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libcifpp
Commit 9160adb1 by Maarten L. Hekkelman
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Merge branch 'develop' into trunk

parents 6c0a4180 3ebf4338
Showing with 280 additions and 110 deletions
CMakeLists.txt
...@@ -37,17 +37,16 @@ include(CheckIncludeFiles) ...@@ -37,17 +37,16 @@ include(CheckIncludeFiles)
include(CheckLibraryExists) include(CheckLibraryExists)
include(CMakePackageConfigHelpers) include(CMakePackageConfigHelpers)
include(Dart) include(Dart)
include(FindFilesystem)
include(GenerateExportHeader) include(GenerateExportHeader)
set(CXX_EXTENSIONS OFF) set(CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 17) set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON) set(CMAKE_CXX_STANDARD_REQUIRED ON)
# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
find_package(Filesystem REQUIRED) find_package(Filesystem REQUIRED)
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
# https://stackoverflow.com/questions/63902528/program-crashes-when-filesystempath-is-destroyed
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
elseif(MSVC) elseif(MSVC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
...@@ -122,20 +121,6 @@ if(MSVC) ...@@ -122,20 +121,6 @@ if(MSVC)
message(STATUS "The library and auxiliary files will be installed in $ENV{LOCALAPPDATA}/${PROJECT_NAME}") 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) set(CMAKE_INSTALL_PREFIX "$ENV{LOCALAPPDATA}/${PROJECT_NAME}" CACHE PATH "..." FORCE)
endif() 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 ${CMAKE_SYSTEM_PROCESSOR}")
endif()
# for mrc, just in case
list(APPEND CMAKE_PREFIX_PATH "$ENV{LOCALAPPDATA}/mrc")
endif() endif()
if(UNIX AND NOT APPLE AND NOT BUILD_FOR_CCP4 AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) if(UNIX AND NOT APPLE AND NOT BUILD_FOR_CCP4 AND CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
...@@ -175,24 +160,18 @@ find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_opt ...@@ -175,24 +160,18 @@ find_package(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_opt
if(NOT MSVC AND Boost_USE_STATIC_LIBS) if(NOT MSVC AND Boost_USE_STATIC_LIBS)
find_package(ZLIB REQUIRED) find_package(ZLIB REQUIRED)
list(APPEND CIFPP_REQUIRED_LIBRARIES ZLIB::ZLIB)
endif() endif()
# Create a revision file, containing the current git version info include(FindFilesystem)
list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPFS_LIBRARY})
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 include(FindAtomic)
git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty) list(APPEND CIFPP_REQUIRED_LIBRARIES ${STDCPPATOMIC_LIBRARY})
else()
SET(BUILD_VERSION_STRING ${PROJECT_VERSION})
endif()
# generate version.h # Create a revision file, containing the current git version info
string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC) include(VersionString)
configure_file("${CMAKE_SOURCE_DIR}/src/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY) write_version_header("LibCIFPP")
# SymOp data table # SymOp data table
if(CIFPP_RECREATE_SYMOP_DATA) if(CIFPP_RECREATE_SYMOP_DATA)
...@@ -200,7 +179,7 @@ if(CIFPP_RECREATE_SYMOP_DATA) ...@@ -200,7 +179,7 @@ if(CIFPP_RECREATE_SYMOP_DATA)
add_executable(symop-map-generator "${CMAKE_SOURCE_DIR}/tools/symop-map-generator.cpp") 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}) target_link_libraries(symop-map-generator Threads::Threads ${Boost_LIBRARIES} ${CIFPP_REQUIRED_LIBRARIES})
if(Boost_INCLUDE_DIR) if(Boost_INCLUDE_DIR)
target_include_directories(symop-map-generator PUBLIC ${Boost_INCLUDE_DIR}) target_include_directories(symop-map-generator PUBLIC ${Boost_INCLUDE_DIR})
endif() endif()
...@@ -271,7 +250,8 @@ target_include_directories(cifpp ...@@ -271,7 +250,8 @@ target_include_directories(cifpp
${CMAKE_BINARY_DIR} ${CMAKE_BINARY_DIR}
) )
target_link_libraries(cifpp Threads::Threads ${Boost_LIBRARIES} std::filesystem ${ZLIB_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") if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
target_link_options(cifpp PRIVATE -undefined dynamic_lookup) target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
...@@ -331,7 +311,7 @@ install(TARGETS cifpp ...@@ -331,7 +311,7 @@ install(TARGETS cifpp
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
if(MSVC) if(MSVC AND BUILD_SHARED_LIBS)
install( install(
FILES $<TARGET_PDB_FILE:${PROJECT_NAME}> FILES $<TARGET_PDB_FILE:${PROJECT_NAME}>
DESTINATION ${CMAKE_INSTALL_LIBDIR} DESTINATION ${CMAKE_INSTALL_LIBDIR}
...@@ -428,7 +408,7 @@ if(CIFPP_BUILD_TESTS) ...@@ -428,7 +408,7 @@ if(CIFPP_BUILD_TESTS)
${CMAKE_CURRENT_BINARY_DIR} # for config.h ${CMAKE_CURRENT_BINARY_DIR} # for config.h
) )
target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp ${Boost_LIBRARIES} std::filesystem ${ZLIB_LIBRARIES}) target_link_libraries(${CIFPP_TEST} PRIVATE Threads::Threads cifpp )
if(CIFPP_USE_RSRC) if(CIFPP_USE_RSRC)
mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic) mrc_target_resources(${CIFPP_TEST} ${CMAKE_SOURCE_DIR}/rsrc/mmcif_pdbx_v50.dic)
......
Config.cmake.in
@PACKAGE_INIT@ @PACKAGE_INIT@
include(CMakeFindDependencyMacro) include(CMakeFindDependencyMacro)
find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex program_options) find_dependency(Threads)
find_dependency(Boost 1.70.0 REQUIRED COMPONENTS system iostreams regex)
if(NOT WIN32) if(NOT WIN32)
find_dependency(ZLIB) find_dependency(ZLIB)
endif() endif()
......
cmake/FindAtomic.cmake 0 → 100644
# Simple check to see if we need a library for std::atomic
if(TARGET std::atomic)
return()
endif()
cmake_minimum_required(VERSION 3.10)
include(CMakePushCheckState)
include(CheckIncludeFileCXX)
include(CheckCXXSourceRuns)
cmake_push_check_state()
set(CMAKE_CXX_STANDARD 17)
check_include_file_cxx("atomic" _CXX_ATOMIC_HAVE_HEADER)
mark_as_advanced(_CXX_ATOMIC_HAVE_HEADER)
set(code [[
#include <atomic>
int main(int argc, char** argv) {
std::atomic<long long> s;
++s;
return 0;
}
]])
check_cxx_source_runs("${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) ...@@ -59,8 +59,10 @@ if(_found)
# Nothing to add... # Nothing to add...
elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED) elseif(CXX_FILESYSTEM_STDCPPFS_NEEDED)
set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME stdc++fs) set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME stdc++fs)
set(STDCPPFS_LIBRARY stdc++fs)
elseif(CXX_FILESYSTEM_CPPFS_NEEDED) elseif(CXX_FILESYSTEM_CPPFS_NEEDED)
set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME c++fs) set_target_properties(std::filesystem PROPERTIES IMPORTED_LIBNAME c++fs)
set(STDCPPFS_LIBRARY c++fs)
endif() endif()
endif() endif()
......
cmake/VersionString.cmake 0 → 100644
# 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++/CifUtils.hpp
...@@ -26,11 +26,7 @@ ...@@ -26,11 +26,7 @@
#pragma once #pragma once
#include <cassert>
#include <filesystem> #include <filesystem>
#include <iostream>
#include <list>
#include <memory>
#include <set> #include <set>
#include <vector> #include <vector>
......
include/cif++/Point.hpp
...@@ -371,8 +371,7 @@ auto DistancePointToLine(const PointF<F> &l1, const PointF<F> &l2, const PointF< ...@@ -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 // a random direction with a distance randomly chosen from a normal
// distribution with a stddev of offset. // distribution with a stddev of offset.
template <typename F> Point Nudge(Point p, float offset);
PointF<F> Nudge(PointF<F> p, F offset);
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// We use quaternions to do rotations in 3d space // We use quaternions to do rotations in 3d space
......
include/cif++/Structure.hpp
...@@ -141,6 +141,8 @@ class Atom ...@@ -141,6 +141,8 @@ class Atom
void set_property(const std::string_view name, const std::string &value) 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); mImpl->set_property(name, value);
} }
...@@ -150,11 +152,16 @@ class Atom ...@@ -150,11 +152,16 @@ class Atom
set_property(name, std::to_string(value)); set_property(name, std::to_string(value));
} }
const std::string &id() const { return mImpl->mID; } const std::string &id() const { return impl().mID; }
AtomType type() const { return mImpl->mType; } AtomType type() const { return impl().mType; }
Point location() const { return mImpl->mLocation; } Point location() const { return impl().mLocation; }
void location(Point p) { mImpl->moveTo(p); } 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 /// \brief Translate the position of this atom by \a t
void translate(Point t); void translate(Point t);
...@@ -169,33 +176,33 @@ class Atom ...@@ -169,33 +176,33 @@ class Atom
void translateRotateAndTranslate(Point t1, Quaternion q, Point t2); void translateRotateAndTranslate(Point t1, Quaternion q, Point t2);
// for direct access to underlying data, be careful! // for direct access to underlying data, be careful!
const cif::Row getRow() const { return mImpl->mRow; } const cif::Row getRow() const { return impl().mRow; }
const cif::Row getRowAniso() const; const cif::Row getRowAniso() const;
bool isSymmetryCopy() const { return mImpl->mSymmetryCopy; } bool isSymmetryCopy() const { return impl().mSymmetryCopy; }
std::string symmetry() const { return mImpl->mSymmetryOperator; } std::string symmetry() const { return impl().mSymmetryOperator; }
const Compound &comp() const { return mImpl->comp(); } const Compound &comp() const { return impl().comp(); }
bool isWater() const { return mImpl->mCompID == "HOH" or mImpl->mCompID == "H2O" or mImpl->mCompID == "WAT"; } bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
int charge() const; int charge() const;
float uIso() const; float uIso() const;
bool getAnisoU(float anisou[6]) const { return mImpl->getAnisoU(anisou); } bool getAnisoU(float anisou[6]) const { return impl().getAnisoU(anisou); }
float occupancy() const; float occupancy() const;
// specifications // specifications
const std::string& labelAtomID() const { return mImpl->mAtomID; } const std::string& labelAtomID() const { return impl().mAtomID; }
const std::string& labelCompID() const { return mImpl->mCompID; } const std::string& labelCompID() const { return impl().mCompID; }
const std::string& labelAsymID() const { return mImpl->mAsymID; } const std::string& labelAsymID() const { return impl().mAsymID; }
std::string labelEntityID() const; std::string labelEntityID() const;
int labelSeqID() const { return mImpl->mSeqID; } int labelSeqID() const { return impl().mSeqID; }
const std::string& labelAltID() const { return mImpl->mAltID; } const std::string& labelAltID() const { return impl().mAltID; }
bool isAlternate() const { return not mImpl->mAltID.empty(); } bool isAlternate() const { return not impl().mAltID.empty(); }
std::string authAtomID() const; std::string authAtomID() const;
std::string authCompID() const; std::string authCompID() const;
std::string authAsymID() const; std::string authAsymID() const;
const std::string& authSeqID() const { return mImpl->mAuthSeqID; } const std::string& authSeqID() const { return impl().mAuthSeqID; }
std::string pdbxAuthInsCode() const; std::string pdbxAuthInsCode() const;
std::string pdbxAuthAltID() const; std::string pdbxAuthAltID() const;
...@@ -218,7 +225,7 @@ class Atom ...@@ -218,7 +225,7 @@ class Atom
std::swap(mImpl, b.mImpl); std::swap(mImpl, b.mImpl);
} }
int compare(const Atom &b) const { return mImpl->compare(*b.mImpl); } int compare(const Atom &b) const { return impl().compare(*b.mImpl); }
bool operator<(const Atom &rhs) const bool operator<(const Atom &rhs) const
{ {
...@@ -232,26 +239,33 @@ class Atom ...@@ -232,26 +239,33 @@ class Atom
void setID(int id); void setID(int id);
const AtomImpl &impl() const
{
if (not mImpl)
throw std::runtime_error("Uninitialized atom, not found?");
return *mImpl;
}
std::shared_ptr<AtomImpl> mImpl; std::shared_ptr<AtomImpl> mImpl;
}; };
template <> template <>
inline std::string Atom::get_property<std::string>(const std::string_view name) const inline std::string Atom::get_property<std::string>(const std::string_view name) const
{ {
return mImpl->get_property(name); return impl().get_property(name);
} }
template <> template <>
inline int Atom::get_property<int>(const std::string_view name) const inline int Atom::get_property<int>(const std::string_view name) const
{ {
auto v = mImpl->get_property(name); auto v = impl().get_property(name);
return v.empty() ? 0 : stoi(v); return v.empty() ? 0 : stoi(v);
} }
template <> template <>
inline float Atom::get_property<float>(const std::string_view name) const inline float Atom::get_property<float>(const std::string_view name) const
{ {
return stof(mImpl->get_property(name)); return stof(impl().get_property(name));
} }
inline void swap(mmcif::Atom &a, mmcif::Atom &b) inline void swap(mmcif::Atom &a, mmcif::Atom &b)
...@@ -559,6 +573,12 @@ class Structure ...@@ -559,6 +573,12 @@ class Structure
/// \brief Get a the single residue for an asym with id \a asymID /// \brief Get a the single residue for an asym with id \a asymID
Residue &getResidue(const std::string &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 // map between auth and label locations
std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID, std::tuple<std::string, int, std::string> MapAuthToLabel(const std::string &asymID,
...@@ -599,6 +619,14 @@ class Structure ...@@ -599,6 +619,14 @@ class Structure
/// \return The newly create asym ID /// \return The newly create asym ID
std::string createNonpoly(const std::string &entity_id, const std::vector<mmcif::Atom> &atoms); 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 /// \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 /// Will asssign new atom_id's to all atoms. Be carefull
void sortAtoms(); void sortAtoms();
......
src/CifUtils.cpp
...@@ -25,19 +25,14 @@ ...@@ -25,19 +25,14 @@
*/ */
#include <atomic> #include <atomic>
#include <chrono>
#include <cmath> #include <cmath>
#include <cstdio>
#include <filesystem>
#include <fstream> #include <fstream>
#include <iomanip>
#include <iostream> #include <iostream>
#include <map> #include <map>
#include <mutex> #include <mutex>
#include <regex> #include <regex>
#include <sstream> #include <sstream>
#include <thread> #include <thread>
#include <tuple>
#if defined(_MSC_VER) #if defined(_MSC_VER)
#define TERM_WIDTH 80 #define TERM_WIDTH 80
...@@ -50,6 +45,8 @@ ...@@ -50,6 +45,8 @@
#include "cif++/CifUtils.hpp" #include "cif++/CifUtils.hpp"
#include "revision.hpp"
namespace ba = boost::algorithm; namespace ba = boost::algorithm;
namespace fs = std::filesystem; namespace fs = std::filesystem;
...@@ -64,39 +61,9 @@ extern int VERBOSE; ...@@ -64,39 +61,9 @@ extern int VERBOSE;
std::string get_version_nr() std::string get_version_nr()
{ {
const std::regex std::ostringstream s;
rxVersionNr1(R"(build-(\d+)-g[0-9a-f]{7}(-dirty)?)"), write_version_string(s, false);
rxVersionNr2(R"(libcifpp-version: (\d+\.\d+\.\d+))"); return s.str();
#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;
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
src/PDB2Cif.cpp
...@@ -657,7 +657,7 @@ class PDBFileParser ...@@ -657,7 +657,7 @@ class PDBFileParser
int mSeqNum; int mSeqNum;
char mIcode; char mIcode;
int mDbSeqNum; int mDbSeqNum = 0;
bool mSeen = false; bool mSeen = false;
std::set<std::string> mAlts; std::set<std::string> mAlts;
...@@ -941,7 +941,10 @@ class PDBFileParser ...@@ -941,7 +941,10 @@ class PDBFileParser
std::string pdb2cifDate(std::string s) std::string pdb2cifDate(std::string s)
{ {
std::error_code ec; 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) std::string pdb2cifAuth(std::string author)
......
src/Structure.cpp
...@@ -1667,6 +1667,16 @@ Residue &Structure::getResidue(const std::string &asymID) ...@@ -1667,6 +1667,16 @@ 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)
{
return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID());
}
const Residue &Structure::getResidue(const mmcif::Atom &atom) const
{
return getResidue(atom.labelAsymID(), atom.labelCompID(), atom.labelSeqID());
}
File &Structure::getFile() const File &Structure::getFile() const
{ {
return mFile; return mFile;
...@@ -2078,7 +2088,8 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve ...@@ -2078,7 +2088,8 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
{ {
auto atom_id = atom_site.getUniqueID(""); auto atom_id = atom_site.getUniqueID("");
auto &&[row, inserted] = atom_site.emplace({{"group_PDB", atom.get_property<std::string>("group_PDB")}, auto &&[row, inserted] = atom_site.emplace({
{"group_PDB", atom.get_property<std::string>("group_PDB")},
{"id", atom_id}, {"id", atom_id},
{"type_symbol", atom.get_property<std::string>("type_symbol")}, {"type_symbol", atom.get_property<std::string>("type_symbol")},
{"label_atom_id", atom.get_property<std::string>("label_atom_id")}, {"label_atom_id", atom.get_property<std::string>("label_atom_id")},
...@@ -2107,6 +2118,53 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve ...@@ -2107,6 +2118,53 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
return asym_id; return asym_id;
} }
std::string Structure::createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info)
{
using namespace cif::literals;
cif::Datablock &db = *mFile.impl().mDb;
auto &struct_asym = db["struct_asym"];
std::string asym_id = struct_asym.getUniqueID();
struct_asym.emplace({{"id", asym_id},
{"pdbx_blank_PDB_chainid_flag", "N"},
{"pdbx_modified", "N"},
{"entity_id", entity_id},
{"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"];
auto &res = mNonPolymers.emplace_back(*this, comp_id, asym_id);
for (auto &atom : atom_info)
{
auto atom_id = atom_site.getUniqueID("");
atom.insert(atom.end(), {
{"group_PDB", "HETATM"},
{"id", atom_id},
{"label_comp_id", comp_id},
{"label_asym_id", asym_id},
{"label_seq_id", ""},
{"label_entity_id", entity_id},
{"auth_comp_id", comp_id},
{"auth_asym_id", asym_id},
{"auth_seq_id", ""},
{"pdbx_PDB_model_num", 1},
{"label_alt_id", ""}
});
auto &&[row, inserted] = atom_site.emplace(atom.begin(), atom.end());
auto &newAtom = mAtoms.emplace_back(std::make_shared<Atom::AtomImpl>(db, atom_id, row));
res.addAtom(newAtom);
}
return asym_id;
}
void Structure::cleanupEmptyCategories() void Structure::cleanupEmptyCategories()
{ {
using namespace cif::literals; using namespace cif::literals;
......
src/revision.hpp.in deleted 100644 → 0
const char kRevision[] = R"(
lib@PROJECT_NAME@-version: @PROJECT_VERSION@
@BUILD_VERSION_STRING@
Date: @BUILD_DATE_TIME@
)";
test/unit-test.cpp
...@@ -1735,12 +1735,12 @@ BOOST_AUTO_TEST_CASE(t1) ...@@ -1735,12 +1735,12 @@ BOOST_AUTO_TEST_CASE(t1)
auto p2 = p1; auto p2 = p1;
Point c1 = CenterPoints(p1); CenterPoints(p1);
for (auto &p : p2) for (auto &p : p2)
p.rotate(q); p.rotate(q);
Point c2 = CenterPoints(p2); CenterPoints(p2);
auto q2 = AlignPoints(p1, p2); auto q2 = AlignPoints(p1, p2);
......
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