update changelog

This reverts commit 07a180991e.

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")
 
@@ -37,17 +37,16 @@ include(CheckIncludeFiles)
 include(CheckLibraryExists)
 include(CMakePackageConfigHelpers)
 include(Dart)
-include(FindFilesystem)
 include(GenerateExportHeader)
 
 set(CXX_EXTENSIONS OFF)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
 find_package(Filesystem REQUIRED)
 
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-	# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
 	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
 elseif(MSVC)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
@@ -122,22 +121,6 @@ if(MSVC)
 		message(STATUS "The library and auxiliary files will be installed in $ENV{LOCALAPPDATA}/${PROJECT_NAME}")
 		set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}/${PROJECT_NAME}" CACHE PATH "..." FORCE)
 	endif()
-
-	# Find out the processor type for the target
-	if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "AMD64")
-		set(COFF_TYPE "x64")
-	elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "i386")
-		set(COFF_TYPE "x86")
-	elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "ARM64")
-		set(COFF_TYPE "arm64")
-	else()
-		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()
 
 if(UNIX AND NOT APPLE AND NOT BUILD_FOR_CCP4 AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
@@ -151,12 +134,12 @@ 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)
-		option(CIFPP_USE_RSRC "Use mrc to create resources" ON)
+	if(MRC_FOUND)
+		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")
@@ -177,25 +160,18 @@ 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::ZLIB)
 endif()
 
+include(FindFilesystem)
+list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPFS_LIBRARY})
+
+include(FindAtomic)
+list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPATOMIC_LIBRARY})
+
 # Create a revision file, containing the current git version info
-
-include(GetGitRevisionDescription)
-option(GENERATE_CUSTOM_VERSION "Generate a custom version string" OFF)
-if(GIT-NOTFOUND OR HEAD-HASH-NOTFOUND OR NOT GENERATE_CUSTOM_VERSION)
-    get_git_head_revision(REFSPEC COMMITHASH)
-
-	# Generate our own version string
-	git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
-else()
-    SET(BUILD_VERSION_STRING ${PROJECT_VERSION})
-endif()
-
-# generate version.h
-string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
-configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
+include(VersionString)
+write_version_header("LibCIFPP")
 
 # SymOp data table
 if(CIFPP_RECREATE_SYMOP_DATA)
@@ -203,7 +179,7 @@ if(CIFPP_RECREATE_SYMOP_DATA)
 
 	add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp")
 
-	target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
+	target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} ${CIFPP_REQUIRED_LIBRARIES})
 	if(Boost_INCLUDE_DIR)
 		target_include_directories(symop-map-generator PUBLIC ${Boost_INCLUDE_DIR})
 	endif()
@@ -274,7 +250,8 @@ target_include_directories(cifpp
 	${CMAKE_BINARY_DIR}
 )
 
-target_link_libraries(cifpp Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
+target_link_libraries(cifpp PUBLIC Threads::Threads Boost::regex Boost::iostreams ${CIFPP_REQUIRED_LIBRARIES})
+# target_link_libraries(cifpp PRIVATE)
 
 if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
     target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
@@ -334,6 +311,13 @@ install(TARGETS cifpp
 	RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 	INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
+if(MSVC AND BUILD_SHARED_LIBS)
+	install(
+		FILES $<TARGET_PDB_FILE:${PROJECT_NAME}>
+		DESTINATION ${CMAKE_INSTALL_LIBDIR}
+		OPTIONAL)
+endif()
+
 install(EXPORT cifppTargets
 	FILE "cifppTargets.cmake"
 	NAMESPACE cifpp::
@@ -407,13 +391,6 @@ 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 ${CMAKE_CURRENT_BINARY_DIR}/cifpp_test_rsrc.obj)
-	endif()
-
 	list(APPEND CIFPP_tests
 		# pdb2cif
 		rename-compound
@@ -424,15 +401,19 @@ if(CIFPP_BUILD_TESTS)
 		set(CIFPP_TEST "${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
 			${CMAKE_CURRENT_BINARY_DIR}  # for config.h
 		)
 
-		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES} ${BZip2_LIBRARIES})
-	
+		target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp )
+
+		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)

Config.cmake.in

@@ -1,10 +1,10 @@
 @PACKAGE_INIT@
 
 include(CMakeFindDependencyMacro)
-find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_options)
+find_dependency(Threads)
+find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex)
 if(NOT WIN32)
 find_dependency(ZLIB)
-find_dependency(BZip2)
 endif()
 
 INCLUDE("${CMAKE_CURRENT_LIST_DIR}/cifppTargets.cmake")

changelog

@@ -1,3 +1,16 @@
+Version 3.0.3
+- Better configuration checks, for atomic e.g.
+- Fixed a problem introduced in refactoring mmcif::Atom
+- Version string creation
+
+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.

cmake/FindAtomic.cmake

@@ -0,0 +1,64 @@
+# Simple check to see if we need a library for std::atomic
+
+if(TARGET std::atomic)
+	return()
+endif()
+
+cmake_minimum_required(VERSION 3.10)
+
+include(CMakePushCheckState)
+include(CheckIncludeFileCXX)
+include(CheckCXXSourceRuns)
+
+cmake_push_check_state()
+
+set(CMAKE_CXX_STANDARD 17)
+
+check_include_file_cxx("atomic" _CXX_ATOMIC_HAVE_HEADER)
+mark_as_advanced(_CXX_ATOMIC_HAVE_HEADER)
+
+set(code [[
+#include <atomic>
+int main(int argc, char** argv) {
+  std::atomic<long long> s;
+  ++s;
+  return 0;
+}
+]])
+
+check_cxx_source_runs("${code}" _CXX_ATOMIC_BUILTIN)
+
+if(_CXX_ATOMIC_BUILTIN)
+	set(_found 1)
+else()
+  list(APPEND CMAKE_REQUIRED_LIBRARIES atomic)
+  list(APPEND FOLLY_LINK_LIBRARIES atomic)
+
+  check_cxx_source_runs("${code}" _CXX_ATOMIC_LIB_NEEDED)
+  if (NOT _CXX_ATOMIC_LIB_NEEDED)
+    message(FATAL_ERROR "unable to link C++ std::atomic code: you may need \
+      to install GNU libatomic")
+  else()
+	set(_found 1)
+  endif()
+endif()
+
+if(_found)
+	add_library(std::atomic INTERFACE IMPORTED)
+	set_property(TARGET std::atomic APPEND PROPERTY INTERFACE_COMPILE_FEATURES cxx_std_14)
+
+	if(_CXX_ATOMIC_BUILTIN)
+		# Nothing to add...
+	elseif(_CXX_ATOMIC_LIB_NEEDED)
+		set_target_properties(std::atomic PROPERTIES IMPORTED_LIBNAME atomic)
+		set(STDCPPATOMIC_LIBRARY atomic)
+	endif()
+endif()
+
+cmake_pop_check_state()
+
+set(Atomic_FOUND ${_found} CACHE BOOL "TRUE if we can run a program using std::atomic" FORCE)
+
+if(Atomic_FIND_REQUIRED AND NOT Atomic_FOUND)
+    message(FATAL_ERROR "Cannot run simple program using std::atomic")
+endif()

cmake/FindFilesystem.cmake

@@ -59,8 +59,10 @@ if(_found)
 		# Nothing to add...
 	elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED)
 		set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME stdc++fs)
+		set(STDCPPFS_LIBRARY stdc++fs)
 	elseif(CXX_FILESYSTEM_CPPFS_NEEDED)
 		set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME c++fs)
+		set(STDCPPFS_LIBRARY c++fs)
 	endif()
 endif()
 

cmake/VersionString.cmake

@@ -0,0 +1,77 @@
+# SPDX-License-Identifier: BSD-2-Clause
+
+# Copyright (c) 2021 NKI/AVL, Netherlands Cancer Institute
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+cmake_minimum_required(VERSION 3.15)
+
+# Create a revision file, containing the current git version info, if any
+function(write_version_header)
+	include(GetGitRevisionDescription)
+	if(NOT(GIT-NOTFOUND OR HEAD-HASH-NOTFOUND))
+		git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
+
+		if(BUILD_VERSION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?")
+			set(BUILD_GIT_TAGREF "${CMAKE_MATCH_2}")
+			if(CMAKE_MATCH_3)
+				set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}*")
+			else()
+				set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}")
+			endif()
+		endif()
+	else()
+		set(BUILD_VERSION_STRING "no git info available")
+	endif()
+
+	include_directories(${CMAKE_BINARY_DIR} PRIVATE)
+	string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
+
+	if(ARGC GREATER 0)
+		set(VAR_PREFIX "${ARGV0}")
+	endif()
+
+	file(WRITE "${CMAKE_BINARY_DIR}/revision.hpp.in" [[// Generated revision file
+
+#pragma once
+
+#include <ostream>
+
+const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@";
+const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@";
+const char k@VAR_PREFIX@VersionGitTag[] = "@BUILD_GIT_TAGREF@";
+const char k@VAR_PREFIX@BuildInfo[] = "@BUILD_VERSION_STRING@";
+const char k@VAR_PREFIX@BuildDate[] = "@BUILD_DATE_TIME@";
+
+inline void write_version_string(std::ostream &os, bool verbose)
+{
+	os << k@VAR_PREFIX@ProjectName << " version " << k@VAR_PREFIX@VersionNumber << std::endl;
+	if (verbose)
+	{
+		os << "build: " << k@VAR_PREFIX@BuildInfo << ' ' << k@VAR_PREFIX@BuildDate << std::endl;
+		if (k@VAR_PREFIX@VersionGitTag[0] != 0)
+			os << "git tag: " << k@VAR_PREFIX@VersionGitTag << std::endl;
+	}
+}
+]])
+	configure_file("${CMAKE_BINARY_DIR}/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
+endfunction()
+

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;

include/cif++/CifUtils.hpp

@@ -26,11 +26,7 @@
 
 #pragma once
 
-#include <cassert>
 #include <filesystem>
-#include <iostream>
-#include <list>
-#include <memory>
 #include <set>
 #include <vector>
 

include/cif++/Point.hpp

@@ -371,8 +371,7 @@ auto DistancePointToLine(const PointF<F> &l1, const PointF<F> &l2, const PointF<
 // a random direction with a distance randomly chosen from a normal
 // distribution with a stddev of offset.
 
-template <typename F>
-PointF<F> Nudge(PointF<F> p, F offset);
+Point Nudge(Point p, float offset);
 
 // --------------------------------------------------------------------
 // We use quaternions to do rotations in 3d space

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; }
 

include/cif++/Structure.hpp

@@ -60,30 +60,108 @@ 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(const Atom &rhs);
+
+	Atom() {}
+
+	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 mImpl_ != nullptr; }
+	explicit operator bool() const { return (bool)mImpl; }
 
 	// 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);
+	Atom &operator=(const Atom &rhs) = default;
 
-	const std::string &id() const;
-	AtomType type() const;
+	template <typename T>
+	T get_property(const std::string_view name) const;
 
-	Point location() const;
-	void location(Point p);
+	void set_property(const std::string_view name, const std::string &value)
+	{
+		if (not mImpl)
+			throw std::logic_error("Error trying to modify an uninitialized atom");
+		mImpl->set_property(name, 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)
+	{
+		set_property(name, std::to_string(value));
+	}
+
+	const std::string &id() const			{ return impl().mID; }
+	AtomType type() const					{ return impl().mType; }
+
+	Point location() const					{ return impl().mLocation; }
+	void location(Point p)
+	{
+		if (not mImpl)
+			throw std::logic_error("Error trying to modify an uninitialized atom");
+		mImpl->moveTo(p);
+	}
 
 	/// \brief Translate the position of this atom by \a t
 	void translate(Point t);
@@ -91,47 +169,40 @@ 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 impl().mRow; }
 	const cif::Row getRowAniso() const;
 
-	// Atom symmetryCopy(const Point& d, const clipper::RTop_orth& rt);
-	bool isSymmetryCopy() const;
-	std::string symmetry() const;
-	// const clipper::RTop_orth& symop() const;
+	bool isSymmetryCopy() const				{ return impl().mSymmetryCopy; }
+	std::string symmetry() const			{ return impl().mSymmetryOperator; }
 
-	const Compound &comp() const;
-	bool isWater() const;
+	const Compound &comp() const			{ return impl().comp(); }
+	bool isWater() const					{ return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
 	int charge() const;
 
 	float uIso() const;
-	bool getAnisoU(float anisou[6]) const;
+	bool getAnisoU(float anisou[6]) const	{ return impl().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;
-	std::string labelCompID() const;
-	std::string labelAsymID() const;
+	const std::string& labelAtomID() const		{ return impl().mAtomID; }
+	const std::string& labelCompID() const		{ return impl().mCompID; }
+	const std::string& labelAsymID() const		{ return impl().mAsymID; }
 	std::string labelEntityID() const;
-	int labelSeqID() const;
-	std::string labelAltID() const;
-	bool isAlternate() const;
+	int labelSeqID() const						{ return impl().mSeqID; }
+	const std::string& labelAltID() const		{ return impl().mAltID; }
+	bool isAlternate() const					{ return not impl().mAltID.empty(); }
 
 	std::string authAtomID() const;
 	std::string authCompID() const;
 	std::string authAsymID() const;
-	std::string authSeqID() const;
+	const std::string& authSeqID() const		{ return impl().mAuthSeqID; }
 	std::string pdbxAuthInsCode() const;
 	std::string pdbxAuthAltID() const;
 
@@ -140,13 +211,6 @@ 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 +222,10 @@ 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 impl().compare(*b.mImpl); }
 
 	bool operator<(const Atom &rhs) const
 	{
@@ -172,14 +236,38 @@ class Atom
 
   private:
 	friend class Structure;
+
 	void setID(int id);
 
-	AtomImpl *impl();
-	const AtomImpl *impl() const;
+	const AtomImpl &impl() const
+	{
+		if (not mImpl)
+			throw std::runtime_error("Uninitialized atom, not found?");
+		return *mImpl;
+	}
 
-	struct AtomImpl *mImpl_;
+	std::shared_ptr<AtomImpl> mImpl;
 };
 
+template <>
+inline std::string Atom::get_property<std::string>(const std::string_view name) const
+{
+	return impl().get_property(name);
+}
+
+template <>
+inline int Atom::get_property<int>(const std::string_view name) const
+{
+	auto v = impl().get_property(name);
+	return v.empty() ? 0 : stoi(v);
+}
+
+template <>
+inline float Atom::get_property<float>(const std::string_view name) const
+{
+	return stof(impl().get_property(name));
+}
+
 inline void swap(mmcif::Atom &a, mmcif::Atom &b)
 {
 	a.swap(b);
@@ -202,19 +290,16 @@ typedef std::vector<Atom> AtomView;
 class Residue
 {
   public:
-	// constructors should be private, but that's not possible for now (needed in emplace)
-
-	// constructor for waters
+	// constructor
 	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 +312,11 @@ 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 +367,8 @@ class Residue
 
 	friend std::ostream &operator<<(std::ostream &os, const Residue &res);
 
+	friend Structure;
+
   protected:
 	Residue() {}
 
@@ -481,6 +573,12 @@ class Structure
 	/// \brief Get a the single residue for an asym with id \a asymID
 	Residue &getResidue(const std::string &asymID);
 
+	/// \brief Get a the residue for atom \a atom
+	Residue &getResidue(const mmcif::Atom &atom);
+
+	/// \brief Get a the residue for atom \a atom
+	const Residue &getResidue(const mmcif::Atom &atom) const;
+
 	// map between auth and label locations
 
 	std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID,
@@ -521,6 +619,14 @@ class Structure
 	/// \return				The newly create asym ID
 	std::string createNonpoly(const std::string &entity_id, const std::vector<mmcif::Atom> &atoms);
 
+	/// \brief Create a new NonPolymer struct_asym with atoms constructed from info in \a atom_info, returns asym_id.
+	/// This method creates new atom records filled with info from the info.
+	///
+	/// \param entity_id	The entity ID of the new nonpoly
+	/// \param atoms		The array of sets of cif::item data containing the data for the atoms.
+	/// \return				The newly create asym ID
+	std::string createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info);
+
 	/// \brief To sort the atoms in order of model > asym-id > res-id > atom-id
 	/// Will asssign new atom_id's to all atoms. Be carefull
 	void sortAtoms();
@@ -531,6 +637,12 @@ 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; }
 

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;
 		}

src/Cif++.cpp

@@ -1,17 +1,17 @@
 /*-
  * 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());
-//	
-//	if (tagsA != tagsB)
-//		std::cout << "Unequal number of fields" << std::endl;
+	//	set<std::string> tagsA(a.fields()), tagsB(b.fields());
+	//
+	//	if (tagsA != tagsB)
+	//		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;
-	std::vector<std::tuple<std::string,compType>> tags;
+
+	typedef std::function<int(const char *, const char *)> compType;
+	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* tb = rb[tag].c_str();	if (strcmp(tb, ".") == 0 or strcmp(tb, "?") == 0) tb = "";
-			
+
+			const char *ta = ra[tag].c_str();
+			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();

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;
 	}
 }
 

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;
 	}
 

src/CifUtils.cpp

@@ -25,19 +25,14 @@
  */
 
 #include <atomic>
-#include <chrono>
 #include <cmath>
-#include <cstdio>
-#include <filesystem>
 #include <fstream>
-#include <iomanip>
 #include <iostream>
 #include <map>
 #include <mutex>
 #include <regex>
 #include <sstream>
 #include <thread>
-#include <tuple>
 
 #if defined(_MSC_VER)
 #define TERM_WIDTH 80
@@ -50,6 +45,8 @@
 
 #include "cif++/CifUtils.hpp"
 
+#include "revision.hpp"
+
 namespace ba = boost::algorithm;
 namespace fs = std::filesystem;
 
@@ -64,39 +61,9 @@ extern int VERBOSE;
 
 std::string get_version_nr()
 {
-	const std::regex
-		rxVersionNr1(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"),
-		rxVersionNr2(R"(libcifpp-version: (\d+\.\d+\.\d+))");
-
-#include "revision.hpp"
-
-	struct membuf : public std::streambuf
-	{
-		membuf(char *data, size_t length) { this->setg(data, data, data + length); }
-	} buffer(const_cast<char *>(kRevision), sizeof(kRevision));
-
-	std::istream is(&buffer);
-
-	std::string line, result;
-
-	while (getline(is, line))
-	{
-		std::smatch m;
-
-		if (std::regex_match(line, m, rxVersionNr1))
-		{
-			result = m[1];
-			if (m[2].matched)
-				result += '*';
-			break;
-		}
-
-		// always the first, replace with more specific if followed by the other info
-		if (std::regex_match(line, m, rxVersionNr2))
-			result = m[1];
-	}
-
-	return result;
+	std::ostringstream s;
+	write_version_string(s, false);
+	return s.str();
 }
 
 // --------------------------------------------------------------------
@@ -1237,7 +1204,7 @@ 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;
 }

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;
 }
 

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;
 	}
 }

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;
 				}
@@ -656,7 +657,7 @@ class PDBFileParser
 		int mSeqNum;
 		char mIcode;
 
-		int mDbSeqNum;
+		int mDbSeqNum = 0;
 		bool mSeen = false;
 		std::set<std::string> mAlts;
 
@@ -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);
 		}
@@ -940,7 +941,10 @@ class PDBFileParser
 	std::string pdb2cifDate(std::string s)
 	{
 		std::error_code ec;
-		return pdb2cifDate(s, ec);
+		auto result = pdb2cifDate(s, ec);
+		if (ec and cif::VERBOSE > 0)
+			std::cerr << "Invalid date(" << s << "): " << ec.message() << std::endl;
+		return result;
 	}
 
 	std::string pdb2cifAuth(std::string author)
@@ -1160,7 +1164,8 @@ 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 +1283,8 @@ 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 +1311,8 @@ 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 +1419,8 @@ 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 +1448,7 @@ 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 +1583,8 @@ 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 +1634,7 @@ 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 +1722,7 @@ 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 +1825,7 @@ 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 +2274,7 @@ 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 +2351,7 @@ 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 +2684,7 @@ 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 +2694,7 @@ 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 +2704,7 @@ 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 +2915,7 @@ 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 +3034,7 @@ 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 +3604,7 @@ 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 +4014,7 @@ 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 +4328,7 @@ 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 +4424,7 @@ 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 +4685,7 @@ 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 +4800,7 @@ 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 +4836,7 @@ 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 +4936,7 @@ void PDBFileParser::ParseConnectivtyAnnotation()
 
 			if (ec)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "Dropping SSBOND " << vI(8, 10) << std::endl;
 				continue;
 			}
@@ -4948,7 +4957,7 @@ 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 +5002,7 @@ 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 +5055,7 @@ 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 +5071,7 @@ 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 +5087,7 @@ 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 +5158,7 @@ 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 +5224,7 @@ void PDBFileParser::ParseMiscellaneousFeatures()
 
 			if (ec)
 			{
-				if (cif::VERBOSE)
+				if (cif::VERBOSE > 0)
 					std::cerr << "skipping struct_site_gen record" << std::endl;
 			}
 			else
@@ -5518,7 +5527,7 @@ 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 +5536,7 @@ 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 +5707,8 @@ 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 +5760,12 @@ 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 +5774,13 @@ void PDBFileParser::Parse(std::istream &is, cif::File &result)
 	}
 	catch (const std::exception &ex)
 	{
-		std::cerr << "Error parsing PDB";
-		if (mRec != nullptr)
-			std::cerr << " at line " << mRec->mLineNr;
-		std::cerr << std::endl;
+		if (cif::VERBOSE >= 0)
+		{
+			std::cerr << "Error parsing PDB";
+			if (mRec != nullptr)
+				std::cerr << " at line " << mRec->mLineNr;
+			std::cerr << std::endl;
+		}
 		throw;
 	}
 }
@@ -5947,7 +5960,7 @@ 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 +6047,6 @@ void ReadPDBFile(std::istream &pdbFile, cif::File &cifFile)
 
 	p.Parse(pdbFile, cifFile);
 
-	if (not cifFile.isValid())
-		// throw std::runtime_error("Resulting mmCIF file is invalid");
+	if (not cifFile.isValid() and cif::VERBOSE >= 0)
 		std::cerr << "Resulting mmCIF file is not valid!" << std::endl;
 }

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
-					  << e.what() << '\n';
+			if (cif::VERBOSE >= 0)
+				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"];

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);
 		}

src/revision.hpp.in

@@ -1,5 +0,0 @@
-const char kRevision[] = R"(
-lib@PROJECT_NAME@-version: @PROJECT_VERSION@
-@BUILD_VERSION_STRING@
-Date: @BUILD_DATE_TIME@
-)";

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;
+// 		}
+// 	}
+// }

test/unit-test.cpp

@@ -1735,12 +1735,12 @@ BOOST_AUTO_TEST_CASE(t1)
 
 	auto p2 = p1;
 
-	Point c1 = CenterPoints(p1);
+	CenterPoints(p1);
 
 	for (auto &p : p2)
 		p.rotate(q);
 	
-	Point c2 = CenterPoints(p2);
+	CenterPoints(p2);
 
 	auto q2 = AlignPoints(p1, p2);