/PDB2Cif.cpp
+++ b/src/PDB2Cif.cpp
@@ -268,7 +268,8 @@ int PDBRecord::vI(int columnFirst, int columnLast)
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Trying to parse '" << std::string(mValue + columnFirst - 7, mValue + columnLast - 7) << '\'' << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Trying to parse '" << std::string(mValue + columnFirst - 7, mValue + columnLast - 7) << '\'' << std::endl;
 		throw;
 	}
@@ -337,7 +338,7 @@ std::tuple<std::string, std::string> SpecificationListParser::GetNextSpecificati
 				}
 				else if (not isspace(ch))
 				{
-					if (cif::VERBOSE)
+					if (cif::VERBOSE > 0)
 						std::cerr << "skipping invalid character in SOURCE ID: " << ch << std::endl;
 				}
 				break;
@@ -354,7 +355,7 @@ std::tuple<std::string, std::string> SpecificationListParser::GetNextSpecificati
 			case eColon:
 				if (ch == ';')
 				{
-					if (cif::VERBOSE)
+					if (cif::VERBOSE > 0)
 						std::cerr << "Empty value for SOURCE: " << id << std::endl;
 					state = eStart;
 				}
@@ -418,7 +419,7 @@ std::tuple<std::string, std::string> SpecificationListParser::GetNextSpecificati
 			case eError:
 				if (ch == ';')
 				{
-					if (cif::VERBOSE)
+					if (cif::VERBOSE > 0)
 						std::cerr << "Skipping invalid header line: '" << std::string(start, mP) << std::endl;
 					state = eStart;
 				}
@@ -832,7 +833,7 @@ class PDBFileParser
 		if (not mChainSeq2AsymSeq.count(key))
 		{
 			ec = error::make_error_code(error::pdbErrors::residueNotFound);
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Residue " << chainID << resSeq << iCode << " could not be mapped" << std::endl;
 		}
 		else
@@ -929,7 +930,7 @@ class PDBFileParser
 		}
 		catch (const std::exception &ex)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << ex.what() << std::endl;
 			ec = error::make_error_code(error::pdbErrors::invalidDate);
 		}
@@ -1160,7 +1161,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
 			if (is.eof())
 				break;
-			std::cerr << "Line number " << lineNr << " is empty!" << std::endl;
+			if (cif::VERBOSE > 0)
+				std::cerr << "Line number " << lineNr << " is empty!" << std::endl;
 			getline(is, lookahead);
 			++lineNr;
@@ -1278,7 +1280,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
 				}
 				catch (const std::exception &ex)
 				{
-					std::cerr << "Dropping FORMUL line (" << (lineNr - 1) << ") with invalid component number '" << value.substr(1, 3) << '\'' << std::endl;
+					if (cif::VERBOSE >= 0)
+						std::cerr << "Dropping FORMUL line (" << (lineNr - 1) << ") with invalid component number '" << value.substr(1, 3) << '\'' << std::endl;
 					continue;
 					// throw_with_nested(std::runtime_error("Invalid component number '" + value.substr(1, 3) + '\''));
 				}
@@ -1305,7 +1308,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
 			}
 			catch (const std::exception &ex)
 			{
-				std::cerr << "Error parsing FORMUL at line " << lineNr << std::endl;
+				if (cif::VERBOSE >= 0)
+					std::cerr << "Error parsing FORMUL at line " << lineNr << std::endl;
 				throw;
 			}
 		}
@@ -1412,7 +1416,8 @@ void PDBFileParser::PreParseInput(std::istream &is)
 	if (not dropped.empty())
 	{
-		std::cerr << "Dropped unsupported records: " << ba::join(dropped, ", ") << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Dropped unsupported records: " << ba::join(dropped, ", ") << std::endl;
 	}
 	if (mData == nullptr)
@@ -1440,7 +1445,7 @@ void PDBFileParser::Match(const std::string &expected, bool throwIfMissing)
 	{
 		if (throwIfMissing)
 			throw std::runtime_error("Expected record " + expected + " but found " + mRec->mName);
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Expected record " + expected + " but found " + mRec->mName << std::endl;
 	}
 }
@@ -1575,7 +1580,8 @@ void PDBFileParser::ParseTitle()
 			if (not iequals(key, "MOL_ID") and mCompounds.empty())
 			{
-				std::cerr << "Ignoring invalid COMPND record" << std::endl;
+				if (cif::VERBOSE >= 0)
+					std::cerr << "Ignoring invalid COMPND record" << std::endl;
 				break;
 			}
@@ -1625,7 +1631,7 @@ void PDBFileParser::ParseTitle()
 		//			auto colon = s.find(": ");
 		//			if (colon == std::string::npos)
 		//			{
-		//				if (cif::VERBOSE)
+		//				if (cif::VERBOSE > 0)
 		//					std::cerr << "invalid source field, missing colon (" << s << ')' << std::endl;
 		//				continue;
 		//			}
@@ -1713,7 +1719,7 @@ void PDBFileParser::ParseTitle()
 	// NUMMDL
 	if (mRec->is("NUMMDL"))
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "skipping unimplemented NUMMDL record" << std::endl;
 		GetNextRecord();
 	}
@@ -1816,7 +1822,7 @@ void PDBFileParser::ParseTitle()
 	// SPRSDE
 	if (mRec->is("SPRSDE"))
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "skipping unimplemented SPRSDE record" << std::endl;
 		GetNextRecord();
 	}
@@ -2265,7 +2271,7 @@ void PDBFileParser::ParseRemarks()
 									state = eMCP;
 								else if (subtopic == "CHIRAL CENTERS")
 									state = eChC;
-								else if (cif::VERBOSE)
+								else if (cif::VERBOSE > 0)
 									throw std::runtime_error("Unknown subtopic in REMARK 500: " + subtopic);
 								headerSeen = false;
@@ -2342,7 +2348,7 @@ void PDBFileParser::ParseRemarks()
 									}
 									catch (const std::exception &ex)
 									{
-										if (cif::VERBOSE)
+										if (cif::VERBOSE > 0)
 											std::cerr << "Dropping REMARK 500 at line " << mRec->mLineNr << " due to invalid symmetry operation" << std::endl;
 										continue;
 									}
@@ -2675,7 +2681,7 @@ void PDBFileParser::ParseRemarks()
 							case sStart:
 								if (s == "SITE")
 									state = sID;
-								else if (cif::VERBOSE)
+								else if (cif::VERBOSE > 0)
 									throw std::runtime_error("Invalid REMARK 800 record, expected SITE");
 								break;
@@ -2685,7 +2691,7 @@ void PDBFileParser::ParseRemarks()
 									id = m[1].str();
 									state = sEvidence;
 								}
-								else if (cif::VERBOSE)
+								else if (cif::VERBOSE > 0)
 									throw std::runtime_error("Invalid REMARK 800 record, expected SITE_IDENTIFIER");
 								break;
@@ -2695,7 +2701,7 @@ void PDBFileParser::ParseRemarks()
 									evidence = m[1].str();
 									state = sDesc;
 								}
-								else if (cif::VERBOSE)
+								else if (cif::VERBOSE > 0)
 									throw std::runtime_error("Invalid REMARK 800 record, expected SITE_IDENTIFIER");
 								break;
@@ -2906,7 +2912,7 @@ void PDBFileParser::ParseRemark200()
 		collectionDate = pdb2cifDate(rm200("DATE OF DATA COLLECTION", diffrnNr), ec);
 		if (ec)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << ec.message() << " for pdbx_collection_date" << std::endl;
 			// The date field can become truncated when multiple values are available
@@ -3025,7 +3031,7 @@ void PDBFileParser::ParseRemark200()
 	else if (inRM200({"HIGHEST RESOLUTION SHELL, RANGE LOW (A)", "COMPLETENESS FOR SHELL (%)",
 	                  "R MERGE FOR SHELL (I)", "R SYM FOR SHELL (I)", "<I/SIGMA(I)> FOR SHELL", "DATA REDUNDANCY IN SHELL"}))
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Not writing reflns_shell record since d_res_high is missing" << std::endl;
 	}
 }
@@ -3595,7 +3601,7 @@ void PDBFileParser::ConstructEntities()
 			{
 				auto &r = chain.mResiduesSeen[lastResidueIndex + 1];
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 				{
 					std::cerr << "Detected residues that cannot be aligned to SEQRES" << std::endl
 							  << "First residue is " << chain.mDbref.chainID << ':' << r.mSeqNum << r.mIcode << std::endl;
@@ -4005,7 +4011,7 @@ void PDBFileParser::ConstructEntities()
 					tie(asym, labelSeq, std::ignore) = MapResidue(seqadv.chainID, seqadv.seqNum, seqadv.iCode, ec);
 					if (ec)
 					{
-						if (cif::VERBOSE)
+						if (cif::VERBOSE > 0)
 							std::cerr << "dropping unmatched SEQADV record" << std::endl;
 						continue;
 					}
@@ -4319,7 +4325,7 @@ void PDBFileParser::ConstructEntities()
 		tie(asymID, seq, std::ignore) = MapResidue(chainID, seqNum, iCode, ec);
 		if (ec) // no need to write a modres if it could not be found
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "dropping unmapped MODRES record" << std::endl;
 			continue;
 		}
@@ -4415,7 +4421,7 @@ void PDBFileParser::ConstructEntities()
 		tie(asymID, seqNr, isPolymer) = MapResidue(unobs.chain, unobs.seq, unobs.iCode, ec);
 		if (ec)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "error mapping unobserved residue" << std::endl;
 			continue;
 		}
@@ -4676,7 +4682,7 @@ void PDBFileParser::ParseSecondaryStructure()
 		if (ec)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Could not map residue for HELIX " << vI(8, 10) << std::endl;
 		}
 		else
@@ -4791,7 +4797,7 @@ void PDBFileParser::ParseSecondaryStructure()
 		if (ec)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Dropping SHEET record " << vI(8, 10) << std::endl;
 		}
 		else
@@ -4827,7 +4833,7 @@ void PDBFileParser::ParseSecondaryStructure()
 				if (ec)
 				{
-					if (cif::VERBOSE)
+					if (cif::VERBOSE > 0)
 						std::cerr << "skipping unmatched pdbx_struct_sheet_hbond record" << std::endl;
 				}
 				else
@@ -4927,7 +4933,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			if (ec)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Dropping SSBOND " << vI(8, 10) << std::endl;
 				continue;
 			}
@@ -4948,7 +4954,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			}
 			catch (const std::exception &ex)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Dropping SSBOND " << vI(8, 10) << " due to invalid symmetry operation" << std::endl;
 				continue;
 			}
@@ -4993,7 +4999,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 		if (mRec->is("LINK  ") or mRec->is("LINKR "))
 		{
-			if (cif::VERBOSE and mRec->is("LINKR "))
+			if (cif::VERBOSE > 0 and mRec->is("LINKR "))
 				std::cerr << "Accepting non-standard LINKR record, but ignoring extra information" << std::endl;
 			//	 1 -  6         Record name    "LINK  "
@@ -5046,7 +5052,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			if (ec)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Dropping LINK record at line " << mRec->mLineNr << std::endl;
 				continue;
 			}
@@ -5062,7 +5068,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 				}
 				catch (const std::invalid_argument &)
 				{
-					if (cif::VERBOSE)
+					if (cif::VERBOSE > 0)
 						std::cerr << "Distance value '" << distance << "' is not a valid float in LINK record" << std::endl;
 					swap(ccp4LinkID, distance); // assume this is a ccp4_link_id... oh really?
 				}
@@ -5078,7 +5084,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			}
 			catch (const std::exception &ex)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Dropping LINK record at line " << mRec->mLineNr << " due to invalid symmetry operation" << std::endl;
 				continue;
 			}
@@ -5149,7 +5155,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 			if (ec)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Dropping CISPEP record at line " << mRec->mLineNr << std::endl;
 				continue;
 			}
@@ -5215,7 +5221,7 @@ void PDBFileParser::ParseMiscellaneousFeatures()
 			if (ec)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "skipping struct_site_gen record" << std::endl;
 			}
 			else
@@ -5518,7 +5524,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 		{
 			if (groupPDB == "HETATM")
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Changing atom from HETATM to ATOM at line " << mRec->mLineNr << std::endl;
 				groupPDB = "ATOM";
 			}
@@ -5527,7 +5533,7 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 		{
 			if (groupPDB == "ATOM")
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Changing atom from ATOM to HETATM at line " << mRec->mLineNr << std::endl;
 				groupPDB = "HETATM";
 			}
@@ -5698,7 +5704,8 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
 		}
 		catch (const std::exception &ex)
 		{
-			std::cerr << "Error parsing REMARK 3" << std::endl;
+			if (cif::VERBOSE >= 0)
+				std::cerr << "Error parsing REMARK 3" << std::endl;
 			throw;
 		}
 		//
@@ -5750,12 +5757,12 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
 				if ((symm1.empty() or symm1 == "1_555") and (symm2.empty() or symm2 == "1_555"))
 					distance = static_cast<float>(mmcif::Distance(mmcif::Point{x1, y1, z1}, mmcif::Point{x2, y2, z2}));
-				else if (cif::VERBOSE)
+				else if (cif::VERBOSE > 0)
 					std::cerr << "Cannot calculate distance for link since one of the atoms is in another dimension" << std::endl;
 			}
 			catch (std::exception &ex)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Error finding atom for LINK distance calculation: " << ex.what() << std::endl;
 			}
@@ -5764,10 +5771,13 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Error parsing PDB";
+		if (cif::VERBOSE >= 0)
-		if (mRec != nullptr)
+		{
-			std::cerr << " at line " << mRec->mLineNr;
+			std::cerr << "Error parsing PDB";
-		std::cerr << std::endl;
+			if (mRec != nullptr)
+				std::cerr << " at line " << mRec->mLineNr;
+			std::cerr << std::endl;
+		}
 		throw;
 	}
 }
@@ -5947,7 +5957,7 @@ int PDBFileParser::PDBChain::AlignResToSeqRes()
 			switch (tb(x, y))
 			{
 				case -1:
-					//					if (cif::VERBOSE)
+					//					if (cif::VERBOSE > 0)
 					//						std::cerr << "A residue found in the ATOM records "
 					//							 << "(" << ry[y].mMonID << " @ " << mDbref.chainID << ":" << ry[y].mSeqNum
 					//							 	<<  ((ry[y].mIcode == ' ' or ry[y].mIcode == 0) ? "" : std::string{ ry[y].mIcode }) << ")"
@@ -6034,7 +6044,6 @@ void ReadPDBFile(std::istream &pdbFile, cif::File &cifFile)
 	p.Parse(pdbFile, cifFile);
-	if (not cifFile.isValid())
+	if (not cifFile.isValid() and cif::VERBOSE >= 0)
-		// throw std::runtime_error("Resulting mmCIF file is invalid");
 		std::cerr << "Resulting mmCIF file is not valid!" << std::endl;
 }
--- a/src/PDB2CifRemark3.cpp
+++ b/src/PDB2CifRemark3.cpp
@@ -1320,7 +1320,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 	if (line != "REFINEMENT.")
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Unexpected data in REMARK 3" << std::endl;
 		return false;
 	}
@@ -1332,7 +1332,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 	if (not std::regex_match(line, m, rxp))
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Expected valid PROGRAM line in REMARK 3" << std::endl;
 		return false;
 	}
@@ -1367,8 +1367,9 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 		}
 		catch(const std::exception& e)
 		{
-			std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
+			if (cif::VERBOSE >= 0)
-					  << e.what() << '\n';
+				std::cerr << "Error parsing REMARK 3 with " << parser->program() << std::endl
+						  << e.what() << '\n';
 			score = 0;
 		}
@@ -1411,7 +1412,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 			tryParser(new TNT_Remark3Parser(program, expMethod, r, db));
 		else if (ba::starts_with(program, "X-PLOR"))
 			tryParser(new XPLOR_Remark3Parser(program, expMethod, r, db));
-		else if (cif::VERBOSE)
+		else if (cif::VERBOSE > 0)
 			std::cerr << "Skipping unknown program (" << program << ") in REMARK 3" << std::endl;
 	}
@@ -1420,7 +1421,8 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 	bool guessProgram = scores.empty() or scores.front().score < 0.9f;;
 	if (guessProgram)
 	{
-		std::cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match" << std::endl;
 		tryParser(new BUSTER_TNT_Remark3Parser("BUSTER-TNT", expMethod, r, db));
 		tryParser(new CNS_Remark3Parser("CNS", expMethod, r, db));
@@ -1444,7 +1446,7 @@ bool Remark3Parser::parse(const std::string& expMethod, PDBRecord* r, cif::Datab
 		auto& best = scores.front();
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "Choosing " << best.parser->program() << " version '" << best.parser->version() << "' as refinement program. Score = " << best.score << std::endl;
 		auto& software = db["software"];

--- a/src/Secondary.cpp
+++ b/src/Secondary.cpp
 /*-
 * 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
@@ -26,14 +26,14 @@
 // Calculate DSSP-like secondary structure information
-#include <numeric>
 #include <iomanip>
+#include <numeric>
 #include <thread>
 #include <boost/algorithm/string.hpp>
-#include "cif++/Structure.hpp"
 #include "cif++/Secondary.hpp"
+#include "cif++/Structure.hpp"
 namespace ba = boost::algorithm;
@@ -47,37 +47,37 @@ struct Res;
 enum ResidueType
 {
 	kUnknownResidue,
 	//
-	kAlanine,				// A	ala
+	kAlanine,       // A	ala
-	kArginine,				// R	arg
+	kArginine,      // R	arg
-	kAsparagine,			// N	asn
+	kAsparagine,    // N	asn
-	kAsparticAcid,			// D	asp
+	kAsparticAcid,  // D	asp
-	kCysteine,				// C	cys
+	kCysteine,      // C	cys
-	kGlutamicAcid,			// E	glu
+	kGlutamicAcid,  // E	glu
-	kGlutamine,				// Q	gln
+	kGlutamine,     // Q	gln
-	kGlycine,				// G	gly
+	kGlycine,       // G	gly
-	kHistidine,				// H	his
+	kHistidine,     // H	his
-	kIsoleucine,			// I	ile
+	kIsoleucine,    // I	ile
-	kLeucine,				// L	leu
+	kLeucine,       // L	leu
-	kLysine,				// K	lys
+	kLysine,        // K	lys
-	kMethionine,			// M	met
+	kMethionine,    // M	met
-	kPhenylalanine,			// F	phe
+	kPhenylalanine, // F	phe
-	kProline,				// P	pro
+	kProline,       // P	pro
-	kSerine,				// S	ser
+	kSerine,        // S	ser
-	kThreonine,				// T	thr
+	kThreonine,     // T	thr
-	kTryptophan,			// W	trp
+	kTryptophan,    // W	trp
-	kTyrosine,				// Y	tyr
+	kTyrosine,      // Y	tyr
-	kValine,				// V	val
+	kValine,        // V	val
 	kResidueTypeCount
 };
 struct ResidueInfo
 {
-	ResidueType		type;
+	ResidueType type;
-	char			code;
+	char code;
-	char			name[4];
+	char name[4];
 };
 const ResidueInfo kResidueInfo[] = {
@@ -109,8 +109,8 @@ ResidueType MapResidue(std::string inName)
 	ba::trim(inName);
 	ResidueType result = kUnknownResidue;
-	for (auto& ri: kResidueInfo)
+	for (auto &ri : kResidueInfo)
 	{
 		if (inName == ri.name)
 		{
@@ -118,37 +118,39 @@ ResidueType MapResidue(std::string inName)
 			break;
 		}
 	}
 	return result;
 }
 struct HBond
 {
-	Res*	residue;
+	Res *residue;
-	double	energy;
+	double energy;
 };
 enum BridgeType
 {
-	btNoBridge, btParallel, btAntiParallel
+	btNoBridge,
+	btParallel,
+	btAntiParallel
 };
 struct Bridge
 {
-	BridgeType				type;
+	BridgeType type;
-	uint32_t				sheet, ladder;
+	uint32_t sheet, ladder;
-	std::set<Bridge*>		link;
+	std::set<Bridge *> link;
-	std::deque<uint32_t>	i, j;
+	std::deque<uint32_t> i, j;
-	std::string				chainI, chainJ;
+	std::string chainI, chainJ;
-	bool			operator<(const Bridge& b) const		{ return chainI < b.chainI or (chainI == b.chainI and i.front() < b.i.front()); }
+	bool operator<(const Bridge &b) const { return chainI < b.chainI or (chainI == b.chainI and i.front() < b.i.front()); }
 };
 struct BridgeParner
 {
-	Res*		residue;
+	Res *residue;
-	uint32_t	ladder;
+	uint32_t ladder;
-	bool		parallel;
+	bool parallel;
 };
 // --------------------------------------------------------------------
@@ -159,7 +161,7 @@ const float
 	kMinimalCADistance = 9.0f,
 	kMinHBondEnergy = -9.9f,
 	kMaxHBondEnergy = -0.5f,
-	kCouplingConstant = -27.888f,	//	= -332 * 0.42 * 0.2
+	kCouplingConstant = -27.888f, //	= -332 * 0.42 * 0.2
 	kMaxPeptideBondLength = 2.5f;
 const float
@@ -172,18 +174,19 @@ const float
 struct Res
 {
-	Res(const Monomer& m, int nr, ChainBreak brk)
+	Res(const Monomer &m, int nr, ChainBreak brk)
-		: mM(m), mNumber(nr)
+		: mM(m)
+		, mNumber(nr)
 		, mType(MapResidue(m.compoundID()))
 		, mChainBreak(brk)
 	{
 		// update the box containing all atoms
-		mBox[0].mX = mBox[0].mY = mBox[0].mZ =  std::numeric_limits<float>::max();
+		mBox[0].mX = mBox[0].mY = mBox[0].mZ = std::numeric_limits<float>::max();
 		mBox[1].mX = mBox[1].mY = mBox[1].mZ = -std::numeric_limits<float>::max();
-		mH = mmcif::Point{ std::numeric_limits<float>::max(), std::numeric_limits<float>::max(), std::numeric_limits<float>::max() };
+		mH = mmcif::Point{std::numeric_limits<float>::max(), std::numeric_limits<float>::max(), std::numeric_limits<float>::max()};
-		for (auto& a: mM.unique_atoms())
+		for (auto &a : mM.unique_atoms())
 		{
 			if (a.labelAtomID() == "CA")
 			{
@@ -227,44 +230,44 @@ struct Res
 	{
 		// assign the Hydrogen
 		mH = mN;
 		if (mType != kProline and mPrev != nullptr)
 		{
 			auto pc = mPrev->mC;
 			auto po = mPrev->mO;
 			float CODistance = static_cast<float>(Distance(pc, po));
-			mH.mX += (pc.mX - po.mX) / CODistance; 
+			mH.mX += (pc.mX - po.mX) / CODistance;
-			mH.mY += (pc.mY - po.mY) / CODistance; 
+			mH.mY += (pc.mY - po.mY) / CODistance;
-			mH.mZ += (pc.mZ - po.mZ) / CODistance; 
+			mH.mZ += (pc.mZ - po.mZ) / CODistance;
 		}
 	}
-	void SetSecondaryStructure(SecondaryStructureType inSS)	{ mSecondaryStructure = inSS; }
+	void SetSecondaryStructure(SecondaryStructureType inSS) { mSecondaryStructure = inSS; }
-	SecondaryStructureType GetSecondaryStructure() const	{ return mSecondaryStructure; }
+	SecondaryStructureType GetSecondaryStructure() const { return mSecondaryStructure; }
-	void SetBetaPartner(uint32_t n, Res& inResidue, uint32_t inLadder, bool inParallel)
+	void SetBetaPartner(uint32_t n, Res &inResidue, uint32_t inLadder, bool inParallel)
 	{
 		assert(n == 0 or n == 1);
 		mBetaPartner[n].residue = &inResidue;
 		mBetaPartner[n].ladder = inLadder;
 		mBetaPartner[n].parallel = inParallel;
 	}
 	BridgeParner GetBetaPartner(uint32_t n) const
 	{
 		assert(n == 0 or n == 1);
 		return mBetaPartner[n];
 	}
-	void SetSheet(uint32_t inSheet)						{ mSheet = inSheet; }
+	void SetSheet(uint32_t inSheet) { mSheet = inSheet; }
-	uint32_t GetSheet() const							{ return mSheet; }
+	uint32_t GetSheet() const { return mSheet; }
-	bool IsBend() const									{ return mBend; }
+	bool IsBend() const { return mBend; }
-	void SetBend(bool inBend)							{ mBend = inBend; }
+	void SetBend(bool inBend) { mBend = inBend; }
 	Helix GetHelixFlag(HelixType helixType) const
 	{
 		size_t stride = static_cast<size_t>(helixType);
@@ -292,7 +295,7 @@ struct Res
 			throw std::runtime_error("Only cysteine residues can form sulphur bridges");
 		mSSBridgeNr = inBridgeNr;
 	}
 	uint8_t GetSSBridgeNr() const
 	{
 		if (mType != kCysteine)
@@ -300,21 +303,20 @@ struct Res
 		return mSSBridgeNr;
 	}
-	double CalculateSurface(const std::vector<Res>& inResidues);
+	double CalculateSurface(const std::vector<Res> &inResidues);
-	double CalculateSurface(const Point& inAtom, float inRadius, const std::vector<Res*>& inNeighbours);
+	double CalculateSurface(const Point &inAtom, float inRadius, const std::vector<Res *> &inNeighbours);
-	bool AtomIntersectsBox(const Point& atom, float inRadius) const
+	bool AtomIntersectsBox(const Point &atom, float inRadius) const
 	{
-		return
+		return atom.mX + inRadius >= mBox[0].mX and
-			atom.mX + inRadius >= mBox[0].mX and
+		       atom.mX - inRadius <= mBox[1].mX and
-			atom.mX - inRadius <= mBox[1].mX and
+		       atom.mY + inRadius >= mBox[0].mY and
-			atom.mY + inRadius >= mBox[0].mY and
+		       atom.mY - inRadius <= mBox[1].mY and
-			atom.mY - inRadius <= mBox[1].mY and
+		       atom.mZ + inRadius >= mBox[0].mZ and
-			atom.mZ + inRadius >= mBox[0].mZ and
+		       atom.mZ - inRadius <= mBox[1].mZ;
-			atom.mZ - inRadius <= mBox[1].mZ;
 	}
-	void ExtendBox(const Point& atom, float inRadius)
+	void ExtendBox(const Point &atom, float inRadius)
 	{
 		if (mBox[0].mX > atom.mX - inRadius)
 			mBox[0].mX = atom.mX - inRadius;
@@ -330,10 +332,10 @@ struct Res
 			mBox[1].mZ = atom.mZ + inRadius;
 	}
-	Res* mNext = nullptr;
+	Res *mNext = nullptr;
-	Res* mPrev = nullptr;
+	Res *mPrev = nullptr;
-	const Monomer& mM;
+	const Monomer &mM;
 	std::string mAltID;
 	int mNumber;
@@ -344,14 +346,14 @@ struct Res
 	Point mCenter;
 	std::vector<Point> mSideChain;
 	double mAccessibility = 0;
 	ResidueType mType;
 	uint8_t mSSBridgeNr = 0;
 	SecondaryStructureType mSecondaryStructure = ssLoop;
 	HBond mHBondDonor[2] = {}, mHBondAcceptor[2] = {};
 	BridgeParner mBetaPartner[2] = {};
 	uint32_t mSheet = 0;
-	Helix mHelixFlags[4] = { Helix::None, Helix::None, Helix::None, Helix::None };	//
+	Helix mHelixFlags[4] = {Helix::None, Helix::None, Helix::None, Helix::None}; //
 	bool mBend = false;
 	ChainBreak mChainBreak = ChainBreak::None;
 };
@@ -360,19 +362,20 @@ struct Res
 class Accumulator
 {
-	public:
+  public:
 	struct candidate
 	{
-		Point	location;
+		Point location;
-		double	radius;
+		double radius;
-		double	distance;
+		double distance;
-		bool operator<(const candidate& rhs) const
+		bool operator<(const candidate &rhs) const
-				{ return distance < rhs.distance; }
+		{
+			return distance < rhs.distance;
+		}
 	};
-	void operator()(const Point& a, const Point& b, double d, double r)
+	void operator()(const Point &a, const Point &b, double d, double r)
 	{
 		double distance = DistanceSquared(a, b);
@@ -384,7 +387,7 @@ class Accumulator
 		if (distance < test and distance > 0.0001)
 		{
-			candidate c = { b - a, r * r, distance };
+			candidate c = {b - a, r * r, distance};
 			m_x.push_back(c);
 			push_heap(m_x.begin(), m_x.end());
@@ -396,19 +399,18 @@ class Accumulator
 		sort_heap(m_x.begin(), m_x.end());
 	}
-	std::vector<candidate>  m_x;
+	std::vector<candidate> m_x;
 };
 // we use a fibonacci sphere to calculate the even distribution of the dots
 class MSurfaceDots
 {
  public:
+	static MSurfaceDots &Instance();
-	static MSurfaceDots&  Instance();
+	size_t size() const { return mPoints.size(); }
+	const Point &operator[](size_t inIx) const { return mPoints[inIx]; }
-	size_t size() const							{ return mPoints.size(); }
+	double weight() const { return mWeight; }
-	const Point& operator[](size_t inIx) const	{ return mPoints[inIx]; }
-	double weight() const						{ return mWeight; }
  private:
 	MSurfaceDots(int32_t inN);
@@ -417,7 +419,7 @@ class MSurfaceDots
 	double mWeight;
 };
-MSurfaceDots& MSurfaceDots::Instance()
+MSurfaceDots &MSurfaceDots::Instance()
 {
 	const int32_t kN = 200;
@@ -442,11 +444,11 @@ MSurfaceDots::MSurfaceDots(int32_t N)
 	}
 }
-double Res::CalculateSurface(const Point& inAtom, float inRadius, const std::vector<Res*>& inNeighbours)
+double Res::CalculateSurface(const Point &inAtom, float inRadius, const std::vector<Res *> &inNeighbours)
 {
 	Accumulator accumulate;
-	for (auto r: inNeighbours)
+	for (auto r : inNeighbours)
 	{
 		if (r->AtomIntersectsBox(inAtom, inRadius))
 		{
@@ -455,7 +457,7 @@ double Res::CalculateSurface(const Point& inAtom, float inRadius, const std::vec
 			accumulate(inAtom, r->mC, inRadius, kRadiusC);
 			accumulate(inAtom, r->mO, inRadius, kRadiusO);
-			for (auto& atom: r->mSideChain)
+			for (auto &atom : r->mSideChain)
 				accumulate(inAtom, atom, inRadius, kRadiusSideAtom);
 		}
 	}
@@ -465,7 +467,7 @@ double Res::CalculateSurface(const Point& inAtom, float inRadius, const std::vec
 	float radius = inRadius + kRadiusWater;
 	double surface = 0;
-	MSurfaceDots& surfaceDots = MSurfaceDots::Instance();
+	MSurfaceDots &surfaceDots = MSurfaceDots::Instance();
 	for (size_t i = 0; i < surfaceDots.size(); ++i)
 	{
@@ -482,51 +484,51 @@ double Res::CalculateSurface(const Point& inAtom, float inRadius, const std::vec
 	return surface * radius * radius;
 }
-double Res::CalculateSurface(const std::vector<Res>& inResidues)
+double Res::CalculateSurface(const std::vector<Res> &inResidues)
 {
-	std::vector<Res*> neighbours;
+	std::vector<Res *> neighbours;
-	for (auto& r: inResidues)
+	for (auto &r : inResidues)
 	{
 		Point center = r.mCenter;
 		double radius = r.mRadius;
 		if (Distance(mCenter, center) < mRadius + radius)
-			neighbours.push_back(const_cast<Res*>(&r));
+			neighbours.push_back(const_cast<Res *>(&r));
 	}
 	mAccessibility = CalculateSurface(mN, kRadiusN, neighbours) +
-					 CalculateSurface(mCAlpha, kRadiusCA, neighbours) +
+	                 CalculateSurface(mCAlpha, kRadiusCA, neighbours) +
-					 CalculateSurface(mC, kRadiusC, neighbours) +
+	                 CalculateSurface(mC, kRadiusC, neighbours) +
-					 CalculateSurface(mO, kRadiusO, neighbours);
+	                 CalculateSurface(mO, kRadiusO, neighbours);
-	for (auto& atom: mSideChain)
+	for (auto &atom : mSideChain)
 		mAccessibility += CalculateSurface(atom, kRadiusSideAtom, neighbours);
 	return mAccessibility;
 }
-void CalculateAccessibilities(std::vector<Res>& inResidues, DSSP_Statistics& stats)
+void CalculateAccessibilities(std::vector<Res> &inResidues, DSSP_Statistics &stats)
 {
 	stats.accessibleSurface = 0;
-	for (auto& residue: inResidues)
+	for (auto &residue : inResidues)
 		stats.accessibleSurface += residue.CalculateSurface(inResidues);
 }
 // --------------------------------------------------------------------
 // TODO: use the angle to improve bond energy calculation.
-double CalculateHBondEnergy(Res& inDonor, Res& inAcceptor)
+double CalculateHBondEnergy(Res &inDonor, Res &inAcceptor)
 {
 	double result = 0;
 	if (inDonor.mType != kProline)
 	{
 		double distanceHO = Distance(inDonor.mH, inAcceptor.mO);
 		double distanceHC = Distance(inDonor.mH, inAcceptor.mC);
 		double distanceNC = Distance(inDonor.mN, inAcceptor.mC);
 		double distanceNO = Distance(inDonor.mN, inAcceptor.mO);
 		if (distanceHO < kMinimalDistance or distanceHC < kMinimalDistance or distanceNC < kMinimalDistance or distanceNO < kMinimalDistance)
 			result = kMinHBondEnergy;
 		else
@@ -550,7 +552,7 @@ double CalculateHBondEnergy(Res& inDonor, Res& inAcceptor)
 	{
 		inDonor.mHBondAcceptor[1].residue = &inAcceptor;
 		inDonor.mHBondAcceptor[1].energy = result;
-	}		
+	}
 	// and acceptor
 	if (result < inAcceptor.mHBondDonor[0].energy)
@@ -563,25 +565,24 @@ double CalculateHBondEnergy(Res& inDonor, Res& inAcceptor)
 	{
 		inAcceptor.mHBondDonor[1].residue = &inDonor;
 		inAcceptor.mHBondDonor[1].energy = result;
-	}		
+	}
 	return result;
 }
 // --------------------------------------------------------------------
-void CalculateHBondEnergies(std::vector<Res>& inResidues)
+void CalculateHBondEnergies(std::vector<Res> &inResidues)
 {
 	// Calculate the HBond energies
 	for (uint32_t i = 0; i + 1 < inResidues.size(); ++i)
 	{
-		auto& ri = inResidues[i];
+		auto &ri = inResidues[i];
 		for (uint32_t j = i + 1; j < inResidues.size(); ++j)
 		{
-			auto& rj = inResidues[j];
+			auto &rj = inResidues[j];
 			if (Distance(ri.mCAlpha, rj.mCAlpha) < kMinimalCADistance)
 			{
 				CalculateHBondEnergy(ri, rj);
@@ -594,7 +595,7 @@ void CalculateHBondEnergies(std::vector<Res>& inResidues)
 // --------------------------------------------------------------------
-bool NoChainBreak(const Res* a, const Res* b)
+bool NoChainBreak(const Res *a, const Res *b)
 {
 	bool result = a->mM.asymID() == b->mM.asymID();
 	for (auto r = a; result and r != b; r = r->mNext)
@@ -608,35 +609,39 @@ bool NoChainBreak(const Res* a, const Res* b)
 	return result;
 }
-bool NoChainBreak(const Res& a, const Res& b)
+bool NoChainBreak(const Res &a, const Res &b)
 {
 	return NoChainBreak(&a, &b);
 }
 // --------------------------------------------------------------------
-bool TestBond(const Res* a, const Res* b)
+bool TestBond(const Res *a, const Res *b)
+{
+	return (a->mHBondAcceptor[0].residue == b and a->mHBondAcceptor[0].energy < kMaxHBondEnergy) or
+	       (a->mHBondAcceptor[1].residue == b and a->mHBondAcceptor[1].energy < kMaxHBondEnergy);
+}
+bool TestBond(DSSP::ResidueInfo const &a, DSSP::ResidueInfo const &b)
 {
-	return
+	return a and b and TestBond(a.mImpl, b.mImpl);
-		(a->mHBondAcceptor[0].residue == b and a->mHBondAcceptor[0].energy < kMaxHBondEnergy) or
-		(a->mHBondAcceptor[1].residue == b and a->mHBondAcceptor[1].energy < kMaxHBondEnergy);
 }
 // --------------------------------------------------------------------
-BridgeType TestBridge(const Res& r1, const Res& r2)
+BridgeType TestBridge(const Res &r1, const Res &r2)
-{										// I.	a	d	II.	a	d		parallel    
+{                                   // I.	a	d	II.	a	d		parallel
-	auto a = r1.mPrev;					//		  \			  /
+	auto a = r1.mPrev;              //		  \			  /
-	auto b = &r1;						//		b	e		b	e
+	auto b = &r1;                   //		b	e		b	e
-	auto c = r1.mNext;					// 		  /			  \                      ..
+	auto c = r1.mNext;              // 		  /			  \                      ..
-	auto d = r2.mPrev;					//		c	f		c	f
+	auto d = r2.mPrev;              //		c	f		c	f
-	auto e = &r2;						//
+	auto e = &r2;                   //
-	auto f = r2.mNext;					// III.	a <- f	IV. a	  f		antiparallel
+	auto f = r2.mNext;              // III.	a <- f	IV. a	  f		antiparallel
-										//		                                   
+	                                //
-	BridgeType result = btNoBridge;		//		b	 e      b <-> e                  
+	BridgeType result = btNoBridge; //		b	 e      b <-> e
-										//                                          
+	                                //
-										//		c -> d		c     d
+	                                //		c -> d		c     d
 	if (a and c and NoChainBreak(a, c) and d and f and NoChainBreak(d, f))
 	{
 		if ((TestBond(c, e) and TestBond(e, a)) or (TestBond(f, b) and TestBond(b, d)))
@@ -644,83 +649,80 @@ BridgeType TestBridge(const Res& r1, const Res& r2)
 		else if ((TestBond(c, d) and TestBond(f, a)) or (TestBond(e, b) and TestBond(b, e)))
 			result = btAntiParallel;
 	}
 	return result;
 }
 // --------------------------------------------------------------------
 // return true if any of the residues in bridge a is identical to any of the residues in bridge b
-bool Linked(const Bridge& a, const Bridge& b)
+bool Linked(const Bridge &a, const Bridge &b)
 {
-	return
+	return find_first_of(a.i.begin(), a.i.end(), b.i.begin(), b.i.end()) != a.i.end() or
-		find_first_of(a.i.begin(), a.i.end(), b.i.begin(), b.i.end()) != a.i.end() or
+	       find_first_of(a.i.begin(), a.i.end(), b.j.begin(), b.j.end()) != a.i.end() or
-		find_first_of(a.i.begin(), a.i.end(), b.j.begin(), b.j.end()) != a.i.end() or
+	       find_first_of(a.j.begin(), a.j.end(), b.i.begin(), b.i.end()) != a.j.end() or
-		find_first_of(a.j.begin(), a.j.end(), b.i.begin(), b.i.end()) != a.j.end() or
+	       find_first_of(a.j.begin(), a.j.end(), b.j.begin(), b.j.end()) != a.j.end();
-		find_first_of(a.j.begin(), a.j.end(), b.j.begin(), b.j.end()) != a.j.end();
 }
 // --------------------------------------------------------------------
-void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
+void CalculateBetaSheets(std::vector<Res> &inResidues, DSSP_Statistics &stats)
 {
 	// Calculate Bridges
 	std::vector<Bridge> bridges;
-	if (inResidues.size() > 4)
+	for (uint32_t i = 1; i + 4 < inResidues.size(); ++i)
 	{
-		for (uint32_t i = 1; i + 4 < inResidues.size(); ++i)
+		auto &ri = inResidues[i];
+		for (uint32_t j = i + 3; j + 1 < inResidues.size(); ++j)
 		{
-			auto& ri = inResidues[i];
+			auto &rj = inResidues[j];
-			for (uint32_t j = i + 3; j + 1 < inResidues.size(); ++j)
+			BridgeType type = TestBridge(ri, rj);
+			if (type == btNoBridge)
+				continue;
+			bool found = false;
+			for (Bridge &bridge : bridges)
 			{
-				auto& rj = inResidues[j];
+				if (type != bridge.type or i != bridge.i.back() + 1)
-				BridgeType type = TestBridge(ri, rj);
-				if (type == btNoBridge)
 					continue;
-				bool found = false;
+				if (type == btParallel and bridge.j.back() + 1 == j)
-				for (Bridge& bridge : bridges)
 				{
-					if (type != bridge.type or i != bridge.i.back() + 1)
+					bridge.i.push_back(i);
-						continue;
+					bridge.j.push_back(j);
+					found = true;
-					if (type == btParallel and bridge.j.back() + 1 == j)
+					break;
-					{
-						bridge.i.push_back(i);
-						bridge.j.push_back(j);
-						found = true;
-						break;
-					}
-					if (type == btAntiParallel and bridge.j.front() - 1 == j)
-					{
-						bridge.i.push_back(i);
-						bridge.j.push_front(j);
-						found = true;
-						break;
-					}
 				}
-				if (not found)
+				if (type == btAntiParallel and bridge.j.front() - 1 == j)
 				{
-					Bridge bridge = {};
-					bridge.type = type;
 					bridge.i.push_back(i);
-					bridge.chainI = ri.mM.asymID();
+					bridge.j.push_front(j);
-					bridge.j.push_back(j);
+					found = true;
-					bridge.chainJ = rj.mM.asymID();
+					break;
-					bridges.push_back(bridge);
 				}
 			}
+			if (not found)
+			{
+				Bridge bridge = {};
+				bridge.type = type;
+				bridge.i.push_back(i);
+				bridge.chainI = ri.mM.asymID();
+				bridge.j.push_back(j);
+				bridge.chainJ = rj.mM.asymID();
+				bridges.push_back(bridge);
+			}
 		}
 	}
 	// extend ladders
 	std::sort(bridges.begin(), bridges.end());
 	for (uint32_t i = 0; i < bridges.size(); ++i)
 	{
 		for (uint32_t j = i + 1; j < bridges.size(); ++j)
@@ -742,7 +744,7 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 			{
 				continue;
 			}
 			bool bulge;
 			if (bridges[i].type == btParallel)
 				bulge = ((jbj - jei < 6 and ibj - iei < 3) or (jbj - jei < 3));
@@ -763,25 +765,25 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 	}
 	// Sheet
-	std::set<Bridge*> ladderset;
+	std::set<Bridge *> ladderset;
-	for (Bridge& bridge : bridges)
+	for (Bridge &bridge : bridges)
 	{
 		ladderset.insert(&bridge);
 		size_t n = bridge.i.size();
 		if (n > kHistogramSize)
 			n = kHistogramSize;
 		if (bridge.type == btParallel)
 			stats.parallelBridgesPerLadderHistogram[n - 1] += 1;
 		else
 			stats.antiparallelBridgesPerLadderHistogram[n - 1] += 1;
 	}
 	uint32_t sheet = 1, ladder = 0;
 	while (not ladderset.empty())
 	{
-		std::set<Bridge*> sheetset;
+		std::set<Bridge *> sheetset;
 		sheetset.insert(*ladderset.begin());
 		ladderset.erase(ladderset.begin());
@@ -789,9 +791,9 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 		while (not done)
 		{
 			done = true;
-			for (Bridge* a : sheetset)
+			for (Bridge *a : sheetset)
 			{
-				for (Bridge* b : ladderset)
+				for (Bridge *b : ladderset)
 				{
 					if (Linked(*a, *b))
 					{
@@ -806,15 +808,15 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 			}
 		}
-		for (Bridge* bridge : sheetset)
+		for (Bridge *bridge : sheetset)
 		{
 			bridge->ladder = ladder;
 			bridge->sheet = sheet;
 			bridge->link = sheetset;
 			++ladder;
 		}
 		size_t nrOfLaddersPerSheet = sheetset.size();
 		if (nrOfLaddersPerSheet > kHistogramSize)
 			nrOfLaddersPerSheet = kHistogramSize;
@@ -822,17 +824,17 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 			stats.laddersPerSheetHistogram[0] += 1;
 		else if (nrOfLaddersPerSheet > 1)
 			stats.laddersPerSheetHistogram[nrOfLaddersPerSheet - 1] += 1;
 		++sheet;
 	}
-	for (Bridge& bridge : bridges)
+	for (Bridge &bridge : bridges)
 	{
 		// find out if any of the i and j set members already have
 		// a bridge assigned, if so, we're assigning bridge 2
 		uint32_t betai = 0, betaj = 0;
 		for (uint32_t l : bridge.i)
 		{
 			if (inResidues[l].GetBetaPartner(0).residue != nullptr)
@@ -850,15 +852,15 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 				break;
 			}
 		}
 		SecondaryStructureType ss = ssBetabridge;
 		if (bridge.i.size() > 1)
 			ss = ssStrand;
 		if (bridge.type == btParallel)
 		{
 			stats.nrOfHBondsInParallelBridges += bridge.i.back() - bridge.i.front() + 2;
 			std::deque<uint32_t>::iterator j = bridge.j.begin();
 			for (uint32_t i : bridge.i)
 				inResidues[i].SetBetaPartner(betai, inResidues[*j++], bridge.ladder, true);
@@ -898,10 +900,10 @@ void CalculateBetaSheets(std::vector<Res>& inResidues, DSSP_Statistics& stats)
 // --------------------------------------------------------------------
-void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, bool inPreferPiHelices = true)
+void CalculateAlphaHelices(std::vector<Res> &inResidues, DSSP_Statistics &stats, bool inPreferPiHelices = true)
 {
 	// Helix and Turn
-	for (HelixType helixType: { HelixType::rh_3_10, HelixType::rh_alpha, HelixType::rh_pi })
+	for (HelixType helixType : {HelixType::rh_3_10, HelixType::rh_alpha, HelixType::rh_pi})
 	{
 		uint32_t stride = static_cast<uint32_t>(helixType) + 3;
@@ -915,7 +917,7 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
 					if (inResidues[j].GetHelixFlag(helixType) == Helix::None)
 						inResidues[j].SetHelixFlag(helixType, Helix::Middle);
 				}
 				if (inResidues[i].GetHelixFlag(helixType) == Helix::End)
 					inResidues[i].SetHelixFlag(helixType, Helix::StartAndEnd);
 				else
@@ -923,8 +925,8 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
 			}
 		}
 	}
-	for (auto& r : inResidues)
+	for (auto &r : inResidues)
 	{
 		double kappa = r.mM.kappa();
 		r.SetBend(kappa != 360 and kappa > 70);
@@ -961,7 +963,7 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
 			bool empty = true;
 			for (uint32_t j = i; empty and j <= i + 4; ++j)
 				empty = inResidues[j].GetSecondaryStructure() == ssLoop or inResidues[j].GetSecondaryStructure() == ssHelix_5 or
-							(inPreferPiHelices and inResidues[j].GetSecondaryStructure() == ssAlphahelix);
+				        (inPreferPiHelices and inResidues[j].GetSecondaryStructure() == ssAlphahelix);
 			if (empty)
 			{
 				for (uint32_t j = i; j <= i + 4; ++j)
@@ -969,19 +971,19 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
 			}
 		}
 	}
 	for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
 	{
 		if (inResidues[i].GetSecondaryStructure() == ssLoop)
 		{
 			bool isTurn = false;
-			for (HelixType helixType: { HelixType::rh_3_10, HelixType::rh_alpha, HelixType::rh_pi })
+			for (HelixType helixType : {HelixType::rh_3_10, HelixType::rh_alpha, HelixType::rh_pi})
 			{
 				uint32_t stride = 3 + static_cast<uint32_t>(helixType);
 				for (uint32_t k = 1; k < stride and not isTurn; ++k)
 					isTurn = (i >= k) and inResidues[i - k].IsHelixStart(helixType);
 			}
 			if (isTurn)
 				inResidues[i].SetSecondaryStructure(ssTurn);
 			else if (inResidues[i].IsBend())
@@ -991,7 +993,7 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
 	std::string asym;
 	size_t helixLength = 0;
-	for (auto r: inResidues)
+	for (auto r : inResidues)
 	{
 		if (r.mM.asymID() != asym)
 		{
@@ -1014,7 +1016,7 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
 // --------------------------------------------------------------------
-void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, int stretch_length)
+void CalculatePPHelices(std::vector<Res> &inResidues, DSSP_Statistics &stats, int stretch_length)
 {
 	size_t N = inResidues.size();
@@ -1049,7 +1051,7 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, in
 				// auto phi_avg = (phi[i + 0] + phi[i + 1]) / 2;
 				// auto phi_sq = (phi[i + 0] - phi_avg) * (phi[i + 0] - phi_avg) +
 				// 			  (phi[i + 1] - phi_avg) * (phi[i + 1] - phi_avg);
 				// if (phi_sq >= 200)
 				// 	continue;
@@ -1065,11 +1067,11 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, in
 					case Helix::None:
 						inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Start);
 						break;
 					case Helix::End:
 						inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Middle);
 						break;
 					default:
 						break;
 				}
@@ -1099,7 +1101,7 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, in
 				// auto phi_sq = (phi[i + 0] - phi_avg) * (phi[i + 0] - phi_avg) +
 				// 			  (phi[i + 1] - phi_avg) * (phi[i + 1] - phi_avg) +
 				// 			  (phi[i + 2] - phi_avg) * (phi[i + 2] - phi_avg);
 				// if (phi_sq >= 300)
 				// 	continue;
@@ -1116,11 +1118,11 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, in
 					case Helix::None:
 						inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Start);
 						break;
 					case Helix::End:
 						inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::StartAndEnd);
 						break;
 					default:
 						break;
 				}
@@ -1133,7 +1135,7 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, in
 				if (inResidues[i + 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop)
 					inResidues[i + 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
 				if (inResidues[i + 2].GetSecondaryStructure() == SecondaryStructureType::ssLoop)
 					inResidues[i + 2].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
@@ -1150,50 +1152,52 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, in
 struct DSSPImpl
 {
-	DSSPImpl(const Structure& s, int min_poly_proline_stretch_length);
+	DSSPImpl(const Structure &s, int min_poly_proline_stretch_length);
-	const Structure&			mStructure;
+	const Structure &mStructure;
-	const std::list<Polymer>&	mPolymers;
+	const std::list<Polymer> &mPolymers;
-	std::vector<Res>			mResidues;
+	std::vector<Res> mResidues;
-	std::vector<std::pair<Res*,Res*>> mSSBonds;
+	std::vector<std::pair<Res *, Res *>> mSSBonds;
 	int m_min_poly_proline_stretch_length;
-	auto findRes(const std::string& asymID, int seqID)
+	auto findRes(const std::string &asymID, int seqID)
 	{
-		return std::find_if(mResidues.begin(), mResidues.end(), [&](auto& r) { return r.mM.asymID() == asymID and r.mM.seqID() == seqID; });
+		return std::find_if(mResidues.begin(), mResidues.end(), [&](auto &r)
+			{ return r.mM.asymID() == asymID and r.mM.seqID() == seqID; });
 	}
 	void calculateSurface();
 	void calculateSecondaryStructure();
-	DSSP_Statistics				mStats = {};
+	DSSP_Statistics mStats = {};
 };
 // --------------------------------------------------------------------
-DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
+DSSPImpl::DSSPImpl(const Structure &s, int min_poly_proline_stretch_length)
 	: mStructure(s)
 	, mPolymers(mStructure.polymers())
 	, m_min_poly_proline_stretch_length(min_poly_proline_stretch_length)
 {
 	size_t nRes = accumulate(mPolymers.begin(), mPolymers.end(),
-		0ULL, [](size_t s, auto& p) { return s + p.size(); });
+		0ULL, [](size_t s, auto &p)
+		{ return s + p.size(); });
 	mStats.nrOfChains = static_cast<uint32_t>(mPolymers.size());
 	mResidues.reserve(nRes);
 	int resNumber = 0;
-	for (auto& p: mPolymers)
+	for (auto &p : mPolymers)
 	{
 		ChainBreak brk = ChainBreak::NewChain;
-		for (auto& m: p)
+		for (auto &m : p)
 		{
 			if (not m.isComplete())
 				continue;
 			++resNumber;
 			if (not mResidues.empty() and
@@ -1219,15 +1223,15 @@ DSSPImpl::DSSPImpl(const Structure& s, int min_poly_proline_stretch_length)
 	{
 		mResidues[i].mNext = &mResidues[i + 1];
 		mResidues[i + 1].mPrev = &mResidues[i];
 		mResidues[i + 1].assignHydrogen();
 	}
 }
 void DSSPImpl::calculateSecondaryStructure()
 {
-	auto& db = mStructure.getFile().data();
+	auto &db = mStructure.getFile().data();
-	for (auto r: db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
+	for (auto r : db["struct_conn"].find(cif::Key("conn_type_id") == "disulf"))
 	{
 		std::string asym1, asym2;
 		int seq1, seq2;
@@ -1236,7 +1240,7 @@ void DSSPImpl::calculateSecondaryStructure()
 		auto r1 = findRes(asym1, seq1);
 		if (r1 == mResidues.end())
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym1 << '/' << seq1 << std::endl;
 			continue;
 			// throw std::runtime_error("Invalid file, missing residue for SS bond");
@@ -1245,7 +1249,7 @@ void DSSPImpl::calculateSecondaryStructure()
 		auto r2 = findRes(asym2, seq2);
 		if (r2 == mResidues.end())
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Missing (incomplete?) residue for SS bond when trying to find " << asym2 << '/' << seq2 << std::endl;
 			continue;
 			// throw std::runtime_error("Invalid file, missing residue for SS bond");
@@ -1261,29 +1265,29 @@ void DSSPImpl::calculateSecondaryStructure()
 	if (cif::VERBOSE > 1)
 	{
-		for (auto& r: mResidues)
+		for (auto &r : mResidues)
 		{
-			auto& m = r.mM;
+			auto &m = r.mM;
-			char helix[5] = { };
+			char helix[5] = {};
-			for (HelixType helixType: { HelixType::rh_3_10, HelixType::rh_alpha, HelixType::rh_pi, HelixType::rh_pp	})
+			for (HelixType helixType : {HelixType::rh_3_10, HelixType::rh_alpha, HelixType::rh_pi, HelixType::rh_pp})
 			{
 				switch (r.GetHelixFlag(helixType))
 				{
-					case Helix::Start:			helix[static_cast<int>(helixType)] = '>'; break;
+					case Helix::Start: helix[static_cast<int>(helixType)] = '>'; break;
-					case Helix::Middle:			helix[static_cast<int>(helixType)] = helixType == HelixType::rh_pp ? 'P' : '3' + static_cast<char>(helixType); break;
+					case Helix::Middle: helix[static_cast<int>(helixType)] = helixType == HelixType::rh_pp ? 'P' : '3' + static_cast<char>(helixType); break;
-					case Helix::StartAndEnd:	helix[static_cast<int>(helixType)] = 'X'; break;
+					case Helix::StartAndEnd: helix[static_cast<int>(helixType)] = 'X'; break;
-					case Helix::End:			helix[static_cast<int>(helixType)] = '<'; break;
+					case Helix::End: helix[static_cast<int>(helixType)] = '<'; break;
-					case Helix::None:			helix[static_cast<int>(helixType)] = ' '; break;
+					case Helix::None: helix[static_cast<int>(helixType)] = ' '; break;
 				}
 			}
 			auto id = m.asymID() + ':' + std::to_string(m.seqID()) + '/' + m.compoundID();
 			std::cerr << id << std::string(12 - id.length(), ' ')
-					<< char(r.mSecondaryStructure) << ' '
+					  << char(r.mSecondaryStructure) << ' '
-					<< helix
+					  << helix
-					<< std::endl;
+					  << std::endl;
 		}
 	}
@@ -1292,11 +1296,11 @@ void DSSPImpl::calculateSecondaryStructure()
 	mStats.nrOfIntraChainSSBridges = 0;
 	uint8_t ssBondNr = 0;
-	for (const auto& [a, b]: mSSBonds)
+	for (const auto &[a, b] : mSSBonds)
 	{
 		if (a == b)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "In the SS bonds list, the residue " << a->mM << " is bonded to itself" << std::endl;
 			continue;
 		}
@@ -1308,7 +1312,7 @@ void DSSPImpl::calculateSecondaryStructure()
 	}
 	mStats.nrOfHBonds = 0;
-	for (auto& r: mResidues)
+	for (auto &r : mResidues)
 	{
 		auto donor = r.mHBondDonor;
@@ -1332,7 +1336,7 @@ void DSSPImpl::calculateSurface()
 // --------------------------------------------------------------------
-const Monomer& DSSP::ResidueInfo::residue() const
+const Monomer &DSSP::ResidueInfo::residue() const
 {
 	return mImpl->mM;
 }
@@ -1377,7 +1381,7 @@ double DSSP::ResidueInfo::accessibility() const
 	return mImpl->mAccessibility;
 }
-std::tuple<DSSP::ResidueInfo,int,bool> DSSP::ResidueInfo::bridgePartner(int i) const
+std::tuple<DSSP::ResidueInfo, int, bool> DSSP::ResidueInfo::bridgePartner(int i) const
 {
 	auto bp = mImpl->GetBetaPartner(i);
@@ -1391,45 +1395,51 @@ int DSSP::ResidueInfo::sheet() const
 	return mImpl->GetSheet();
 }
-std::tuple<DSSP::ResidueInfo,double> DSSP::ResidueInfo::acceptor(int i) const
+std::tuple<DSSP::ResidueInfo, double> DSSP::ResidueInfo::acceptor(int i) const
 {
-	auto& a = mImpl->mHBondAcceptor[i];
+	auto &a = mImpl->mHBondAcceptor[i];
-	return { ResidueInfo(a.residue), a.energy };
+	return {ResidueInfo(a.residue), a.energy};
 }
-std::tuple<DSSP::ResidueInfo,double> DSSP::ResidueInfo::donor(int i) const
+std::tuple<DSSP::ResidueInfo, double> DSSP::ResidueInfo::donor(int i) const
 {
-	auto& d = mImpl->mHBondDonor[i];
+	auto &d = mImpl->mHBondDonor[i];
-	return { ResidueInfo(d.residue), d.energy };
+	return {ResidueInfo(d.residue), d.energy};
 }
 // --------------------------------------------------------------------
-DSSP::iterator::iterator(Res* res)
+DSSP::iterator::iterator(Res *res)
 	: mCurrent(res)
 {
 }
-DSSP::iterator::iterator(const iterator& i)
+DSSP::iterator::iterator(const iterator &i)
 	: mCurrent(i.mCurrent)
 {
 }
-DSSP::iterator& DSSP::iterator::operator=(const iterator& i)
+DSSP::iterator &DSSP::iterator::operator=(const iterator &i)
 {
 	mCurrent = i.mCurrent;
 	return *this;
 }
-DSSP::iterator& DSSP::iterator::operator++()
+DSSP::iterator &DSSP::iterator::operator++()
 {
 	++mCurrent.mImpl;
 	return *this;
 }
+DSSP::iterator &DSSP::iterator::operator--()
+{
+	--mCurrent.mImpl;
+	return *this;
+}
 // --------------------------------------------------------------------
-DSSP::DSSP(const Structure& s, int min_poly_proline_stretch, bool calculateSurfaceAccessibility)
+DSSP::DSSP(const Structure &s, int min_poly_proline_stretch, bool calculateSurfaceAccessibility)
 	: mImpl(new DSSPImpl(s, min_poly_proline_stretch))
 {
 	if (calculateSurfaceAccessibility)
@@ -1455,7 +1465,7 @@ DSSP::iterator DSSP::begin() const
 DSSP::iterator DSSP::end() const
 {
 	// careful now, MSVC is picky when it comes to dereferencing iterators that are at the end.
-	Res* res = nullptr;
+	Res *res = nullptr;
 	if (not mImpl->mResidues.empty())
 	{
 		res = mImpl->mResidues.data();
@@ -1465,55 +1475,58 @@ DSSP::iterator DSSP::end() const
 	return iterator(res);
 }
-SecondaryStructureType DSSP::operator()(const std::string& inAsymID, int inSeqID) const
+SecondaryStructureType DSSP::operator()(const std::string &inAsymID, int inSeqID) const
 {
 	SecondaryStructureType result = ssLoop;
 	auto i = find_if(mImpl->mResidues.begin(), mImpl->mResidues.end(),
-		[&](auto& r) { return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
+		[&](auto &r)
+		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 	if (i != mImpl->mResidues.end())
 		result = i->mSecondaryStructure;
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 	return result;
 }
-SecondaryStructureType DSSP::operator()(const Monomer& m) const
+SecondaryStructureType DSSP::operator()(const Monomer &m) const
 {
 	return operator()(m.asymID(), m.seqID());
 }
-double DSSP::accessibility(const std::string& inAsymID, int inSeqID) const
+double DSSP::accessibility(const std::string &inAsymID, int inSeqID) const
 {
 	SecondaryStructureType result = ssLoop;
 	auto i = find_if(mImpl->mResidues.begin(), mImpl->mResidues.end(),
-		[&](auto& r) { return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
+		[&](auto &r)
+		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 	if (i != mImpl->mResidues.end())
 		result = i->mSecondaryStructure;
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 	return result;
 }
-double DSSP::accessibility(const Monomer& m) const
+double DSSP::accessibility(const Monomer &m) const
 {
 	return accessibility(m.asymID(), m.seqID());
 }
-bool DSSP::isAlphaHelixEndBeforeStart(const Monomer& m) const
+bool DSSP::isAlphaHelixEndBeforeStart(const Monomer &m) const
 {
 	return isAlphaHelixEndBeforeStart(m.asymID(), m.seqID());
 }
-bool DSSP::isAlphaHelixEndBeforeStart(const std::string& inAsymID, int inSeqID) const
+bool DSSP::isAlphaHelixEndBeforeStart(const std::string &inAsymID, int inSeqID) const
 {
 	auto i = find_if(mImpl->mResidues.begin(), mImpl->mResidues.end(),
-		[&](auto& r) { return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
+		[&](auto &r)
+		{ return r.mM.asymID() == inAsymID and r.mM.seqID() == inSeqID; });
 	bool result = false;
 	if (i != mImpl->mResidues.end() and i + 1 != mImpl->mResidues.end())
 		result = i->GetHelixFlag(HelixType::rh_alpha) == Helix::End and (i + 1)->GetHelixFlag(HelixType::rh_alpha) == Helix::Start;
-	else if (cif::VERBOSE)
+	else if (cif::VERBOSE > 0)
 		std::cerr << "Could not find secondary structure for " << inAsymID << ':' << inSeqID << std::endl;
 	return result;
@@ -1524,4 +1537,4 @@ DSSP_Statistics DSSP::GetStatistics() const
 	return mImpl->mStats;
 }
-}
+} // namespace mmcif
--- a/src/Structure.cpp
+++ b/src/Structure.cpp
 /*-
 * 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
@@ -108,8 +108,8 @@ void FileImpl::load_data(const char *data, size_t length)
 	// And validate, otherwise lots of functionality won't work
 	//	if (mData.getValidator() == nullptr)
 	mData.loadDictionary("mmcif_pdbx_v50");
-	if (not mData.isValid())
+	if (not mData.isValid() and cif::VERBOSE >= 0)
-		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
+		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
 }
 void FileImpl::load(const std::filesystem::path &path)
@@ -140,14 +140,14 @@ void FileImpl::load(const std::filesystem::path &path)
 		{
 			try
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "unrecognized file extension, trying cif" << std::endl;
 				mData.load(in);
 			}
 			catch (const cif::CifParserError &e)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Not cif, trying plain old PDB" << std::endl;
 				// pffft...
@@ -169,7 +169,8 @@ void FileImpl::load(const std::filesystem::path &path)
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Error trying to load file " << path << std::endl;
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Error trying to load file " << path << std::endl;
 		throw;
 	}
@@ -179,8 +180,8 @@ void FileImpl::load(const std::filesystem::path &path)
 	// And validate, otherwise lots of functionality won't work
 	//	if (mData.getValidator() == nullptr)
 	mData.loadDictionary("mmcif_pdbx_v50");
-	if (not mData.isValid())
+	if (not mData.isValid() and cif::VERBOSE >= 0)
-		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE ? "." : " use --verbose option to see errors") << std::endl;
+		std::cerr << "Invalid mmCIF file" << (cif::VERBOSE > 0 ? "." : " use --verbose option to see errors") << std::endl;
 }
 void FileImpl::save(const std::filesystem::path &path)
@@ -202,494 +203,237 @@ void FileImpl::save(const std::filesystem::path &path)
 // --------------------------------------------------------------------
 // Atom
-struct AtomImpl
+Atom::AtomImpl::AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row)
+	: mDb(db)
+	, mID(id)
+	, mRefcount(1)
+	, mRow(row)
+	, mCompound(nullptr)
 {
-	AtomImpl(const AtomImpl &i)
+	prefetch();
-		: mDb(i.mDb)
+}
-		, mID(i.mID)
-		, mType(i.mType)
-		, mAtomID(i.mAtomID)
-		, mCompID(i.mCompID)
-		, mAsymID(i.mAsymID)
-		, mSeqID(i.mSeqID)
-		, mAltID(i.mAltID)
-		, mLocation(i.mLocation)
-		, mRefcount(1)
-		, mRow(i.mRow)
-		, mCachedRefs(i.mCachedRefs)
-		, mCompound(i.mCompound)
-		, mRadius(i.mRadius)
-		, mSymmetryCopy(i.mSymmetryCopy)
-		, mClone(true)
-	// , mRTop(i.mRTop), mD(i.mD)
-	{
-	}
-	AtomImpl(cif::Datablock &db, const std::string &id)
-		: mDb(db)
-		, mID(id)
-		, mRefcount(1)
-		, mCompound(nullptr)
-	{
-		auto &cat = db["atom_site"];
-		mRow = cat[cif::Key("id") == mID];
-		prefetch();
-	}
-	AtomImpl(cif::Datablock &db, cif::Row &row)
-		: mDb(db)
-		, mID(row["id"].as<std::string>())
-		, mRefcount(1)
-		, mRow(row)
-		, mCompound(nullptr)
-	{
-		prefetch();
-	}
-	AtomImpl(cif::Datablock &db, const std::string &id, cif::Row row)
+// constructor for a symmetry copy of an atom
-		: mDb(db)
+Atom::AtomImpl::AtomImpl(const AtomImpl &impl, const Point &loc, const std::string &sym_op)
-		, mID(id)
+	: mDb(impl.mDb)
-		, mRefcount(1)
+	, mID(impl.mID)
-		, mRow(row)
+	, mType(impl.mType)
-		, mCompound(nullptr)
-	{
-		prefetch();
-	}
-	AtomImpl(const AtomImpl &impl, const Point &loc, const std::string &sym_op)
+	, mAtomID(impl.mAtomID)
-		: mDb(impl.mDb)
+	, mCompID(impl.mCompID)
-		, mID(impl.mID)
+	, mAsymID(impl.mAsymID)
-		, mType(impl.mType)
+	, mSeqID(impl.mSeqID)
-		, mAtomID(impl.mAtomID)
+	, mAltID(impl.mAltID)
-		, mCompID(impl.mCompID)
+	, mAuthSeqID(impl.mAuthSeqID)
-		, mAsymID(impl.mAsymID)
-		, mSeqID(impl.mSeqID)
-		, mAltID(impl.mAltID)
-		, mLocation(loc)
-		, mRefcount(1)
-		, mRow(impl.mRow)
-		, mCachedRefs(impl.mCachedRefs)
-		, mCompound(impl.mCompound)
-		, mRadius(impl.mRadius)
-		, mSymmetryCopy(true)
-		, mSymmetryOperator(sym_op)
-	{
-	}
-	void prefetch()
+	, mLocation(loc)
-	{
+	, mRefcount(1)
-		// Prefetch some data
+	, mRow(impl.mRow)
-		std::string symbol;
+	, mCachedRefs(impl.mCachedRefs)
-		cif::tie(symbol, mAtomID, mCompID, mAsymID, mSeqID, mAltID) =
+	, mCompound(impl.mCompound)
-			mRow.get("type_symbol", "label_atom_id", "label_comp_id", "label_asym_id", "label_seq_id", "label_alt_id");
+	, mSymmetryCopy(true)
+	, mSymmetryOperator(sym_op)
+{
+}
-		if (symbol != "X")
+void Atom::AtomImpl::prefetch()
-			mType = AtomTypeTraits(symbol).type();
+{
+	// Prefetch some data
+	std::string symbol;
+	cif::tie(symbol, mAtomID, mCompID, mAsymID, mSeqID, mAltID, mAuthSeqID) =
+		mRow.get("type_symbol", "label_atom_id", "label_comp_id", "label_asym_id", "label_seq_id", "label_alt_id", "auth_seq_id");
-		float x, y, z;
+	if (symbol != "X")
-		cif::tie(x, y, z) = mRow.get("Cartn_x", "Cartn_y", "Cartn_z");
+		mType = AtomTypeTraits(symbol).type();
-		mLocation = Point(x, y, z);
+	float x, y, z;
+	cif::tie(x, y, z) = mRow.get("Cartn_x", "Cartn_y", "Cartn_z");
-		std::string compID;
+	mLocation = Point(x, y, z);
-		cif::tie(compID) = mRow.get("label_comp_id");
+}
-		// mCompound = CompoundFactory::instance().create(compID);
+int Atom::AtomImpl::compare(const AtomImpl &b) const
-	}
+{
+	int d = mAsymID.compare(b.mAsymID);
+	if (d == 0)
+		d = mSeqID - b.mSeqID;
+	if (d == 0)
+		d = mAtomID.compare(b.mAtomID);
+	if (d == 0)
+		d = mAuthSeqID.compare(b.mAuthSeqID);
-	void reference()
+	return d;
-	{
+}
-		++mRefcount;
-	}
-	void release()
+bool Atom::AtomImpl::getAnisoU(float anisou[6]) const
-	{
+{
-		if (--mRefcount <= 0)
+	bool result = false;
-			delete this;
-	}
-	bool getAnisoU(float anisou[6]) const
+	auto cat = mDb.get("atom_site_anisotrop");
+	if (cat)
 	{
-		bool result = false;
+		try
-		auto cat = mDb.get("atom_site_anisotrop");
-		if (cat)
 		{
-			try
+			auto r = cat->find1(cif::Key("id") == mID);
-			{
+			cif::tie(anisou[0], anisou[1], anisou[2], anisou[3], anisou[4], anisou[5]) =
-				auto r = cat->find1(cif::Key("id") == mID);
+				r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]");
-				cif::tie(anisou[0], anisou[1], anisou[2], anisou[3], anisou[4], anisou[5]) =
+			result = true;
-					r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]");
-				result = true;
-			}
-			catch(const std::exception& e)
-			{
-			}
 		}
+		catch (const std::exception &e)
-		return result;
-	}
-	void moveTo(const Point &p)
-	{
-		assert(not mSymmetryCopy);
-		if (mSymmetryCopy)
-			throw std::runtime_error("Moving symmetry copy");
-		if (not mClone)
 		{
-			property("Cartn_x", std::to_string(p.getX()));
-			property("Cartn_y", std::to_string(p.getY()));
-			property("Cartn_z", std::to_string(p.getZ()));
 		}
-		//		boost::format kPosFmt("%.3f");
-		//
-		//		mRow["Cartn_x"] = (kPosFmt % p.getX()).str();
-		//		mRow["Cartn_y"] = (kPosFmt % p.getY()).str();
-		//		mRow["Cartn_z"] = (kPosFmt % p.getZ()).str();
-		mLocation = p;
 	}
-	const Compound &comp() const
+	return result;
-	{
+}
-		if (mCompound == nullptr)
-		{
-			std::string compID;
-			cif::tie(compID) = mRow.get("label_comp_id");
-			mCompound = CompoundFactory::instance().create(compID);
-			if (cif::VERBOSE and mCompound == nullptr)
-				std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
-		}
-		if (mCompound == nullptr)
-			throw std::runtime_error("no compound");
-		return *mCompound;
-	}
-	bool isWater() const
+void Atom::AtomImpl::moveTo(const Point &p)
-	{
+{
-		// mCompound may still be null here, and besides, this check is not that exciting anyway
+	assert(not mSymmetryCopy);
-		return mCompID == "HOH" or mCompID == "H2O" or mCompID == "WAT";
+	if (mSymmetryCopy)
-	}
+		throw std::runtime_error("Moving symmetry copy");
-	float radius() const
+	if (not mClone)
 	{
-		return mRadius;
+		mRow.assign("Cartn_x", std::to_string(p.getX()), true, false);
+		mRow.assign("Cartn_y", std::to_string(p.getY()), true, false);
+		mRow.assign("Cartn_z", std::to_string(p.getZ()), true, false);
 	}
-	const std::string property(const std::string_view name) const
+	mLocation = p;
-	{
+}
-		for (auto &&[tag, ref] : mCachedRefs)
-		{
-			if (tag == name)
-				return ref.as<std::string>();
-		}
-		mCachedRefs.emplace_back(name, mRow[name]);
-		return std::get<1>(mCachedRefs.back()).as<std::string>();
-	}
-	void property(const std::string_view name, const std::string &value)
+const Compound &Atom::AtomImpl::comp() const
+{
+	if (mCompound == nullptr)
 	{
-		for (auto &&[tag, ref] : mCachedRefs)
+		std::string compID;
-		{
+		cif::tie(compID) = mRow.get("label_comp_id");
-			if (tag != name)
-				continue;
-			ref = value;
-			return;
-		}
-		mCachedRefs.emplace_back(name, mRow[name]);
+		mCompound = CompoundFactory::instance().create(compID);
-		std::get<1>(mCachedRefs.back()) = value;
-	}
-	int compare(const AtomImpl &b) const
+		if (cif::VERBOSE > 0 and mCompound == nullptr)
-	{
+			std::cerr << "Compound not found: '" << compID << '\'' << std::endl;
-		int d = mAsymID.compare(b.mAsymID);
-		if (d == 0)
-			d = mSeqID - b.mSeqID;
-		if (d == 0)
-			d = mAtomID.compare(b.mAtomID);
-		return d;
 	}
-	void swapAtomLabels(AtomImpl &b)
+	if (mCompound == nullptr)
-	{
+		throw std::runtime_error("no compound");
-		std::swap(mAtomID, b.mAtomID);
-	}
-	const cif::Datablock &mDb;
-	std::string mID;
-	AtomType mType;
-	std::string mAtomID;
-	std::string mCompID;
-	std::string mAsymID;
-	int mSeqID;
-	std::string mAltID;
-	Point mLocation;
-	int mRefcount;
-	cif::Row mRow;
-	mutable std::vector<std::tuple<std::string,cif::detail::ItemReference>> mCachedRefs;
+	return *mCompound;
-	mutable const Compound *mCompound = nullptr;
-	float mRadius = std::nanf("4");
-	bool mSymmetryCopy = false;
-	bool mClone = false;
-	std::string mSymmetryOperator = "1_555";
-	// clipper::RTop_orth	mRTop;
-	// Point				mD;
-	// int32_t				mRTix;
-};
-//Atom::Atom(const File& f, const std::string& id)
-//	: mImpl(new AtomImpl(f, id))
-//{
-//}
-//
-Atom::Atom()
-	: mImpl_(nullptr)
-{
 }
-Atom::Atom(AtomImpl *impl)
+const std::string Atom::AtomImpl::get_property(const std::string_view name) const
-	: mImpl_(impl)
 {
-}
+	for (auto &&[tag, ref] : mCachedRefs)
+	{
-Atom::Atom(cif::Datablock &db, cif::Row &row)
+		if (tag == name)
-	: mImpl_(new AtomImpl(db, row))
+			return ref.as<std::string>();
-{
+	}
-}
-AtomImpl *Atom::impl()
-{
-	if (mImpl_ == nullptr)
-		throw std::runtime_error("atom is not set");
-	return mImpl_;
-}
-const AtomImpl *Atom::impl() const
-{
-	if (mImpl_ == nullptr)
-		throw std::runtime_error("atom is not set");
-	return mImpl_;
-}
-Atom Atom::clone() const
+	mCachedRefs.emplace_back(name, mRow[name]);
-{
+	return std::get<1>(mCachedRefs.back()).as<std::string>();
-	return Atom(mImpl_ ? new AtomImpl(*mImpl_) : nullptr);
 }
-Atom::Atom(const Atom &rhs, const Point &loc, const std::string &sym_op)
+void Atom::AtomImpl::set_property(const std::string_view name, const std::string &value)
-	: mImpl_(new AtomImpl(*rhs.mImpl_, loc, sym_op))
 {
-}
+	for (auto &&[tag, ref] : mCachedRefs)
+	{
+		if (tag != name)
+			continue;
-Atom::Atom(const Atom &rhs)
+		ref = value;
-	: mImpl_(rhs.mImpl_)
+		return;
-{
+	}
-	if (mImpl_)
-		mImpl_->reference();
-}
-Atom::~Atom()
+	mCachedRefs.emplace_back(name, mRow[name]);
-{
+	std::get<1>(mCachedRefs.back()) = value;
-	if (mImpl_)
-		mImpl_->release();
 }
-Atom &Atom::operator=(const Atom &rhs)
+Atom::Atom(cif::Datablock &db, cif::Row &row)
+	: Atom(std::make_shared<AtomImpl>(db, row["id"].as<std::string>(), row))
 {
-	if (this != &rhs)
-	{
-		if (mImpl_)
-			mImpl_->release();
-		mImpl_ = rhs.mImpl_;
-		if (mImpl_)
-			mImpl_->reference();
-	}
-	return *this;
 }
-const cif::Row Atom::getRow() const
+Atom::Atom(const Atom &rhs, const Point &loc, const std::string &sym_op)
+	: Atom(std::make_shared<AtomImpl>(*rhs.mImpl, loc, sym_op))
 {
-	return mImpl_->mRow;
 }
 const cif::Row Atom::getRowAniso() const
 {
-	auto &db = mImpl_->mDb;
+	auto &db = mImpl->mDb;
 	auto cat = db.get("atom_site_anisotrop");
 	if (not cat)
 		return {};
 	else
-		return cat->find1(cif::Key("id") == mImpl_->mID);
+		return cat->find1(cif::Key("id") == mImpl->mID);
-}
-template <>
-std::string Atom::property<std::string>(const std::string_view name) const
-{
-	return impl()->property(name);
-}
-template <>
-int Atom::property<int>(const std::string_view name) const
-{
-	auto v = impl()->property(name);
-	return v.empty() ? 0 : stoi(v);
-}
-template <>
-float Atom::property<float>(const std::string_view name) const
-{
-	return stof(impl()->property(name));
-}
-void Atom::property(const std::string_view name, const std::string &value)
-{
-	impl()->property(name, value);
-}
-const std::string &Atom::id() const
-{
-	return impl()->mID;
-}
-AtomType Atom::type() const
-{
-	return impl()->mType;
-}
-int Atom::charge() const
-{
-	return property<int>("pdbx_formal_charge");
 }
 float Atom::uIso() const
 {
 	float result;
-	if (not property<std::string>("U_iso_or_equiv").empty())
+	if (not get_property<std::string>("U_iso_or_equiv").empty())
-		result = property<float>("U_iso_or_equiv");
+		result = get_property<float>("U_iso_or_equiv");
-	else if (not property<std::string>("B_iso_or_equiv").empty())
+	else if (not get_property<std::string>("B_iso_or_equiv").empty())
-		result = property<float>("B_iso_or_equiv") / static_cast<float>(8 * kPI * kPI);
+		result = get_property<float>("B_iso_or_equiv") / static_cast<float>(8 * kPI * kPI);
 	else
 		throw std::runtime_error("Missing B_iso or U_iso");
 	return result;
 }
-bool Atom::getAnisoU(float anisou[6]) const
+std::string Atom::labelID() const
-{
-	return impl()->getAnisoU(anisou);
-}
-float Atom::occupancy() const
 {
-	return property<float>("occupancy");
+	return mImpl->mCompID + '_' + mImpl->mAsymID + '_' + std::to_string(mImpl->mSeqID) + ':' + mImpl->mAtomID;
 }
-std::string Atom::labelAtomID() const
+std::string Atom::pdbID() const
 {
-	return impl()->mAtomID;
+	return get_property<std::string>("auth_comp_id") + '_' +
+	       get_property<std::string>("auth_asym_id") + '_' +
+	       get_property<std::string>("auth_seq_id") +
+	       get_property<std::string>("pdbx_PDB_ins_code");
 }
-std::string Atom::labelCompID() const
+int Atom::charge() const
 {
-	return impl()->mCompID;
+	return get_property<int>("pdbx_formal_charge");
 }
-std::string Atom::labelAsymID() const
+float Atom::occupancy() const
 {
-	return impl()->mAsymID;
+	return get_property<float>("occupancy");
 }
 std::string Atom::labelEntityID() const
 {
-	return property<std::string>("label_entity_id");
+	return get_property<std::string>("label_entity_id");
-}
-std::string Atom::labelAltID() const
-{
-	return impl()->mAltID;
-}
-bool Atom::isAlternate() const
-{
-	return not impl()->mAltID.empty();
-}
-int Atom::labelSeqID() const
-{
-	return impl()->mSeqID;
-}
-std::string Atom::authAsymID() const
-{
-	return property<std::string>("auth_asym_id");
 }
 std::string Atom::authAtomID() const
 {
-	return property<std::string>("auth_atom_id");
+	return get_property<std::string>("auth_atom_id");
-}
-std::string Atom::pdbxAuthAltID() const
-{
-	return property<std::string>("pdbx_auth_alt_id");
-}
-std::string Atom::pdbxAuthInsCode() const
-{
-	return property<std::string>("pdbx_PDB_ins_code");
 }
 std::string Atom::authCompID() const
 {
-	return property<std::string>("auth_comp_id");
+	return get_property<std::string>("auth_comp_id");
 }
-std::string Atom::authSeqID() const
+std::string Atom::authAsymID() const
-{
-	return property<std::string>("auth_seq_id");
-}
-std::string Atom::labelID() const
-{
-	return property<std::string>("label_comp_id") + '_' + impl()->mAsymID + '_' + std::to_string(impl()->mSeqID) + ':' + impl()->mAtomID;
-}
-std::string Atom::pdbID() const
 {
-	return property<std::string>("auth_comp_id") + '_' +
+	return get_property<std::string>("auth_asym_id");
-	       property<std::string>("auth_asym_id") + '_' +
-	       property<std::string>("auth_seq_id") +
-	       property<std::string>("pdbx_PDB_ins_code");
 }
-Point Atom::location() const
+std::string Atom::pdbxAuthInsCode() const
 {
-	return impl()->mLocation;
+	return get_property<std::string>("pdbx_PDB_ins_code");
 }
-void Atom::location(Point p)
+std::string Atom::pdbxAuthAltID() const
 {
-	impl()->moveTo(p);
+	return get_property<std::string>("pdbx_auth_alt_id");
 }
 void Atom::translate(Point t)
@@ -706,80 +450,32 @@ void Atom::rotate(Quaternion q)
 	location(loc);
 }
-// Atom Atom::symmetryCopy(const Point& d, const clipper::RTop_orth& rt)
+void Atom::translateAndRotate(Point t, Quaternion q)
-// {
-// 	return Atom(new AtomImpl(*impl(), d, rt));
-// }
-// bool Atom::isSymmetryCopy() const
-// {
-// 	return impl()->mSymmetryCopy;
-// }
-// std::string Atom::symmetry() const
-// {
-// 	return clipper::Symop(impl()->mRTop).format() + "\n" + impl()->mRTop.format();
-// }
-bool Atom::isSymmetryCopy() const
 {
-	return mImpl_->mSymmetryCopy;
+	auto loc = location();
-}
+	loc += t;
+	loc.rotate(q);
-std::string Atom::symmetry() const
+	location(loc);
-{
-	return mImpl_->mSymmetryOperator;
-}
-// const clipper::RTop_orth& Atom::symop() const
-// {
-// 	return impl()->mRTop;
-// }
-const Compound &Atom::comp() const
-{
-	return impl()->comp();
 }
-bool Atom::isWater() const
+void Atom::translateRotateAndTranslate(Point t1, Quaternion q, Point t2)
 {
-	return impl()->isWater();
+	auto loc = location();
+	loc += t1;
+	loc.rotate(q);
+	loc += t2;
+	location(loc);
 }
 bool Atom::operator==(const Atom &rhs) const
 {
-	return impl() == rhs.impl() or
+	return mImpl == rhs.mImpl or
-	       (&impl()->mDb == &rhs.impl()->mDb and impl()->mID == rhs.impl()->mID);
+	       (&mImpl->mDb == &rhs.mImpl->mDb and mImpl->mID == rhs.mImpl->mID);
-}
-// clipper::Atom Atom::toClipper() const
-// {
-// 	return impl()->toClipper();
-// }
-// void Atom::calculateRadius(float resHigh, float resLow, float perc)
-// {
-// 	AtomShape shape(*this, resHigh, resLow, false);
-// 	impl()->mRadius = shape.radius();
-// 	// verbose
-// 	if (cif::VERBOSE > 1)
-// 		cout << "Calculated radius for " << AtomTypeTraits(impl()->mType).name() << " with charge " << charge() << " is " << impl()->mRadius << std::endl;
-// }
-float Atom::radius() const
-{
-	return impl()->mRadius;
-}
-int Atom::compare(const Atom &b) const
-{
-	return impl() == b.impl() ? 0 : impl()->compare(*b.impl());
 }
 void Atom::setID(int id)
 {
-	impl()->mID = std::to_string(id);
+	mImpl->mID = std::to_string(id);
 }
 std::ostream &operator<<(std::ostream &os, const Atom &atom)
@@ -797,66 +493,6 @@ std::ostream &operator<<(std::ostream &os, const Atom &atom)
 // --------------------------------------------------------------------
 // residue
-// First constructor used to be for waters only, but now accepts sugars as well.
-Residue::Residue(const Structure &structure, const std::string &compoundID,
-	const std::string &asymID, const std::string &authSeqID)
-	: mStructure(&structure)
-	, mCompoundID(compoundID)
-	, mAsymID(asymID)
-	, mAuthSeqID(authSeqID)
-{
-	for (auto &a : mStructure->atoms())
-	{
-		if (a.labelAsymID() != mAsymID or
-			a.labelCompID() != mCompoundID)
-			continue;
-		if (compoundID == "HOH")
-		{
-			if (not mAuthSeqID.empty() and a.authSeqID() != mAuthSeqID)
-				continue;
-		}
-		else
-		{
-			if (mSeqID > 0 and a.labelSeqID() != mSeqID)
-				continue;
-		}
-		mAtoms.push_back(a);
-	}
-	assert(not mAtoms.empty());
-}
-Residue::Residue(const Structure &structure, const std::string &compoundID, const std::string &asymID)
-	: Residue(structure, compoundID, asymID, 0, {})
-{
-}
-Residue::Residue(const Structure &structure, const std::string &compoundID,
-	const std::string &asymID, int seqID, const std::string &authSeqID)
-	: mStructure(&structure)
-	, mCompoundID(compoundID)
-	, mAsymID(asymID)
-	, mSeqID(seqID)
-	, mAuthSeqID(authSeqID)
-{
-	assert(mCompoundID != "HOH");
-	for (auto &a : mStructure->atoms())
-	{
-		if (mSeqID > 0 and a.labelSeqID() != mSeqID)
-			continue;
-		if (a.labelAsymID() != mAsymID or
-			a.labelCompID() != mCompoundID)
-			continue;
-		mAtoms.push_back(a);
-	}
-}
 Residue::Residue(Residue &&rhs)
 	: mStructure(rhs.mStructure)
 	, mCompoundID(std::move(rhs.mCompoundID))
@@ -865,13 +501,13 @@ Residue::Residue(Residue &&rhs)
 	, mAuthSeqID(rhs.mAuthSeqID)
 	, mAtoms(std::move(rhs.mAtoms))
 {
-	//std::cerr << "move constructor residue" << std::endl;
+	// std::cerr << "move constructor residue" << std::endl;
 	rhs.mStructure = nullptr;
 }
 Residue &Residue::operator=(Residue &&rhs)
 {
-	//std::cerr << "move assignment residue" << std::endl;
+	// std::cerr << "move assignment residue" << std::endl;
 	mStructure = rhs.mStructure;
 	rhs.mStructure = nullptr;
 	mCompoundID = std::move(rhs.mCompoundID);
@@ -885,7 +521,7 @@ Residue &Residue::operator=(Residue &&rhs)
 Residue::~Residue()
 {
-	//std::cerr << "~Residue" << std::endl;
+	// std::cerr << "~Residue" << std::endl;
 }
 std::string Residue::entityID() const
@@ -999,7 +635,7 @@ AtomView Residue::unique_atoms() const
 			firstAlt = alt;
 		else if (alt != firstAlt)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "skipping alternate atom " << atom << std::endl;
 			continue;
 		}
@@ -1145,11 +781,6 @@ std::ostream &operator<<(std::ostream &os, const Residue &res)
 // --------------------------------------------------------------------
 // monomer
-//Monomer::Monomer(Monomer&& rhs)
-//	: Residue(std::move(rhs)), mPolymer(rhs.mPolymer), mIndex(rhs.mIndex)
-//{
-//}
 Monomer::Monomer(const Polymer &polymer, size_t index, int seqID, const std::string &authSeqID, const std::string &compoundID)
 	: Residue(*polymer.structure(), compoundID, polymer.asymID(), seqID, authSeqID)
 	, mPolymer(&polymer)
@@ -1162,23 +793,11 @@ Monomer::Monomer(Monomer &&rhs)
 	, mPolymer(rhs.mPolymer)
 	, mIndex(rhs.mIndex)
 {
-	std::cerr << "move constructor monomer" << std::endl;
-	//	mStructure = rhs.mStructure;			rhs.mStructure = nullptr;
-	//	mCompoundID = std::move(rhs.mCompoundID);
-	//	mAsymID = std::move(rhs.mAsymID);
-	//	mSeqID = rhs.mSeqID;
-	//	mAtoms = std::move(rhs.mAtoms);
-	//
-	//	mPolymer = rhs.mPolymer; rhs.mPolymer = nullptr;
-	//	mIndex = rhs.mIndex;
 	rhs.mPolymer = nullptr;
 }
 Monomer &Monomer::operator=(Monomer &&rhs)
 {
-	std::cerr << "move assignment monomer" << std::endl;
 	Residue::operator=(std::move(rhs));
 	mPolymer = rhs.mPolymer;
 	rhs.mPolymer = nullptr;
@@ -1222,7 +841,7 @@ float Monomer::phi() const
 	}
 	catch (const std::exception &ex)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << ex.what() << std::endl;
 	}
@@ -1244,7 +863,7 @@ float Monomer::psi() const
 	}
 	catch (const std::exception &ex)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << ex.what() << std::endl;
 	}
@@ -1268,7 +887,7 @@ float Monomer::alpha() const
 	}
 	catch (const std::exception &ex)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << ex.what() << std::endl;
 	}
@@ -1296,7 +915,7 @@ float Monomer::kappa() const
 	}
 	catch (const std::exception &ex)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "When trying to calculate kappa for " << asymID() << ':' << seqID() << ": "
 					  << ex.what() << std::endl;
 	}
@@ -1319,7 +938,7 @@ float Monomer::tco() const
 	}
 	catch (const std::exception &ex)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "When trying to calculate tco for " << asymID() << ':' << seqID() << ": "
 					  << ex.what() << std::endl;
 	}
@@ -1338,7 +957,7 @@ float Monomer::omega() const
 	}
 	catch (const std::exception &ex)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "When trying to calculate omega for " << asymID() << ':' << seqID() << ": "
 					  << ex.what() << std::endl;
 	}
@@ -1409,7 +1028,7 @@ float Monomer::chi(size_t nr) const
 	}
 	catch (const std::exception &e)
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << e.what() << std::endl;
 		result = 0;
 	}
@@ -1550,94 +1169,6 @@ bool Monomer::isCis(const mmcif::Monomer &a, const mmcif::Monomer &b)
 // --------------------------------------------------------------------
 // polymer
-//
-//Polymer::iterator::iterator(const Polymer& p, uint32_t index)
-//	: mPolymer(&p), mIndex(index), mCurrent(p, index)
-//{
-//	auto& polySeq = mPolymer->mPolySeq;
-//
-//	if (index < polySeq.size())
-//	{
-//		int seqID;
-//		std::string asymID, monID;
-//		cif::tie(asymID, seqID, monID) =
-//			polySeq[mIndex].get("asym_id", "seq_id", "mon_id");
-//
-//		mCurrent = Monomer(*mPolymer, index, seqID, monID, "");
-//	}
-//}
-//
-//Monomer Polymer::operator[](size_t index) const
-//{
-//	if (index >= mPolySeq.size())
-//		throw out_of_range("Invalid index for residue in polymer");
-//
-//	std::string compoundID;
-//	int seqID;
-//
-//	auto r = mPolySeq[index];
-//
-//	cif::tie(seqID, compoundID) =
-//		r.get("seq_id", "mon_id");
-//
-//	return Monomer(const_cast<Polymer&>(*this), index, seqID, compoundID, "");
-//}
-//
-//Polymer::iterator::iterator(const iterator& rhs)
-//	: mPolymer(rhs.mPolymer), mIndex(rhs.mIndex), mCurrent(rhs.mCurrent)
-//{
-//}
-//
-//Polymer::iterator& Polymer::iterator::operator++()
-//{
-//	auto& polySeq = mPolymer->mPolySeq;
-//
-//	if (mIndex < polySeq.size())
-//		++mIndex;
-//
-//	if (mIndex < polySeq.size())
-//	{
-//		int seqID;
-//		std::string asymID, monID;
-//		cif::tie(asymID, seqID, monID) =
-//			polySeq[mIndex].get("asym_id", "seq_id", "mon_id");
-//
-//		mCurrent = Monomer(*mPolymer, mIndex, seqID, monID, "");
-//	}
-//
-//	return *this;
-//}
-//Polymer::Polymer(const Structure& s, const std::string& asymID)
-//	: mStructure(const_cast<Structure*>(&s)), mAsymID(asymID)
-//	, mPolySeq(s.category("pdbx_poly_seq_scheme").find(cif::Key("asym_id") == mAsymID))
-//{
-//	mEntityID = mPolySeq.front()["entity_id"].as<std::string>();
-//
-//#if DEBUG
-//	for (auto r: mPolySeq)
-//		assert(r["entity_id"] == mEntityID);
-//#endif
-//
-//}
-//Polymer::Polymer(Polymer&& rhs)
-//	: std::vector<Monomer>(std::move(rhs))
-//	, mStructure(rhs.mStructure)
-//	, mEntityID(std::move(rhs.mEntityID)), mAsymID(std::move(rhs.mAsymID)), mPolySeq(std::move(rhs.mPolySeq))
-//{
-//	rhs.mStructure = nullptr;
-//}
-//
-//Polymer& Polymer::operator=(Polymer&& rhs)
-//{
-//	std::vector<Monomer>::operator=(std::move(rhs));
-//	mStructure = rhs.mStructure;			rhs.mStructure = nullptr;
-//	mEntityID = std::move(rhs.mEntityID);
-//	mAsymID = std::move(rhs.mAsymID);
-//	mPolySeq = std::move(rhs.mPolySeq);
-//	return *this;
-//}
 Polymer::Polymer(const Structure &s, const std::string &entityID, const std::string &asymID)
 	: mStructure(const_cast<Structure *>(&s))
@@ -1663,7 +1194,7 @@ Polymer::Polymer(const Structure &s, const std::string &entityID, const std::str
 			ix[seqID] = index;
 			emplace_back(*this, index, seqID, authSeqID, compoundID);
 		}
-		else if (cif::VERBOSE)
+		else if (cif::VERBOSE > 0)
 		{
 			Monomer m{*this, index, seqID, authSeqID, compoundID};
 			std::cerr << "Dropping alternate residue " << m << std::endl;
@@ -1745,7 +1276,7 @@ File::~File()
 	delete mImpl;
 }
-cif::Datablock& File::createDatablock(const std::string_view name)
+cif::Datablock &File::createDatablock(const std::string_view name)
 {
 	auto db = new cif::Datablock(name);
@@ -1808,7 +1339,7 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 		cif::tie(model_nr) = atomCat.front().get("pdbx_PDB_model_num");
 		if (model_nr and *model_nr != mModelNr)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << std::endl;
 			mModelNr = *model_nr;
 			loadAtomsForModel(options);
@@ -1816,7 +1347,10 @@ Structure::Structure(File &f, size_t modelNr, StructureOpenOptions options)
 	}
 	if (mAtoms.empty())
-		std::cerr << "Warning: no atoms loaded" << std::endl;
+	{
+		if (cif::VERBOSE >= 0)
+			std::cerr << "Warning: no atoms loaded" << std::endl;
+	}
 	else
 		loadData();
 }
@@ -1839,11 +1373,10 @@ void Structure::loadAtomsForModel(StructureOpenOptions options)
 		if ((options bitand StructureOpenOptions::SkipHydrogen) and type_symbol == "H")
 			continue;
-		mAtoms.emplace_back(new AtomImpl(*db, id, a));
+		mAtoms.emplace_back(std::make_shared<Atom::AtomImpl>(*db, id, a));
 	}
 }
 Structure::Structure(const Structure &s)
 	: mFile(s.mFile)
 	, mModelNr(s.mModelNr)
@@ -1884,7 +1417,7 @@ void Structure::loadData()
 			r.get("asym_id", "mon_id", "pdb_seq_num");
 		if (monID == "HOH")
-			mNonPolymers.emplace_back(*this, monID, asymID, pdbSeqNum);
+			mNonPolymers.emplace_back(*this, monID, asymID, 0, pdbSeqNum);
 		else if (mNonPolymers.empty() or mNonPolymers.back().asymID() != asymID)
 			mNonPolymers.emplace_back(*this, monID, asymID);
 	}
@@ -1897,7 +1430,43 @@ void Structure::loadData()
 		cif::tie(asymID, monID, num) =
 			r.get("asym_id", "mon_id", "num");
-		mBranchResidues.emplace_back(*this, monID, asymID, num);
+		mBranchResidues.emplace_back(*this, monID, asymID, 0, num);
+	}
+	// place atoms in residues
+	using key_type = std::tuple<std::string, std::string, int>;
+	using map_type = std::map<key_type, Residue *>;
+	map_type resMap;
+	for (auto &poly : mPolymers)
+	{
+		for (auto &res : poly)
+			resMap[{res.asymID(), res.compoundID(), res.seqID()}] = &res;
+	}
+	for (auto &res : mNonPolymers)
+		resMap[{res.asymID(), res.compoundID(), (res.isWater() ? std::stoi(res.mAuthSeqID) : res.seqID())}] = &res;
+	for (auto &res : mBranchResidues)
+		resMap[{res.asymID(), res.compoundID(), res.seqID()}] = &res;
+	for (auto &atom : mAtoms)
+	{
+		key_type k(atom.labelAsymID(), atom.labelCompID(), atom.isWater() ? std::stoi(atom.authSeqID()) : atom.labelSeqID());
+		auto ri = resMap.find(k);
+		if (ri == resMap.end())
+		{
+			if (cif::VERBOSE > 0)
+				std::cerr << "Missing residue for atom " << atom << std::endl;
+			assert(false);
+			continue;
+		}
+		ri->second->addAtom(atom);
 	}
 }
@@ -1948,7 +1517,7 @@ AtomView Structure::waters() const
 	for (auto &a : mAtoms)
 	{
-		if (a.property<std::string>("label_entity_id") == waterEntityID)
+		if (a.get_property<std::string>("label_entity_id") == waterEntityID)
 			result.push_back(a);
 	}
@@ -2021,7 +1590,7 @@ Atom Structure::getAtomByPositionAndType(Point p, std::string_view type, std::st
 		if (a.labelCompID() != res_type)
 			continue;
 		if (a.labelAtomID() != type)
 			continue;
@@ -2077,7 +1646,7 @@ const Residue &Structure::getResidue(const std::string &asymID, const std::strin
 Residue &Structure::getResidue(const std::string &asymID, const std::string &compID, int seqID)
 {
-	return const_cast<Residue&>(const_cast<Structure const&>(*this).getResidue(asymID, compID, seqID));
+	return const_cast<Residue &>(const_cast<Structure const &>(*this).getResidue(asymID, compID, seqID));
 }
 const Residue &Structure::getResidue(const std::string &asymID) const
@@ -2095,7 +1664,7 @@ const Residue &Structure::getResidue(const std::string &asymID) const
 Residue &Structure::getResidue(const std::string &asymID)
 {
-	return const_cast<Residue&>(const_cast<Structure const&>(*this).getResidue(asymID));
+	return const_cast<Residue &>(const_cast<Structure const &>(*this).getResidue(asymID));
 }
 Residue &Structure::getResidue(const mmcif::Atom &atom)
@@ -2291,8 +1860,7 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
 	auto r = chemComp.find(cif::Key("id") == compoundID);
 	if (r.empty())
 	{
-		chemComp.emplace({
+		chemComp.emplace({{"id", compoundID},
-			{"id", compoundID},
 			{"name", compound->name()},
 			{"formula", compound->formula()},
 			{"formula_weight", compound->formulaWeight()},
@@ -2308,19 +1876,17 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
 		{
 			entity_id = pdbxEntityNonpoly.find1<std::string>("comp_id"_key == compoundID, "entity_id");
 		}
-		catch(const std::exception& ex)
+		catch (const std::exception &ex)
 		{
 			auto &entity = db["entity"];
 			entity_id = entity.getUniqueID("");
-			entity.emplace({
+			entity.emplace({{"id", entity_id},
-				{"id", entity_id},
 				{"type", "non-polymer"},
 				{"pdbx_description", compound->name()},
 				{"formula_weight", compound->formulaWeight()}});
-			pdbxEntityNonpoly.emplace({
+			pdbxEntityNonpoly.emplace({{"entity_id", entity_id},
-				{"entity_id", entity_id},
 				{"name", compound->name()},
 				{"comp_id", compoundID}});
 		}
@@ -2329,65 +1895,6 @@ std::string Structure::insertCompound(const std::string &compoundID, bool isEnti
 	return entity_id;
 }
-// // --------------------------------------------------------------------
-// Structure::residue_iterator::residue_iterator(const Structure* s, poly_iterator polyIter, size_t polyResIndex, size_t nonPolyIndex)
-// 	: mStructure(*s), mPolyIter(polyIter), mPolyResIndex(polyResIndex), mNonPolyIndex(nonPolyIndex)
-// {
-// 	while (mPolyIter != mStructure.mPolymers.end() and mPolyResIndex == mPolyIter->size())
-// 		++mPolyIter;
-// }
-// auto Structure::residue_iterator::operator*() -> reference
-// {
-// 	if (mPolyIter != mStructure.mPolymers.end())
-// 		return (*mPolyIter)[mPolyResIndex];
-// 	else
-// 		return mStructure.mNonPolymers[mNonPolyIndex];
-// }
-// auto Structure::residue_iterator::operator->() -> pointer
-// {
-// 	if (mPolyIter != mStructure.mPolymers.end())
-// 		return &(*mPolyIter)[mPolyResIndex];
-// 	else
-// 		return &mStructure.mNonPolymers[mNonPolyIndex];
-// }
-// Structure::residue_iterator& Structure::residue_iterator::operator++()
-// {
-// 	if (mPolyIter != mStructure.mPolymers.end())
-// 	{
-// 		++mPolyResIndex;
-// 		if (mPolyResIndex >= mPolyIter->size())
-// 		{
-// 			++mPolyIter;
-// 			mPolyResIndex = 0;
-// 		}
-// 	}
-// 	else
-// 		++mNonPolyIndex;
-// 	return *this;
-// }
-// Structure::residue_iterator Structure::residue_iterator::operator++(int)
-// {
-// 	auto result = *this;
-// 	operator++();
-// 	return result;
-// }
-// bool Structure::residue_iterator::operator==(const Structure::residue_iterator& rhs) const
-// {
-// 	return mPolyIter == rhs.mPolyIter and mPolyResIndex == rhs.mPolyResIndex and mNonPolyIndex == rhs.mNonPolyIndex;
-// }
-// bool Structure::residue_iterator::operator!=(const Structure::residue_iterator& rhs) const
-// {
-// 	return mPolyIter != rhs.mPolyIter or mPolyResIndex != rhs.mPolyResIndex or mNonPolyIndex != rhs.mNonPolyIndex;
-// }
 // --------------------------------------------------------------------
 void Structure::removeAtom(Atom &a)
@@ -2434,7 +1941,7 @@ void Structure::swapAtoms(Atom &a1, Atom &a2)
 	auto l2 = r2["label_atom_id"];
 	l1.swap(l2);
-	a1.impl()->swapAtomLabels(*a2.impl());
+	std::swap(a1.mImpl->mAtomID, a2.mImpl->mAtomID);
 	auto l3 = r1["auth_atom_id"];
 	auto l4 = r2["auth_atom_id"];
@@ -2524,7 +2031,8 @@ void Structure::changeResidue(Residue &res, const std::string &newCompound,
 			{ return a.labelAtomID() == a1; });
 		if (i == atoms.end())
 		{
-			std::cerr << "Missing atom for atom ID " << a1 << std::endl;
+			if (cif::VERBOSE >= 0)
+				std::cerr << "Missing atom for atom ID " << a1 << std::endl;
 			continue;
 		}
@@ -2564,50 +2072,47 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 	auto &struct_asym = db["struct_asym"];
 	std::string asym_id = struct_asym.getUniqueID();
-	struct_asym.emplace({
+	struct_asym.emplace({{"id", asym_id},
-		{ "id", asym_id },
+		{"pdbx_blank_PDB_chainid_flag", "N"},
-		{ "pdbx_blank_PDB_chainid_flag", "N" },
+		{"pdbx_modified", "N"},
-		{ "pdbx_modified", "N" },
+		{"entity_id", entity_id},
-		{ "entity_id", entity_id },
+		{"details", "?"}});
-		{ "details", "?" }
-	});
 	std::string comp_id = db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
 	auto &atom_site = db["atom_site"];
-	for (auto& atom: atoms)
+	auto &res = mNonPolymers.emplace_back(*this, comp_id, asym_id);
+	for (auto &atom : atoms)
 	{
 		auto atom_id = atom_site.getUniqueID("");
-		auto &&[row, inserted ] = atom_site.emplace({
+		auto &&[row, inserted] = atom_site.emplace({{"group_PDB", atom.get_property<std::string>("group_PDB")},
-			{ "group_PDB",			atom.property<std::string>("group_PDB") },
+			{"id", atom_id},
-			{ "id",					atom_id },
+			{"type_symbol", atom.get_property<std::string>("type_symbol")},
-			{ "type_symbol",		atom.property<std::string>("type_symbol") },
+			{"label_atom_id", atom.get_property<std::string>("label_atom_id")},
-			{ "label_atom_id",		atom.property<std::string>("label_atom_id") },
+			{"label_alt_id", atom.get_property<std::string>("label_alt_id")},
-			{ "label_alt_id",		atom.property<std::string>("label_alt_id") },
+			{"label_comp_id", comp_id},
-			{ "label_comp_id",		comp_id },
+			{"label_asym_id", asym_id},
-			{ "label_asym_id",		asym_id },
+			{"label_entity_id", entity_id},
-			{ "label_entity_id",	entity_id },
+			{"label_seq_id", "."},
-			{ "label_seq_id",		"." },
+			{"pdbx_PDB_ins_code", ""},
-			{ "pdbx_PDB_ins_code",	"" },
+			{"Cartn_x", atom.get_property<std::string>("Cartn_x")},
-			{ "Cartn_x",			atom.property<std::string>("Cartn_x") },
+			{"Cartn_y", atom.get_property<std::string>("Cartn_y")},
-			{ "Cartn_y",			atom.property<std::string>("Cartn_y") },
+			{"Cartn_z", atom.get_property<std::string>("Cartn_z")},
-			{ "Cartn_z",			atom.property<std::string>("Cartn_z") },
+			{"occupancy", atom.get_property<std::string>("occupancy")},
-			{ "occupancy",			atom.property<std::string>("occupancy") },
+			{"B_iso_or_equiv", atom.get_property<std::string>("B_iso_or_equiv")},
-			{ "B_iso_or_equiv",		atom.property<std::string>("B_iso_or_equiv") },
+			{"pdbx_formal_charge", atom.get_property<std::string>("pdbx_formal_charge")},
-			{ "pdbx_formal_charge",	atom.property<std::string>("pdbx_formal_charge") },
+			{"auth_seq_id", ""},
-			{ "auth_seq_id",		"" },
+			{"auth_comp_id", comp_id},
-			{ "auth_comp_id",		comp_id },
+			{"auth_asym_id", asym_id},
-			{ "auth_asym_id",		asym_id },
+			{"auth_atom_id", atom.get_property<std::string>("label_atom_id")},
-			{ "auth_atom_id",		atom.property<std::string>("label_atom_id") },
+			{"pdbx_PDB_model_num", 1}});
-			{ "pdbx_PDB_model_num",	1 }
-		});
+		auto &newAtom = mAtoms.emplace_back(std::make_shared<Atom::AtomImpl>(db, atom_id, row));
+		res.addAtom(newAtom);
-		mAtoms.emplace_back(new AtomImpl(db, atom_id, row));
+	}
-	}
-	mNonPolymers.emplace_back(*this, comp_id, asym_id);
 	return asym_id;
 }
@@ -2685,7 +2190,7 @@ void Structure::cleanupEmptyCategories()
 		{
 			// is this correct?
 			std::set<std::string> asym_ids;
-			for (const auto &[ asym_id ] : db["pdbx_branch_scheme"].find<std::string>("entity_id"_key == id, "asym_id"))
+			for (const auto &[asym_id] : db["pdbx_branch_scheme"].find<std::string>("entity_id"_key == id, "asym_id"))
 				asym_ids.insert(asym_id);
 			count = asym_ids.size();
 		}
@@ -2696,14 +2201,26 @@ void Structure::cleanupEmptyCategories()
 void Structure::translate(Point t)
 {
-	for (auto& a: mAtoms)
+	for (auto &a : mAtoms)
 		a.translate(t);
 }
 void Structure::rotate(Quaternion q)
 {
-	for (auto& a: mAtoms)
+	for (auto &a : mAtoms)
 		a.rotate(q);
 }
+void Structure::translateAndRotate(Point t, Quaternion q)
+{
+	for (auto &a : mAtoms)
+		a.translateAndRotate(t, q);
+}
+void Structure::translateRotateAndTranslate(Point t1, Quaternion q, Point t2)
+{
+	for (auto &a : mAtoms)
+		a.translateRotateAndTranslate(t1, q, t2);
+}
 } // namespace mmcif
--- a/src/TlsParser.cpp
+++ b/src/TlsParser.cpp
@@ -248,7 +248,7 @@ struct TLSSelectionNot : public TLSSelection
 		for (auto& r: residues)
 			r.selected = not r.selected;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "NOT" << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -267,7 +267,7 @@ struct TLSSelectionAll : public TLSSelection
 		for (auto& r: residues)
 			r.selected = true;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "ALL" << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -287,7 +287,7 @@ struct TLSSelectionChain : public TLSSelectionAll
 		for (auto& r: residues)
 			r.selected = allChains or r.chainID == m_chain;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "CHAIN " << m_chain << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -307,7 +307,7 @@ struct TLSSelectionResID : public TLSSelectionAll
 		for (auto& r: residues)
 			r.selected = r.seqNr == m_seq_nr and r.iCode == m_icode;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "ResID " << m_seq_nr << (m_icode ? std::string { m_icode} : "") << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -331,7 +331,7 @@ struct TLSSelectionRangeSeq : public TLSSelectionAll
 						  (r.seqNr <= m_last or m_last == kResidueNrWildcard));
 		}
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Range " << m_first << ':' << m_last << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -374,7 +374,7 @@ struct TLSSelectionRangeID : public TLSSelectionAll
 			}
 		}
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Through " << m_first << ':' << m_last << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -407,7 +407,7 @@ struct TLSSelectionUnion : public TLSSelection
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 			ri->selected = ai->selected or bi->selected;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Union" << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -440,7 +440,7 @@ struct TLSSelectionIntersection : public TLSSelection
 		for (auto ai = a.begin(), bi = b.begin(), ri = residues.begin(); ri != residues.end(); ++ai, ++bi, ++ri)
 			ri->selected = ai->selected and bi->selected;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Intersection" << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -462,7 +462,7 @@ struct TLSSelectionByName : public TLSSelectionAll
 		for (auto& r: residues)
 			r.selected = r.name == m_name;
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Name " << m_name << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -488,7 +488,7 @@ struct TLSSelectionByElement : public TLSSelectionAll
 		for (auto& r: residues)
 			r.selected = iequals(r.name, m_element);
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 		{
 			std::cout << std::string(indentLevel * 2, ' ') << "Element " << m_element << std::endl;
 			DumpSelection(residues, indentLevel);
@@ -890,7 +890,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::Parse()
 	Match(pt_EOLN);
-	if (extraParenthesis)
+	if (extraParenthesis and cif::VERBOSE > 0)
 		std::cerr << "WARNING: too many closing parenthesis in TLS selection statement" << std::endl;
 	return result;
@@ -931,7 +931,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
 		case '(':
 			Match('(');
 			result = ParseAtomSelection();
-			if (m_lookahead == pt_EOLN)
+			if (m_lookahead == pt_EOLN and cif::VERBOSE > 0)
 				std::cerr << "WARNING: missing closing parenthesis in TLS selection statement" << std::endl;
 			else
 				Match(')');
@@ -1033,7 +1033,7 @@ TLSSelectionPtr TLSSelectionParserImplPhenix::ParseFactor()
 					result.reset(new TLSSelectionRangeID(from, to, icode_from, icode_to));
 				else
 				{
-					if (cif::VERBOSE and (icode_from or icode_to))
+					if (cif::VERBOSE > 0 and (icode_from or icode_to))
 						std::cerr << "Warning, ignoring insertion codes" << std::endl;
 					result.reset(new TLSSelectionRangeSeq(from, to));
@@ -1231,7 +1231,8 @@ TLSSelectionPtr TLSSelectionParserImplBuster::ParseGroup()
 				std::tie(chain2, seqNr2) = ParseAtom();
 				if (chain1 != chain2)
 				{
-					std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
+					if (cif::VERBOSE > 0)
+						std::cerr << "Warning, ranges over multiple chains detected" << std::endl;
 					TLSSelectionPtr sc1(new TLSSelectionChain(chain1));
 					TLSSelectionPtr sr1(new TLSSelectionRangeSeq(seqNr1, kResidueNrWildcard));
@@ -1289,7 +1290,7 @@ std::tuple<std::string,int> TLSSelectionParserImplBuster::ParseAtom()
 			Match(':');
 			std::string atom = m_value_s;
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Warning: ignoring atom ID '" << atom << "' in TLS selection" << std::endl;
 			Match(bt_IDENT);
@@ -1810,7 +1811,8 @@ class TLSSelectionParser
 		}
 		catch (const std::exception& ex)
 		{
-			std::cerr << "ParseError: " << ex.what() << std::endl;
+			if (cif::VERBOSE >= 0)
+				std::cerr << "ParseError: " << ex.what() << std::endl;
 		}
 		return result;
@@ -1834,14 +1836,14 @@ TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::str
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 		}
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to PHENIX" << std::endl;
 			result = phenix.Parse(selection);
 		}
@@ -1852,35 +1854,35 @@ TLSSelectionPtr ParseSelectionDetails(const std::string& program, const std::str
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to BUSTER" << std::endl;
 			result = buster.Parse(selection);
 		}
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 		}
 	}
 	else
 	{
-		if (cif::VERBOSE)
+		if (cif::VERBOSE > 0)
 			std::cerr << "No known program specified, trying PHENIX" << std::endl;
 		result = phenix.Parse(selection);
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to BUSTER" << std::endl;
 			result = buster.Parse(selection);
 		}
 		if (not result)
 		{
-			if (cif::VERBOSE)
+			if (cif::VERBOSE > 0)
 				std::cerr << "Falling back to old BUSTER" << std::endl;
 			result = busterOld.Parse(selection);
 		}

--- a/test/structure-test.cpp
+++ b/test/structure-test.cpp
@@ -179,3 +179,23 @@ _struct_asym.details                       ?
 				<< structure.getFile().data() << std::endl;
 	}
 }
+// // --------------------------------------------------------------------
+// BOOST_AUTO_TEST_CASE(test_load_1)
+// {
+// 	mmcif::File cf(gTestDir / "5v3g.cif.gz");
+// 	mmcif::Structure s(cf);
+// 	for (auto &poly : s.polymers())
+// 	{
+// 		std::cout << std::string(80, '=') << std::endl;
+// 		for (auto &res : poly)
+// 		{
+// 			std::cout << res << std::endl;
+// 			for (auto &atom : res.atoms())
+// 				std::cout << "  " << atom << std::endl;
+// 		}
+// 	}
+// }