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libcifpp
Commit 15db026e by Maarten L. Hekkelman
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Merge branch 'develop' of github.com:PDB-REDO/libcifpp into develop

parents 19f2fd75 627d3b9d
Showing with 439 additions and 511 deletions
.gitignore
......@@ -7,3 +7,4 @@ CMakeSettings.json
msvc/
src/revision.hpp
test/test-create_sugar_?.cif
Testing/
CMakeLists.txt
......@@ -35,10 +35,13 @@ include(CheckIncludeFiles)
include(CheckLibraryExists)
include(CMakePackageConfigHelpers)
include(CheckCXXSourceCompiles)
include(GenerateExportHeader)
set(CXX_EXTENSIONS OFF)
set(CMAKE_CXX_STANDARD 20)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# set(CMAKE_CXX_VISIBILITY_PRESET hidden)
# set(CMAKE_VISIBILITY_INLINES_HIDDEN 1)
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers")
......@@ -224,7 +227,6 @@ set(project_headers
${PROJECT_SOURCE_DIR}/include/cif++/datablock.hpp
${PROJECT_SOURCE_DIR}/include/cif++/file.hpp
${PROJECT_SOURCE_DIR}/include/cif++/validate.hpp
${PROJECT_SOURCE_DIR}/include/cif++/list.hpp
${PROJECT_SOURCE_DIR}/include/cif++/iterator.hpp
${PROJECT_SOURCE_DIR}/include/cif++/parser.hpp
${PROJECT_SOURCE_DIR}/include/cif++/forward_decl.hpp
......@@ -249,6 +251,7 @@ set(project_headers
add_library(cifpp ${project_sources} ${project_headers} ${PROJECT_SOURCE_DIR}/src/symop_table_data.hpp)
add_library(cifpp::cifpp ALIAS cifpp)
generate_export_header(cifpp EXPORT_FILE_NAME cif++/exports.hpp)
if(BOOST_REGEX)
target_compile_definitions(cifpp PRIVATE USE_BOOST_REGEX=1 BOOST_REGEX_STANDALONE=1)
......@@ -263,7 +266,7 @@ set_target_properties(cifpp PROPERTIES POSITION_INDEPENDENT_CODE ON)
target_include_directories(cifpp
PUBLIC
"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>"
"$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include;${PROJECT_BINARY_DIR}>"
"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
)
......@@ -343,6 +346,12 @@ install(
COMPONENT Devel
)
install(
FILES ${PROJECT_BINARY_DIR}/cif++/exports.hpp
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/cif++
COMPONENT Devel
)
install(FILES
${PROJECT_SOURCE_DIR}/rsrc/mmcif_ddl.dic
${PROJECT_SOURCE_DIR}/rsrc/mmcif_pdbx.dic
......
changelog
Version 5.0.6
- Fix file::contains, using iequals
- Fix is_cis
Version 5.0.5
- Fix code to work on 32 bit machines
......
include/cif++/atom_type.hpp
......@@ -204,7 +204,7 @@ struct atom_type_info
float radii[kRadiusTypeCount];
};
extern const atom_type_info kKnownAtoms[];
extern CIFPP_EXPORT const atom_type_info kKnownAtoms[];
// --------------------------------------------------------------------
// AtomTypeTraits
......
include/cif++/category.hpp
......@@ -26,8 +26,6 @@
#pragma once
#include <array>
#include <cif++/forward_decl.hpp>
#include <cif++/condition.hpp>
......@@ -35,6 +33,8 @@
#include <cif++/row.hpp>
#include <cif++/validate.hpp>
#include <array>
// TODO: implement all of:
// https://en.cppreference.com/w/cpp/named_req/Container
// https://en.cppreference.com/w/cpp/named_req/SequenceContainer
......
include/cif++/compound.hpp
......@@ -29,15 +29,15 @@
/// \file This file contains the definition for the class compound, encapsulating
/// the information found for compounds in the CCD.
#include <cif++.hpp>
#include <cif++/atom_type.hpp>
#include <cif++/point.hpp>
#include <map>
#include <set>
#include <tuple>
#include <vector>
#include <cif++.hpp>
#include <cif++/atom_type.hpp>
#include <cif++/point.hpp>
namespace cif
{
......@@ -180,7 +180,7 @@ class compound_factory
~compound_factory();
static const std::map<std::string, char> kAAMap, kBaseMap;
static CIFPP_EXPORT const std::map<std::string, char> kAAMap, kBaseMap;
private:
compound_factory();
......@@ -195,4 +195,4 @@ class compound_factory
std::shared_ptr<compound_factory_impl> m_impl;
};
} // namespace pdbx
} // namespace cif
include/cif++/condition.hpp
......@@ -26,14 +26,14 @@
#pragma once
#include <cif++/row.hpp>
#include <cassert>
#include <functional>
#include <iostream>
#include <regex>
#include <utility>
#include <cif++/row.hpp>
namespace cif
{
......@@ -859,4 +859,4 @@ namespace literals
}
} // namespace literals
} // namespace cif
\ No newline at end of file
} // namespace cif
include/cif++/datablock.hpp
......@@ -26,9 +26,8 @@
#pragma once
#include <cif++/forward_decl.hpp>
#include <cif++/category.hpp>
#include <cif++/forward_decl.hpp>
namespace cif
{
......@@ -88,7 +87,7 @@ class datablock : public std::list<category>
}
// --------------------------------------------------------------------
bool operator==(const datablock &rhs) const;
private:
......
include/cif++/file.hpp
......@@ -28,6 +28,7 @@
#include <list>
#include <cif++/exports.hpp>
#include <cif++/datablock.hpp>
#include <cif++/parser.hpp>
......
include/cif++/forward_decl.hpp
......@@ -26,6 +26,8 @@
#pragma once
#include <cif++/exports.hpp>
#include <string>
#include <vector>
......
include/cif++/item.hpp
......@@ -26,6 +26,12 @@
#pragma once
#include <cif++/exports.hpp>
#include <cif++/forward_decl.hpp>
#include <cif++/text.hpp>
#include <cif++/utilities.hpp>
#include <cassert>
#include <charconv>
#include <cstring>
#include <iomanip>
......@@ -35,9 +41,6 @@
#include <optional>
#include <utility>
#include <cif++/forward_decl.hpp>
#include <cif++/text.hpp>
/// \file item.hpp
/// This file contains the declaration of item but also the item_value and item_handle
/// These handle the storage of and access to the data for a single data field.
......@@ -45,8 +48,6 @@
namespace cif
{
extern int VERBOSE;
// --------------------------------------------------------------------
/// \brief item is a transient class that is used to pass data into rows
/// but it also takes care of formatting data.
......@@ -353,7 +354,7 @@ struct item_handle
{
}
static const item_handle s_null_item;
static CIFPP_EXPORT const item_handle s_null_item;
friend void swap(item_handle a, item_handle b)
{
......
include/cif++/list.hpp deleted 100644 → 0
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2022 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.
*/
#pragma once
#include <memory>
namespace cif
{
// --------------------------------------------------------------------
template<typename Allocator = std::allocator<void>>
class list
{
public:
protected:
struct list_item
{
list_item *m_next = nullptr;
};
using list_item_allocator_type = typename std::allocator_traits<Alloc>::template rebind_alloc<list_item>;
using list_item_allocator_traits = std::allocator_traits<item_allocator_type>;
list_item_allocator_traits::pointer get_item()
{
list_item_allocator_type ia(get_allocator());
return list_item_allocator_traits::allocate(ia, 1);
}
template<typename ...Arguments>
list_item *create_list_item(uint16_t column_ix, Arguments... args)
{
auto p = this->get_item();
list_item_allocator_type ia(get_allocator());
list_item_allocator_traits::construct(ia, p, std::forward<Arguments>(args)...);
return p;
}
void delete_list_item(list_item *iv)
{
list_item_allocator_type ia(get_allocator());
list_item_allocator_traits::destroy(ia, iv);
list_item_allocator_traits::deallocate(ia, iv, 1);
}
list_item *m_head = nullptr, *m_tail = nullptr;
};
} // namespace cif
include/cif++/model.hpp
......@@ -26,10 +26,10 @@
#pragma once
#include <numeric>
#include <cif++/atom_type.hpp>
#include <numeric>
#if __cpp_lib_format
#include <format>
#endif
......
include/cif++/parser.hpp
......@@ -26,11 +26,11 @@
#pragma once
#include <cif++/row.hpp>
#include <map>
#include <regex>
#include <cif++/row.hpp>
namespace cif
{
......@@ -94,7 +94,7 @@ class sac_parser
static bool is_unquoted_string(std::string_view text)
{
bool result = is_ordinary(text.front());
bool result = text.empty() or is_ordinary(text.front());
if (result)
{
......
include/cif++/pdb/tls.hpp
......@@ -26,19 +26,15 @@
#pragma once
#include <cif++.hpp>
#include <string>
#include <tuple>
#include <vector>
#include <cif++.hpp>
namespace cif
{
extern const int
kResidueNrWildcard,
kNoSeqNum;
struct tls_selection;
struct tls_residue;
......
include/cif++/point.hpp
......@@ -26,6 +26,8 @@
#pragma once
#include <cif++/exports.hpp>
#include <cmath>
#include <complex>
#include <functional>
......
include/cif++/symmetry.hpp
......@@ -26,6 +26,8 @@
#pragma once
#include <cif++/exports.hpp>
#include <array>
#include <cstdint>
#include <string>
......@@ -50,8 +52,8 @@ struct space_group
int nr;
};
extern const space_group kSpaceGroups[];
extern const std::size_t kNrOfSpaceGroups;
extern CIFPP_EXPORT const space_group kSpaceGroups[];
extern CIFPP_EXPORT const std::size_t kNrOfSpaceGroups;
// --------------------------------------------------------------------
......@@ -139,8 +141,8 @@ struct symop_datablock
static_assert(sizeof(symop_datablock) == sizeof(uint64_t), "Size of symop_data is wrong");
extern const symop_datablock kSymopNrTable[];
extern const std::size_t kSymopNrTableSize;
extern CIFPP_EXPORT const symop_datablock kSymopNrTable[];
extern CIFPP_EXPORT const std::size_t kSymopNrTableSize;
// --------------------------------------------------------------------
......
include/cif++/text.hpp
......@@ -26,6 +26,8 @@
#pragma once
#include <cif++/exports.hpp>
#include <charconv>
#include <cmath>
#include <limits>
......@@ -34,7 +36,6 @@
#include <tuple>
#include <vector>
#if __has_include(<experimental/type_traits>)
#include <experimental/type_traits>
#else
......@@ -249,7 +250,7 @@ typedef std::set<std::string, iless> iset;
// --------------------------------------------------------------------
// This really makes a difference, having our own tolower routines
extern const uint8_t kCharToLowerMap[256];
extern CIFPP_EXPORT const uint8_t kCharToLowerMap[256];
inline char tolower(int ch)
{
......@@ -448,8 +449,8 @@ std::to_chars_result to_chars(char *first, char *last, FloatType &value, chars_f
template <typename FloatType, std::enable_if_t<std::is_floating_point_v<FloatType>, int> = 0>
std::to_chars_result to_chars(char *first, char *last, FloatType &value, chars_format fmt, int precision)
{
int size = last - first;
int r;
int size = static_cast<int>(last - first);
int r = 0;
switch (fmt)
{
......
include/cif++/utilities.hpp
......@@ -26,6 +26,8 @@
#pragma once
#include <cif++/exports.hpp>
#include <filesystem>
#ifndef STDOUT_FILENO
......@@ -50,7 +52,7 @@
namespace cif
{
extern int VERBOSE;
extern CIFPP_EXPORT int VERBOSE;
// the git 'build' number
std::string get_version_nr();
......
include/cif++/validate.hpp
......@@ -26,13 +26,13 @@
#pragma once
#include <cif++/text.hpp>
#include <filesystem>
#include <list>
#include <mutex>
#include <utility>
#include <cif++/text.hpp>
namespace cif
{
......
src/atom_type.cpp
......@@ -182,24 +182,24 @@ const struct ionic_radii
{ F, { kNA, kNA, 119, kNA, kNA, kNA, kNA, kNA, kNA, 22, kNA } }, // Fluorine
{ Na, { kNA, kNA, kNA, 116, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Sodium
{ Mg, { kNA, kNA, kNA, kNA, 86, kNA, kNA, kNA, kNA, kNA, kNA } }, // Magnesium
{ Al, { kNA, kNA, kNA, kNA, kNA, 67.5, kNA, kNA, kNA, kNA, kNA } }, // Aluminium
{ Al, { kNA, kNA, kNA, kNA, kNA, 67.5f, kNA, kNA, kNA, kNA, kNA } }, // Aluminium
{ Si, { kNA, kNA, kNA, kNA, kNA, kNA, 54, kNA, kNA, kNA, kNA } }, // Silicon
{ P, { kNA, kNA, kNA, kNA, kNA, 58, kNA, 52, kNA, kNA, kNA } }, // Phosphorus
{ S, { kNA, 170, kNA, kNA, kNA, kNA, 51, kNA, 43, kNA, kNA } }, // Sulfur
{ Cl, { kNA, kNA, 181, kNA, kNA, kNA, kNA, 26, kNA, 41, kNA } }, // Chlorine
{ K, { kNA, kNA, kNA, 152, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Potassium
{ Ca, { kNA, kNA, kNA, kNA, 114, kNA, kNA, kNA, kNA, kNA, kNA } }, // Calcium
{ Sc, { kNA, kNA, kNA, kNA, kNA, 88.5, kNA, kNA, kNA, kNA, kNA } }, // Scandium
{ Ti, { kNA, kNA, kNA, kNA, 100, 81, 74.5, kNA, kNA, kNA, kNA } }, // Titanium
{ Sc, { kNA, kNA, kNA, kNA, kNA, 88.5f, kNA, kNA, kNA, kNA, kNA } }, // Scandium
{ Ti, { kNA, kNA, kNA, kNA, 100, 81, 74.5f, kNA, kNA, kNA, kNA } }, // Titanium
{ V, { kNA, kNA, kNA, kNA, 93, 78, 72, 68, kNA, kNA, kNA } }, // Vanadium
{ Cr, { kNA, kNA, kNA, kNA, 87, 75.5, 69, 63, 58, kNA, kNA } }, // Chromium ls
{ Cr, { kNA, kNA, kNA, kNA, 87, 75.5f, 69, 63, 58, kNA, kNA } }, // Chromium ls
// { Cr,{ kNA, kNA, kNA, kNA, 94, kNA, kNA, kNA, kNA, kNA, kNA } }, // Chromium hs
{ Mn, { kNA, kNA, kNA, kNA, 81, 72, 67, 47, 39.5, 60, kNA } }, // Manganese ls
// { Mn,{ kNA, kNA, kNA, kNA, 97, 78.5, kNA, kNA, kNA, kNA, kNA } }, // Manganese hs
{ Fe, { kNA, kNA, kNA, kNA, 75, 69, 72.5, kNA, 39, kNA, kNA } }, // Iron ls
// { Fe,{ kNA, kNA, kNA, kNA, 92, 78.5, kNA, kNA, kNA, kNA, kNA } }, // Iron hs
{ Co, { kNA, kNA, kNA, kNA, 79, 68.5, kNA, kNA, kNA, kNA, kNA } }, // Cobalt ls
// { Co,{ kNA, kNA, kNA, kNA, 88.5, 75, 67, kNA, kNA, kNA, kNA } }, // Cobalt hs
{ Mn, { kNA, kNA, kNA, kNA, 81, 72, 67, 47, 39.5f, 60, kNA } }, // Manganese ls
// { Mn,{ kNA, kNA, kNA, kNA, 97, 78.5f, kNA, kNA, kNA, kNA, kNA } }, // Manganese hs
{ Fe, { kNA, kNA, kNA, kNA, 75, 69, 72.5f, kNA, 39, kNA, kNA } }, // Iron ls
// { Fe,{ kNA, kNA, kNA, kNA, 92, 78.5f, kNA, kNA, kNA, kNA, kNA } }, // Iron hs
{ Co, { kNA, kNA, kNA, kNA, 79, 68.5f, kNA, kNA, kNA, kNA, kNA } }, // Cobalt ls
// { Co,{ kNA, kNA, kNA, kNA, 88.5f, 75, 67, kNA, kNA, kNA, kNA } }, // Cobalt hs
{ Ni, { kNA, kNA, kNA, kNA, 83, 70, 62, kNA, kNA, kNA, kNA } }, // Nickel ls
// { Ni,{ kNA, kNA, kNA, kNA, kNA, 74, kNA, kNA, kNA, kNA, kNA } }, // Nickel hs
{ Cu, { kNA, kNA, kNA, 91, 87, 68, kNA, kNA, kNA, kNA, kNA } }, // Copper
......@@ -215,10 +215,10 @@ const struct ionic_radii
{ Zr, { kNA, kNA, kNA, kNA, kNA, kNA, 86, kNA, kNA, kNA, kNA } }, // Zirconium
{ Nb, { kNA, kNA, kNA, kNA, kNA, 86, 82, 78, kNA, kNA, kNA } }, // Niobium
{ Mo, { kNA, kNA, kNA, kNA, kNA, 83, 79, 75, 73, kNA, kNA } }, // Molybdenum
{ Tc, { kNA, kNA, kNA, kNA, kNA, kNA, 78.5, 74, kNA, 70, kNA } }, // Technetium
{ Ru, { kNA, kNA, kNA, kNA, kNA, 82, 76, 70.5, kNA, 52, 150 } }, // Ruthenium
{ Rh, { kNA, kNA, kNA, kNA, kNA, 80.5, 74, 69, kNA, kNA, kNA } }, // Rhodium
{ Pd, { kNA, kNA, kNA, 73, 100, 90, 75.5, kNA, kNA, kNA, kNA } }, // Palladium
{ Tc, { kNA, kNA, kNA, kNA, kNA, kNA, 78.5f, 74, kNA, 70, kNA } }, // Technetium
{ Ru, { kNA, kNA, kNA, kNA, kNA, 82, 76, 70.5f, kNA, 52, 150 } }, // Ruthenium
{ Rh, { kNA, kNA, kNA, kNA, kNA, 80.5f, 74, 69, kNA, kNA, kNA } }, // Rhodium
{ Pd, { kNA, kNA, kNA, 73, 100, 90, 75.5f, kNA, kNA, kNA, kNA } }, // Palladium
{ Ag, { kNA, kNA, kNA, 129, 108, 89, kNA, kNA, kNA, kNA, kNA } }, // Silver
{ Cd, { kNA, kNA, kNA, kNA, 109, kNA, kNA, kNA, kNA, kNA, kNA } }, // Cadmium
{ In, { kNA, kNA, kNA, kNA, kNA, 94, kNA, kNA, kNA, kNA, kNA } }, // Indium
......@@ -229,32 +229,32 @@ const struct ionic_radii
{ Xe, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 62 } }, // Xenon
{ Cs, { kNA, kNA, kNA, 167, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Caesium
{ Ba, { kNA, kNA, kNA, kNA, 149, kNA, kNA, kNA, kNA, kNA, kNA } }, // Barium
{ La, { kNA, kNA, kNA, kNA, kNA, 117.2, kNA, kNA, kNA, kNA, kNA } }, // Lanthanum
{ La, { kNA, kNA, kNA, kNA, kNA, 117.2f, kNA, kNA, kNA, kNA, kNA } }, // Lanthanum
{ Ce, { kNA, kNA, kNA, kNA, kNA, 115, 101, kNA, kNA, kNA, kNA } }, // Cerium
{ Pr, { kNA, kNA, kNA, kNA, kNA, 113, 99, kNA, kNA, kNA, kNA } }, // Praseodymium
{ Nd, { kNA, kNA, kNA, kNA, 143, 112.3, kNA, kNA, kNA, kNA, kNA } }, // Neodymium
{ Nd, { kNA, kNA, kNA, kNA, 143, 112.3f, kNA, kNA, kNA, kNA, kNA } }, // Neodymium
{ Pm, { kNA, kNA, kNA, kNA, kNA, 111, kNA, kNA, kNA, kNA, kNA } }, // Promethium
{ Sm, { kNA, kNA, kNA, kNA, 136, 109.8, kNA, kNA, kNA, kNA, kNA } }, // Samarium
{ Eu, { kNA, kNA, kNA, kNA, 131, 108.7, kNA, kNA, kNA, kNA, kNA } }, // Europium
{ Gd, { kNA, kNA, kNA, kNA, kNA, 107.8, kNA, kNA, kNA, kNA, kNA } }, // Gadolinium
{ Tb, { kNA, kNA, kNA, kNA, kNA, 106.3, 90, kNA, kNA, kNA, kNA } }, // Terbium
{ Dy, { kNA, kNA, kNA, kNA, 121, 105.2, kNA, kNA, kNA, kNA, kNA } }, // Dysprosium
{ Ho, { kNA, kNA, kNA, kNA, kNA, 104.1, kNA, kNA, kNA, kNA, kNA } }, // Holmium
{ Sm, { kNA, kNA, kNA, kNA, 136, 109.8f, kNA, kNA, kNA, kNA, kNA } }, // Samarium
{ Eu, { kNA, kNA, kNA, kNA, 131, 108.7f, kNA, kNA, kNA, kNA, kNA } }, // Europium
{ Gd, { kNA, kNA, kNA, kNA, kNA, 107.8f, kNA, kNA, kNA, kNA, kNA } }, // Gadolinium
{ Tb, { kNA, kNA, kNA, kNA, kNA, 106.3f, 90, kNA, kNA, kNA, kNA } }, // Terbium
{ Dy, { kNA, kNA, kNA, kNA, 121, 105.2f, kNA, kNA, kNA, kNA, kNA } }, // Dysprosium
{ Ho, { kNA, kNA, kNA, kNA, kNA, 104.1f, kNA, kNA, kNA, kNA, kNA } }, // Holmium
{ Er, { kNA, kNA, kNA, kNA, kNA, 103, kNA, kNA, kNA, kNA, kNA } }, // Erbium
{ Tm, { kNA, kNA, kNA, kNA, 117, 102, kNA, kNA, kNA, kNA, kNA } }, // Thulium
{ Yb, { kNA, kNA, kNA, kNA, 116, 100.8, kNA, kNA, kNA, kNA, kNA } }, // Ytterbium
{ Lu, { kNA, kNA, kNA, kNA, kNA, 100.1, kNA, kNA, kNA, kNA, kNA } }, // Lutetium
{ Yb, { kNA, kNA, kNA, kNA, 116, 100.8f, kNA, kNA, kNA, kNA, kNA } }, // Ytterbium
{ Lu, { kNA, kNA, kNA, kNA, kNA, 100.1f, kNA, kNA, kNA, kNA, kNA } }, // Lutetium
{ Hf, { kNA, kNA, kNA, kNA, kNA, kNA, 85, kNA, kNA, kNA, kNA } }, // Hafnium
{ Ta, { kNA, kNA, kNA, kNA, kNA, 86, 82, 78, kNA, kNA, kNA } }, // Tantalum
{ W, { kNA, kNA, kNA, kNA, kNA, kNA, 80, 76, 74, kNA, kNA } }, // Tungsten
{ Re, { kNA, kNA, kNA, kNA, kNA, kNA, 77, 72, 69, 67, kNA } }, // Rhenium
{ Os, { kNA, kNA, kNA, kNA, kNA, kNA, 77, 71.5, 68.5, 66.5, 53 } }, // Osmium
{ Ir, { kNA, kNA, kNA, kNA, kNA, 82, 76.5, 71, kNA, kNA, kNA } }, // Iridium
{ Pt, { kNA, kNA, kNA, kNA, 94, kNA, 76.5, 71, kNA, kNA, kNA } }, // Platinum
{ Os, { kNA, kNA, kNA, kNA, kNA, kNA, 77, 71.5f, 68.5f, 66.5f, 53 } }, // Osmium
{ Ir, { kNA, kNA, kNA, kNA, kNA, 82, 76.5f, 71, kNA, kNA, kNA } }, // Iridium
{ Pt, { kNA, kNA, kNA, kNA, 94, kNA, 76.5f, 71, kNA, kNA, kNA } }, // Platinum
{ Au, { kNA, kNA, kNA, 151, kNA, 99, kNA, 71, kNA, kNA, kNA } }, // Gold
{ Hg, { kNA, kNA, kNA, 133, 116, kNA, kNA, kNA, kNA, kNA, kNA } }, // Mercury
{ Tl, { kNA, kNA, kNA, 164, kNA, 102.5, kNA, kNA, kNA, kNA, kNA } }, // Thallium
{ Pb, { kNA, kNA, kNA, kNA, 133, kNA, 91.5, kNA, kNA, kNA, kNA } }, // Lead
{ Tl, { kNA, kNA, kNA, 164, kNA, 102.5f, kNA, kNA, kNA, kNA, kNA } }, // Thallium
{ Pb, { kNA, kNA, kNA, kNA, 133, kNA, 91.5f, kNA, kNA, kNA, kNA } }, // Lead
{ Bi, { kNA, kNA, kNA, kNA, kNA, 117, kNA, 90, kNA, kNA, kNA } }, // Bismuth
{ Po, { kNA, kNA, kNA, kNA, kNA, kNA, 108, kNA, 81, kNA, kNA } }, // Polonium
{ At, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 76, kNA } }, // Astatine
......@@ -263,16 +263,16 @@ const struct ionic_radii
{ Ac, { kNA, kNA, kNA, kNA, kNA, 126, kNA, kNA, kNA, kNA, kNA } }, // Actinium
{ Th, { kNA, kNA, kNA, kNA, kNA, kNA, 108, kNA, kNA, kNA, kNA } }, // Thorium
{ Pa, { kNA, kNA, kNA, kNA, kNA, 116, 104, 92, kNA, kNA, kNA } }, // Protactinium
{ U, { kNA, kNA, kNA, kNA, kNA, 116.5, 103, 90, 87, kNA, kNA } }, // Uranium
{ U, { kNA, kNA, kNA, kNA, kNA, 116.5f, 103, 90, 87, kNA, kNA } }, // Uranium
{ Np, { kNA, kNA, kNA, kNA, 124, 115, 101, 89, 86, 85, kNA } }, // Neptunium
{ Pu, { kNA, kNA, kNA, kNA, kNA, 114, 100, 88, 85, kNA, kNA } }, // Plutonium
{ Am, { kNA, kNA, kNA, kNA, 140, 111.5, 99, kNA, kNA, kNA, kNA } }, // Americium
{ Am, { kNA, kNA, kNA, kNA, 140, 111.5f, 99, kNA, kNA, kNA, kNA } }, // Americium
{ Cm, { kNA, kNA, kNA, kNA, kNA, 111, 99, kNA, kNA, kNA, kNA } }, // Curium
{ Bk, { kNA, kNA, kNA, kNA, kNA, 110, 97, kNA, kNA, kNA, kNA } }, // Berkelium
{ Cf, { kNA, kNA, kNA, kNA, kNA, 109, 96.1, kNA, kNA, kNA, kNA } }, // Californium
{ Es, { kNA, kNA, kNA, kNA, kNA, 92.8, kNA, kNA, kNA, kNA, kNA } }, // Einsteinium
{ Cf, { kNA, kNA, kNA, kNA, kNA, 109, 96.1f, kNA, kNA, kNA, kNA } }, // Californium
{ Es, { kNA, kNA, kNA, kNA, kNA, 92.8f, kNA, kNA, kNA, kNA, kNA } }, // Einsteinium
}, kEffectiveIonicRadii[] = {
{ H, { kNA, kNA, 139.9, -18, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Hydrogen
{ H, { kNA, kNA, 139.9f, -18, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Hydrogen
{ Li, { kNA, kNA, kNA, 76, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Lithium
{ Be, { kNA, kNA, kNA, kNA, 45, kNA, kNA, kNA, kNA, kNA, kNA } }, // Beryllium
{ B, { kNA, kNA, kNA, kNA, kNA, 27, kNA, kNA, kNA, kNA, kNA } }, // Boron
......@@ -282,24 +282,24 @@ const struct ionic_radii
{ F, { kNA, kNA, 133, kNA, kNA, kNA, kNA, kNA, kNA, 8, kNA } }, // Fluorine
{ Na, { kNA, kNA, kNA, 102, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Sodium
{ Mg, { kNA, kNA, kNA, kNA, 72, kNA, kNA, kNA, kNA, kNA, kNA } }, // Magnesium
{ Al, { kNA, kNA, kNA, kNA, kNA, 53.5, kNA, kNA, kNA, kNA, kNA } }, // Aluminium
{ Al, { kNA, kNA, kNA, kNA, kNA, 53.5f, kNA, kNA, kNA, kNA, kNA } }, // Aluminium
{ Si, { kNA, kNA, kNA, kNA, kNA, kNA, 40, kNA, kNA, kNA, kNA } }, // Silicon
{ P, { 212, kNA, kNA, kNA, kNA, 44, kNA, 38, kNA, kNA, kNA } }, // Phosphorus
{ S, { kNA, 184, kNA, kNA, kNA, kNA, 37, kNA, 29, kNA, kNA } }, // Sulfur
{ Cl, { kNA, kNA, 181, kNA, kNA, kNA, kNA, 12, kNA, 27, kNA } }, // Chlorine
{ K, { kNA, kNA, kNA, 138, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Potassium
{ Ca, { kNA, kNA, kNA, kNA, 100, kNA, kNA, kNA, kNA, kNA, kNA } }, // Calcium
{ Sc, { kNA, kNA, kNA, kNA, kNA, 74.5, kNA, kNA, kNA, kNA, kNA } }, // Scandium
{ Ti, { kNA, kNA, kNA, kNA, 86, 67, 60.5, kNA, kNA, kNA, kNA } }, // Titanium
{ Sc, { kNA, kNA, kNA, kNA, kNA, 74.5f, kNA, kNA, kNA, kNA, kNA } }, // Scandium
{ Ti, { kNA, kNA, kNA, kNA, 86, 67, 60.5f, kNA, kNA, kNA, kNA } }, // Titanium
{ V, { kNA, kNA, kNA, kNA, 79, 64, 58, 54, kNA, kNA, kNA } }, // Vanadium
{ Cr, { kNA, kNA, kNA, kNA, 73, 61.5, 55, 49, 44, kNA, kNA } }, // Chromium ls
{ Cr, { kNA, kNA, kNA, kNA, 73, 61.5f, 55, 49, 44, kNA, kNA } }, // Chromium ls
{ Cr, { kNA, kNA, kNA, kNA, 80, kNA, kNA, kNA, kNA, kNA, kNA } }, // Chromium hs
{ Mn, { kNA, kNA, kNA, kNA, 67, 58, 53, 33, 25.5, 46, kNA } }, // Manganese ls
{ Mn, { kNA, kNA, kNA, kNA, 83, 64.5, kNA, kNA, kNA, kNA, kNA } }, // Manganese hs
{ Fe, { kNA, kNA, kNA, kNA, 61, 55, 58.5, kNA, 25, kNA, kNA } }, // Iron ls
{ Fe, { kNA, kNA, kNA, kNA, 78, 64.5, kNA, kNA, kNA, kNA, kNA } }, // Iron hs
{ Co, { kNA, kNA, kNA, kNA, 65, 54.5, kNA, kNA, kNA, kNA, kNA } }, // Cobalt ls
{ Co, { kNA, kNA, kNA, kNA, 74.5, 61, 53, kNA, kNA, kNA, kNA } }, // Cobalt hs
{ Mn, { kNA, kNA, kNA, kNA, 67, 58, 53, 33, 25.5f, 46, kNA } }, // Manganese ls
{ Mn, { kNA, kNA, kNA, kNA, 83, 64.5f, kNA, kNA, kNA, kNA, kNA } }, // Manganese hs
{ Fe, { kNA, kNA, kNA, kNA, 61, 55, 58.5f, kNA, 25, kNA, kNA } }, // Iron ls
{ Fe, { kNA, kNA, kNA, kNA, 78, 64.5f, kNA, kNA, kNA, kNA, kNA } }, // Iron hs
{ Co, { kNA, kNA, kNA, kNA, 65, 54.5f, kNA, kNA, kNA, kNA, kNA } }, // Cobalt ls
{ Co, { kNA, kNA, kNA, kNA, 74.5f, 61, 53, kNA, kNA, kNA, kNA } }, // Cobalt hs
{ Ni, { kNA, kNA, kNA, kNA, 69, 56, 48, kNA, kNA, kNA, kNA } }, // Nickel ls
{ Ni, { kNA, kNA, kNA, kNA, kNA, 60, kNA, kNA, kNA, kNA, kNA } }, // Nickel hs
{ Cu, { kNA, kNA, kNA, 77, 73, 54, kNA, kNA, kNA, kNA, kNA } }, // Copper
......@@ -315,10 +315,10 @@ const struct ionic_radii
{ Zr, { kNA, kNA, kNA, kNA, kNA, kNA, 72, kNA, kNA, kNA, kNA } }, // Zirconium
{ Nb, { kNA, kNA, kNA, kNA, kNA, 72, 68, 64, kNA, kNA, kNA } }, // Niobium
{ Mo, { kNA, kNA, kNA, kNA, kNA, 69, 65, 61, 59, kNA, kNA } }, // Molybdenum
{ Tc, { kNA, kNA, kNA, kNA, kNA, kNA, 64.5, 60, kNA, 56, kNA } }, // Technetium
{ Ru, { kNA, kNA, kNA, kNA, kNA, 68, 62, 56.5, kNA, 38, 36 } }, // Ruthenium
{ Rh, { kNA, kNA, kNA, kNA, kNA, 66.5, 60, 55, kNA, kNA, kNA } }, // Rhodium
{ Pd, { kNA, kNA, kNA, 59, 86, 76, 61.5, kNA, kNA, kNA, kNA } }, // Palladium
{ Tc, { kNA, kNA, kNA, kNA, kNA, kNA, 64.5f, 60, kNA, 56, kNA } }, // Technetium
{ Ru, { kNA, kNA, kNA, kNA, kNA, 68, 62, 56.5f, kNA, 38, 36 } }, // Ruthenium
{ Rh, { kNA, kNA, kNA, kNA, kNA, 66.5f, 60, 55, kNA, kNA, kNA } }, // Rhodium
{ Pd, { kNA, kNA, kNA, 59, 86, 76, 61.5f, kNA, kNA, kNA, kNA } }, // Palladium
{ Ag, { kNA, kNA, kNA, 115, 94, 75, kNA, kNA, kNA, kNA, kNA } }, // Silver
{ Cd, { kNA, kNA, kNA, kNA, 95, kNA, kNA, kNA, kNA, kNA, kNA } }, // Cadmium
{ In, { kNA, kNA, kNA, kNA, kNA, 80, kNA, kNA, kNA, kNA, kNA } }, // Indium
......@@ -329,48 +329,48 @@ const struct ionic_radii
{ Xe, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 48 } }, // Xenon
{ Cs, { kNA, kNA, kNA, 167, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Caesium
{ Ba, { kNA, kNA, kNA, kNA, 135, kNA, kNA, kNA, kNA, kNA, kNA } }, // Barium
{ La, { kNA, kNA, kNA, kNA, kNA, 103.2, kNA, kNA, kNA, kNA, kNA } }, // Lanthanum
{ La, { kNA, kNA, kNA, kNA, kNA, 103.2f, kNA, kNA, kNA, kNA, kNA } }, // Lanthanum
{ Ce, { kNA, kNA, kNA, kNA, kNA, 101, 87, kNA, kNA, kNA, kNA } }, // Cerium
{ Pr, { kNA, kNA, kNA, kNA, kNA, 99, 85, kNA, kNA, kNA, kNA } }, // Praseodymium
{ Nd, { kNA, kNA, kNA, kNA, 129, 98.3, kNA, kNA, kNA, kNA, kNA } }, // Neodymium
{ Nd, { kNA, kNA, kNA, kNA, 129, 98.3f, kNA, kNA, kNA, kNA, kNA } }, // Neodymium
{ Pm, { kNA, kNA, kNA, kNA, kNA, 97, kNA, kNA, kNA, kNA, kNA } }, // Promethium
{ Sm, { kNA, kNA, kNA, kNA, 122, 95.8, kNA, kNA, kNA, kNA, kNA } }, // Samarium
{ Eu, { kNA, kNA, kNA, kNA, 117, 94.7, kNA, kNA, kNA, kNA, kNA } }, // Europium
{ Gd, { kNA, kNA, kNA, kNA, kNA, 93.5, kNA, kNA, kNA, kNA, kNA } }, // Gadolinium
{ Tb, { kNA, kNA, kNA, kNA, kNA, 92.3, 76, kNA, kNA, kNA, kNA } }, // Terbium
{ Dy, { kNA, kNA, kNA, kNA, 107, 91.2, kNA, kNA, kNA, kNA, kNA } }, // Dysprosium
{ Ho, { kNA, kNA, kNA, kNA, kNA, 90.1, kNA, kNA, kNA, kNA, kNA } }, // Holmium
{ Sm, { kNA, kNA, kNA, kNA, 122, 95.8f, kNA, kNA, kNA, kNA, kNA } }, // Samarium
{ Eu, { kNA, kNA, kNA, kNA, 117, 94.7f, kNA, kNA, kNA, kNA, kNA } }, // Europium
{ Gd, { kNA, kNA, kNA, kNA, kNA, 93.5f, kNA, kNA, kNA, kNA, kNA } }, // Gadolinium
{ Tb, { kNA, kNA, kNA, kNA, kNA, 92.3f, 76, kNA, kNA, kNA, kNA } }, // Terbium
{ Dy, { kNA, kNA, kNA, kNA, 107, 91.2f, kNA, kNA, kNA, kNA, kNA } }, // Dysprosium
{ Ho, { kNA, kNA, kNA, kNA, kNA, 90.1f, kNA, kNA, kNA, kNA, kNA } }, // Holmium
{ Er, { kNA, kNA, kNA, kNA, kNA, 89, kNA, kNA, kNA, kNA, kNA } }, // Erbium
{ Tm, { kNA, kNA, kNA, kNA, 103, 88, kNA, kNA, kNA, kNA, kNA } }, // Thulium
{ Yb, { kNA, kNA, kNA, kNA, 102, 86.8, kNA, kNA, kNA, kNA, kNA } }, // Ytterbium
{ Lu, { kNA, kNA, kNA, kNA, kNA, 86.1, kNA, kNA, kNA, kNA, kNA } }, // Lutetium
{ Yb, { kNA, kNA, kNA, kNA, 102, 86.8f, kNA, kNA, kNA, kNA, kNA } }, // Ytterbium
{ Lu, { kNA, kNA, kNA, kNA, kNA, 86.1f, kNA, kNA, kNA, kNA, kNA } }, // Lutetium
{ Hf, { kNA, kNA, kNA, kNA, kNA, kNA, 71, kNA, kNA, kNA, kNA } }, // Hafnium
{ Ta, { kNA, kNA, kNA, kNA, kNA, 72, 68, 64, kNA, kNA, kNA } }, // Tantalum
{ W, { kNA, kNA, kNA, kNA, kNA, kNA, 66, 62, 60, kNA, kNA } }, // Tungsten
{ Re, { kNA, kNA, kNA, kNA, kNA, kNA, 63, 58, 55, 53, kNA } }, // Rhenium
{ Os, { kNA, kNA, kNA, kNA, kNA, kNA, 63, 57.5, 54.5, 52.5, 39 } }, // Osmium
{ Ir, { kNA, kNA, kNA, kNA, kNA, 68, 62.5, 57, kNA, kNA, kNA } }, // Iridium
{ Pt, { kNA, kNA, kNA, kNA, 80, kNA, 62.5, 57, kNA, kNA, kNA } }, // Platinum
{ Os, { kNA, kNA, kNA, kNA, kNA, kNA, 63, 57.5f, 54.5f, 52.5f, 39 } }, // Osmium
{ Ir, { kNA, kNA, kNA, kNA, kNA, 68, 62.5f, 57, kNA, kNA, kNA } }, // Iridium
{ Pt, { kNA, kNA, kNA, kNA, 80, kNA, 62.5f, 57, kNA, kNA, kNA } }, // Platinum
{ Au, { kNA, kNA, kNA, 137, kNA, 85, kNA, 57, kNA, kNA, kNA } }, // Gold
{ Hg, { kNA, kNA, kNA, 119, 102, kNA, kNA, kNA, kNA, kNA, kNA } }, // Mercury
{ Tl, { kNA, kNA, kNA, 150, kNA, 88.5, kNA, kNA, kNA, kNA, kNA } }, // Thallium
{ Pb, { kNA, kNA, kNA, kNA, 119, kNA, 77.5, kNA, kNA, kNA, kNA } }, // Lead
{ Tl, { kNA, kNA, kNA, 150, kNA, 88.5f, kNA, kNA, kNA, kNA, kNA } }, // Thallium
{ Pb, { kNA, kNA, kNA, kNA, 119, kNA, 77.5f, kNA, kNA, kNA, kNA } }, // Lead
{ Bi, { kNA, kNA, kNA, kNA, kNA, 103, kNA, 76, kNA, kNA, kNA } }, // Bismuth
{ Po, { kNA, 223, kNA, kNA, kNA, kNA, 94, kNA, 67, kNA, kNA } }, // Polonium
{ At, { kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, kNA, 62, kNA } }, // Astatine
{ Fr, { kNA, kNA, kNA, 180, kNA, kNA, kNA, kNA, kNA, kNA, kNA } }, // Francium
{ Ra, { kNA, kNA, kNA, kNA, 148, kNA, kNA, kNA, kNA, kNA, kNA } }, // Radium
{ Ac, { kNA, kNA, kNA, kNA, kNA, 106.5, kNA, kNA, kNA, kNA, kNA } }, // Actinium
{ Ac, { kNA, kNA, kNA, kNA, kNA, 106.5f, kNA, kNA, kNA, kNA, kNA } }, // Actinium
{ Th, { kNA, kNA, kNA, kNA, kNA, kNA, 94, kNA, kNA, kNA, kNA } }, // Thorium
{ Pa, { kNA, kNA, kNA, kNA, kNA, 104, 90, 78, kNA, kNA, kNA } }, // Protactinium
{ U, { kNA, kNA, kNA, kNA, kNA, 102.5, 89, 76, 73, kNA, kNA } }, // Uranium
{ U, { kNA, kNA, kNA, kNA, kNA, 102.5f, 89, 76, 73, kNA, kNA } }, // Uranium
{ Np, { kNA, kNA, kNA, kNA, 110, 101, 87, 75, 72, 71, kNA } }, // Neptunium
{ Pu, { kNA, kNA, kNA, kNA, kNA, 100, 86, 74, 71, kNA, kNA } }, // Plutonium
{ Am, { kNA, kNA, kNA, kNA, 126, 97.5, 85, kNA, kNA, kNA, kNA } }, // Americium
{ Am, { kNA, kNA, kNA, kNA, 126, 97.5f, 85, kNA, kNA, kNA, kNA } }, // Americium
{ Cm, { kNA, kNA, kNA, kNA, kNA, 97, 85, kNA, kNA, kNA, kNA } }, // Curium
{ Bk, { kNA, kNA, kNA, kNA, kNA, 96, 83, kNA, kNA, kNA, kNA } }, // Berkelium
{ Cf, { kNA, kNA, kNA, kNA, kNA, 95, 82.1, kNA, kNA, kNA, kNA } }, // Californium
{ Es, { kNA, kNA, kNA, kNA, kNA, 83.5, kNA, kNA, kNA, kNA, kNA } }, // Einsteinium
{ Cf, { kNA, kNA, kNA, kNA, kNA, 95, 82.1f, kNA, kNA, kNA, kNA } }, // Californium
{ Es, { kNA, kNA, kNA, kNA, kNA, 83.5f, kNA, kNA, kNA, kNA, kNA } }, // Einsteinium
};
......
src/category.cpp
......@@ -24,14 +24,14 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <numeric>
#include <stack>
#include <cif++/category.hpp>
#include <cif++/datablock.hpp>
#include <cif++/parser.hpp>
#include <cif++/utilities.hpp>
#include <numeric>
#include <stack>
// TODO: Find out what the rules are exactly for linked items, the current implementation
// is inconsistent. It all depends whether a link is satified if a field taking part in the
// set of linked items is null at one side and not null in the other.
......@@ -1241,10 +1241,10 @@ size_t category::erase(condition &&cond, std::function<void(row_handle)> &&visit
for (auto &&[childCat, link] : m_child_links)
{
auto cond = get_children_condition(*ri, *childCat);
if (not cond)
auto ccond = get_children_condition(*ri, *childCat);
if (not ccond)
continue;
potential_orphans[childCat] = std::move(potential_orphans[childCat]) or std::move(cond);
potential_orphans[childCat] = std::move(potential_orphans[childCat]) or std::move(ccond);
}
save_value sv(m_validator);
......
src/compound.cpp
......@@ -24,16 +24,15 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cif++/compound.hpp>
#include <filesystem>
#include <fstream>
#include <map>
#include <mutex>
#include <numeric>
#include <shared_mutex>
#include <filesystem>
#include <fstream>
#include <cif++/compound.hpp>
namespace fs = std::filesystem;
namespace cif
......
src/item.cpp
......@@ -24,10 +24,10 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cassert>
#include <cif++/row.hpp>
#include <cassert>
namespace cif
{
......
src/model.cpp
......@@ -34,8 +34,6 @@
namespace fs = std::filesystem;
extern int VERBOSE;
namespace cif::mm
{
......@@ -954,7 +952,7 @@ float monomer::omega(const monomer &a, const monomer &b)
bool monomer::is_cis(const monomer &a, const monomer &b)
{
return omega(a, b) < 30.0f;
return std::abs(omega(a, b)) < 30.0f;
}
// --------------------------------------------------------------------
......@@ -1155,7 +1153,7 @@ branch::branch(structure &structure, const std::string &asym_id, const std::stri
auto &branch_scheme = db["pdbx_branch_scheme"];
auto &branch_link = db["pdbx_entity_branch_link"];
for (const auto &entity_id : struct_asym.find<std::string>("id"_key == asym_id, "entity_id"))
for (const auto &asym_entity_id : struct_asym.find<std::string>("id"_key == asym_id, "entity_id"))
{
for (const auto &[comp_id, num] : branch_scheme.find<std::string, int>(
"asym_id"_key == asym_id, "mon_id", "pdb_seq_num"))
......@@ -1164,7 +1162,7 @@ branch::branch(structure &structure, const std::string &asym_id, const std::stri
}
for (const auto &[num1, num2, atom1, atom2] : branch_link.find<size_t, size_t, std::string, std::string>(
"entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
"entity_id"_key == asym_entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
{
// if (not iequals(atom1, "c1"))
// throw std::runtime_error("invalid pdbx_entity_branch_link");
......@@ -1238,7 +1236,7 @@ sugar &branch::construct_sugar(const std::string &compound_id)
{"type", compound->type()}});
}
sugar &result = emplace_back(*this, compound_id, m_asym_id, size() + 1);
sugar &result = emplace_back(*this, compound_id, m_asym_id, static_cast<int>(size() + 1));
db["pdbx_branch_scheme"].emplace({
{"asym_id", result.get_asym_id()},
......@@ -2388,180 +2386,180 @@ branch &structure::create_branch()
return m_branches.emplace_back(*this, asym_id, entity_id);
}
branch &structure::create_branch(std::vector<row_initializer> atoms)
{
// // sanity check
// for (auto &nag_atom : atoms)
// {
// for (const auto &[name, value] : nag_atom)
// {
// if (name == "label_comp_id" and value != "NAG")
// throw std::logic_error("The first sugar in a branch should be a NAG");
// }
// }
// using namespace literals;
// auto &branch = create_branch();
// auto asym_id = branch.get_asym_id();
// auto entity_id = branch.get_entity_id();
// auto &sugar = branch.emplace_back(branch, "NAG", asym_id, 1);
// auto &atom_site = m_db["atom_site"];
// for (auto &atom : atoms)
// {
// auto atom_id = atom_site.get_unique_id("");
// atom.set_value("id", atom_id);
// atom.set_value("label_asym_id", asym_id);
// atom.set_value("auth_asym_id", asym_id);
// atom.set_value("label_entity_id", entity_id);
// atom.set_value({ "auth_seq_id", 1 });
// atom.set_value_if_empty({"group_PDB", "HETATM"});
// atom.set_value_if_empty({"label_comp_id", "NAG"});
// atom.set_value_if_empty({"label_seq_id", "."});
// atom.set_value_if_empty({"auth_comp_id", "NAG"});
// atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
// atom.set_value_if_empty({"label_alt_id", ""});
// auto row = atom_site.emplace(atom.begin(), atom.end());
// auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
// sugar.add_atom(newAtom);
// }
// // // now we can create the entity and get the real ID
// // auto entity_id = create_entity_for_branch(branch);
// // assert(not entity_id.empty());
// for (auto &a : sugar.atoms())
// a.set_property("label_entity_id", entity_id);
// m_db["pdbx_branch_scheme"].emplace({
// {"asym_id", asym_id},
// {"entity_id", entity_id},
// {"num", 1},
// {"mon_id", "NAG"},
// {"pdb_asym_id", asym_id},
// {"pdb_seq_num", 1},
// {"pdb_mon_id", "NAG"},
// branch &structure::create_branch(std::vector<row_initializer> atoms)
// {
// // // sanity check
// // for (auto &nag_atom : atoms)
// // {
// // for (const auto &[name, value] : nag_atom)
// // {
// // if (name == "label_comp_id" and value != "NAG")
// // throw std::logic_error("The first sugar in a branch should be a NAG");
// // }
// // }
// // using namespace literals;
// // auto &branch = create_branch();
// // auto asym_id = branch.get_asym_id();
// // auto entity_id = branch.get_entity_id();
// // auto &sugar = branch.emplace_back(branch, "NAG", asym_id, 1);
// // auto &atom_site = m_db["atom_site"];
// // for (auto &atom : atoms)
// // {
// // auto atom_id = atom_site.get_unique_id("");
// // atom.set_value("id", atom_id);
// // atom.set_value("label_asym_id", asym_id);
// // atom.set_value("auth_asym_id", asym_id);
// // atom.set_value("label_entity_id", entity_id);
// // atom.set_value({ "auth_seq_id", 1 });
// // atom.set_value_if_empty({"group_PDB", "HETATM"});
// // atom.set_value_if_empty({"label_comp_id", "NAG"});
// // atom.set_value_if_empty({"label_seq_id", "."});
// // atom.set_value_if_empty({"auth_comp_id", "NAG"});
// // atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
// // atom.set_value_if_empty({"label_alt_id", ""});
// // auto row = atom_site.emplace(atom.begin(), atom.end());
// // auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
// // sugar.add_atom(newAtom);
// // }
// // // // now we can create the entity and get the real ID
// // // auto entity_id = create_entity_for_branch(branch);
// // // assert(not entity_id.empty());
// // for (auto &a : sugar.atoms())
// // a.set_property("label_entity_id", entity_id);
// // m_db["pdbx_branch_scheme"].emplace({
// // {"asym_id", asym_id},
// // {"entity_id", entity_id},
// // {"num", 1},
// // {"mon_id", "NAG"},
// // {"pdb_asym_id", asym_id},
// // {"pdb_seq_num", 1},
// // {"pdb_mon_id", "NAG"},
// // // TODO: need fix, collect from nag_atoms?
// // {"auth_asym_id", asym_id},
// // {"auth_mon_id", "NAG"},
// // {"auth_seq_num", 1},
// // {"hetero", "n"}
// // });
// // return branch;
// }
// // TODO: need fix, collect from nag_atoms?
// {"auth_asym_id", asym_id},
// {"auth_mon_id", "NAG"},
// {"auth_seq_num", 1},
// branch &structure::extend_branch(const std::string &asym_id, std::vector<row_initializer> atom_info,
// int link_sugar, const std::string &link_atom)
// {
// // // sanity check
// // std::string compoundID;
// {"hetero", "n"}
// });
// // for (auto &atom : atom_info)
// // {
// // for (const auto &[name, value] : atom)
// // {
// // if (name != "label_comp_id")
// // continue;
// return branch;
}
// // if (compoundID.empty())
// // compoundID = value;
// // else if (value != compoundID)
// // throw std::logic_error("All atoms should be of the same type");
// // }
// // }
branch &structure::extend_branch(const std::string &asym_id, std::vector<row_initializer> atom_info,
int link_sugar, const std::string &link_atom)
{
// // sanity check
// std::string compoundID;
// // using namespace literals;
// for (auto &atom : atom_info)
// {
// for (const auto &[name, value] : atom)
// {
// if (name != "label_comp_id")
// continue;
// // // auto &branch = m_branches.emplace_back(*this, asym_id);
// // auto tmp_entity_id = m_db["entity"].get_unique_id("");
// if (compoundID.empty())
// compoundID = value;
// else if (value != compoundID)
// throw std::logic_error("All atoms should be of the same type");
// }
// }
// // auto &atom_site = m_db["atom_site"];
// using namespace literals;
// // auto bi = std::find_if(m_branches.begin(), m_branches.end(), [asym_id](branch &b)
// // { return b.get_asym_id() == asym_id; });
// // if (bi == m_branches.end())
// // throw std::logic_error("Create a branch first!");
// // auto &branch = m_branches.emplace_back(*this, asym_id);
// auto tmp_entity_id = m_db["entity"].get_unique_id("");
// // branch &branch = *bi;
// auto &atom_site = m_db["atom_site"];
// // int sugarNum = static_cast<int>(branch.size() + 1);
// auto bi = std::find_if(m_branches.begin(), m_branches.end(), [asym_id](branch &b)
// { return b.get_asym_id() == asym_id; });
// if (bi == m_branches.end())
// throw std::logic_error("Create a branch first!");
// // auto &sugar = branch.emplace_back(branch, compoundID, asym_id, sugarNum);
// branch &branch = *bi;
// // for (auto &atom : atom_info)
// // {
// // auto atom_id = atom_site.get_unique_id("");
// int sugarNum = static_cast<int>(branch.size() + 1);
// // atom.set_value("id", atom_id);
// // atom.set_value("label_asym_id", asym_id);
// // atom.set_value("auth_asym_id", asym_id);
// // atom.set_value("label_entity_id", tmp_entity_id);
// // atom.set_value({"auth_seq_id", sugarNum });
// auto &sugar = branch.emplace_back(branch, compoundID, asym_id, sugarNum);
// // atom.set_value_if_empty({"group_PDB", "HETATM"});
// // atom.set_value_if_empty({"label_comp_id", compoundID});
// // atom.set_value_if_empty({"auth_comp_id", compoundID});
// // atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
// // atom.set_value_if_empty({"label_alt_id", ""});
// for (auto &atom : atom_info)
// {
// auto atom_id = atom_site.get_unique_id("");
// // auto row = atom_site.emplace(atom.begin(), atom.end());
// atom.set_value("id", atom_id);
// atom.set_value("label_asym_id", asym_id);
// atom.set_value("auth_asym_id", asym_id);
// atom.set_value("label_entity_id", tmp_entity_id);
// atom.set_value({"auth_seq_id", sugarNum });
// // auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
// // sugar.add_atom(newAtom);
// // }
// atom.set_value_if_empty({"group_PDB", "HETATM"});
// atom.set_value_if_empty({"label_comp_id", compoundID});
// atom.set_value_if_empty({"auth_comp_id", compoundID});
// atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
// atom.set_value_if_empty({"label_alt_id", ""});
// // sugar.set_link(branch.at(link_sugar - 1).get_atom_by_atom_id(link_atom));
// auto row = atom_site.emplace(atom.begin(), atom.end());
// // auto entity_id = create_entity_for_branch(branch);
// auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
// sugar.add_atom(newAtom);
// }
// // // Update the entity id of the asym
// // auto &struct_asym = m_db["struct_asym"];
// // auto r = struct_asym.find1("id"_key == asym_id);
// // r["entity_id"] = entity_id;
// sugar.set_link(branch.at(link_sugar - 1).get_atom_by_atom_id(link_atom));
// // for (auto &s2 : branch)
// // {
// // for (auto atom : s2.atoms())
// // atom.set_property("label_entity_id", entity_id);
// // }
// auto entity_id = create_entity_for_branch(branch);
// // auto &pdbx_branch_scheme = m_db["pdbx_branch_scheme"];
// // pdbx_branch_scheme.erase("asym_id"_key == asym_id);
// // Update the entity id of the asym
// auto &struct_asym = m_db["struct_asym"];
// auto r = struct_asym.find1("id"_key == asym_id);
// r["entity_id"] = entity_id;
// // for (auto &s2 : branch)
// // {
// // pdbx_branch_scheme.emplace({
// // {"asym_id", asym_id},
// // {"entity_id", entity_id},
// // {"num", s2.num()},
// // {"mon_id", s2.get_compound_id()},
// for (auto &s2 : branch)
// {
// for (auto atom : s2.atoms())
// atom.set_property("label_entity_id", entity_id);
// }
// // {"pdb_asym_id", asym_id},
// // {"pdb_seq_num", s2.num()},
// // {"pdb_mon_id", s2.get_compound_id()},
// auto &pdbx_branch_scheme = m_db["pdbx_branch_scheme"];
// pdbx_branch_scheme.erase("asym_id"_key == asym_id);
// // // TODO: need fix, collect from nag_atoms?
// // {"auth_asym_id", asym_id},
// // {"auth_mon_id", s2.get_compound_id()},
// // {"auth_seq_num", s2.get_auth_seq_id()},
// for (auto &s2 : branch)
// {
// pdbx_branch_scheme.emplace({
// {"asym_id", asym_id},
// {"entity_id", entity_id},
// {"num", s2.num()},
// {"mon_id", s2.get_compound_id()},
// {"pdb_asym_id", asym_id},
// {"pdb_seq_num", s2.num()},
// {"pdb_mon_id", s2.get_compound_id()},
// // TODO: need fix, collect from nag_atoms?
// {"auth_asym_id", asym_id},
// {"auth_mon_id", s2.get_compound_id()},
// {"auth_seq_num", s2.get_auth_seq_id()},
// {"hetero", "n"}
// });
// }
// // {"hetero", "n"}
// // });
// // }
// return branch;
}
// // return branch;
// }
std::string structure::create_entity_for_branch(branch &branch)
{
......
src/parser.cpp
......@@ -24,22 +24,16 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cassert>
#include <iostream>
#include <map>
#include <regex>
#include <stack>
#include <cif++/utilities.hpp>
#include <cif++/forward_decl.hpp>
#include <cif++/parser.hpp>
#include <cif++/file.hpp>
namespace cif
{
extern int VERBOSE;
}
#include <cassert>
#include <iostream>
#include <map>
#include <regex>
#include <stack>
namespace cif
{
......
src/pdb/cif2pdb.cpp
......@@ -24,6 +24,10 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cif++.hpp>
#include <cif++/pdb/cif2pdb.hpp>
#include <cif++/gzio.hpp>
#include <cmath>
#include <deque>
#include <iomanip>
......@@ -31,9 +35,6 @@
#include <regex>
#include <set>
#include <cif++.hpp>
#include <cif++/pdb/cif2pdb.hpp>
#include <cif++/gzio.hpp>
namespace cif::pdb
{
......
src/pdb/pdb2cif.cpp
......@@ -24,17 +24,16 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <iomanip>
#include <map>
#include <set>
#include <stack>
#include <cif++.hpp>
#include <cif++/pdb/pdb2cif.hpp>
#include <cif++/pdb/pdb2cif_remark_3.hpp>
#include <cif++/gzio.hpp>
#include <iomanip>
#include <map>
#include <set>
#include <stack>
using cif::category;
using cif::datablock;
using cif::iequals;
......
src/pdb/pdb2cif_remark_3.cpp
......@@ -25,12 +25,11 @@
*/
#include <cif++.hpp>
#include <cif++/pdb/pdb2cif_remark_3.hpp>
#include <map>
#include <set>
#include <cif++/pdb/pdb2cif_remark_3.hpp>
namespace cif::pdb
{
......
src/pdb/tls.cpp
......@@ -27,12 +27,12 @@
// #include <sys/ioctl.h>
// #include <termios.h>
#include <iomanip>
#include <iostream>
#include <cif++.hpp>
#include <cif++/pdb/tls.hpp>
#include <iomanip>
#include <iostream>
namespace cif
{
......
src/point.cpp
......@@ -24,11 +24,11 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cif++/point.hpp>
#include <cassert>
#include <random>
#include <cif++/point.hpp>
namespace cif
{
......@@ -369,7 +369,7 @@ quaternion construct_for_dihedral_angle(point p1, point p2, point p3, point p4,
float dh = dihedral_angle(p1, p2, p3, p4);
for (int iteration = 0; iteration < 100; ++iteration)
{
float delta = std::fmod(angle - dh, 360);
float delta = std::fmod(angle - dh, 360.0f);
if (delta < -180)
delta += 360;
......
src/symmetry.cpp
......@@ -24,10 +24,10 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <stdexcept>
#include <cif++/symmetry.hpp>
#include <stdexcept>
#include "./symop_table_data.hpp"
namespace cif
......
src/text.cpp
......@@ -24,11 +24,11 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cif++/text.hpp>
#include <algorithm>
#include <cassert>
#include <cif++/text.hpp>
namespace cif
{
......
src/utilities.cpp
......@@ -24,6 +24,9 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cif++/utilities.hpp>
#include "revision.hpp"
#include <atomic>
#include <cassert>
#include <cmath>
......@@ -44,10 +47,6 @@
#include <termios.h>
#endif
#include <cif++/utilities.hpp>
#include "revision.hpp"
namespace fs = std::filesystem;
// --------------------------------------------------------------------
......@@ -408,9 +407,9 @@ struct rsrc_imp
#if _MSC_VER
extern "C" const mrsrc::rsrc_imp *gResourceIndexDefault[1] = {};
extern "C" const char *gResourceDataDefault[1] = {};
extern "C" const char *gResourceNameDefault[1] = {};
extern "C" CIFPP_EXPORT const mrsrc::rsrc_imp *gResourceIndexDefault[1] = {};
extern "C" CIFPP_EXPORT const char *gResourceDataDefault[1] = {};
extern "C" CIFPP_EXPORT const char *gResourceNameDefault[1] = {};
extern "C" const mrsrc::rsrc_imp gResourceIndex[];
extern "C" const char gResourceData[];
......
src/validate.cpp
......@@ -24,6 +24,11 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <cif++/dictionary_parser.hpp>
#include <cif++/validate.hpp>
#include <cif++/utilities.hpp>
#include <cif++/gzio.hpp>
#include <cassert>
#include <fstream>
#include <iostream>
......@@ -41,12 +46,6 @@ using boost::regex;
using std::regex;
#endif
#include <cif++/dictionary_parser.hpp>
#include <cif++/validate.hpp>
#include <cif++/utilities.hpp>
#include <cif++/gzio.hpp>
namespace cif
{
......
test/sugar-test.cpp
......@@ -96,87 +96,87 @@ BOOST_AUTO_TEST_CASE(sugar_name_1)
}
}
// --------------------------------------------------------------------
// // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_sugar_1)
{
using namespace cif::literals;
// BOOST_AUTO_TEST_CASE(create_sugar_1)
// {
// using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
cif::file file(example.string());
cif::mm::structure s(file);
// const std::filesystem::path example(gTestDir / "1juh.cif.gz");
// cif::file file(example.string());
// cif::mm::structure s(file);
// collect atoms from asym L first
auto &NAG = s.get_residue("L");
auto nagAtoms = NAG.atoms();
// // collect atoms from asym L first
// auto &NAG = s.get_residue("L");
// auto nagAtoms = NAG.atoms();
std::vector<cif::row_initializer> ai;
// std::vector<cif::row_initializer> ai;
auto &db = s.get_datablock();
auto &as = db["atom_site"];
// auto &db = s.get_datablock();
// auto &as = db["atom_site"];
// NOTE, row_initializer does not actually hold the data, so copy it first
// before it gets destroyed by remove_residue
// // NOTE, row_initializer does not actually hold the data, so copy it first
// // before it gets destroyed by remove_residue
for (auto r : as.find("label_asym_id"_key == "L"))
/*auto &ri = */ai.emplace_back(r);
// for (auto r : as.find("label_asym_id"_key == "L"))
// /*auto &ri = */ai.emplace_back(r);
s.remove_residue(NAG);
// s.remove_residue(NAG);
auto &branch = s.create_branch(ai);
// auto &branch = s.create_branch(ai);
BOOST_CHECK_EQUAL(branch.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(branch.size(), 1);
// BOOST_CHECK_EQUAL(branch.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose");
// BOOST_CHECK_EQUAL(branch.size(), 1);
BOOST_CHECK_EQUAL(branch[0].atoms().size(), nagAtoms.size());
// BOOST_CHECK_EQUAL(branch[0].atoms().size(), nagAtoms.size());
BOOST_CHECK(file.is_valid());
// BOOST_CHECK(file.is_valid());
file.save(gTestDir / "test-create_sugar_1.cif");
}
// file.save(gTestDir / "test-create_sugar_1.cif");
// }
// --------------------------------------------------------------------
// // --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(create_sugar_2)
{
using namespace cif::literals;
// BOOST_AUTO_TEST_CASE(create_sugar_2)
// {
// using namespace cif::literals;
const std::filesystem::path example(gTestDir / "1juh.cif.gz");
cif::file file(example.string());
cif::mm::structure s(file);
// const std::filesystem::path example(gTestDir / "1juh.cif.gz");
// cif::file file(example.string());
// cif::mm::structure s(file);
// Get branch for H
auto &bH = s.get_branch_by_asym_id("H");
// // Get branch for H
// auto &bH = s.get_branch_by_asym_id("H");
BOOST_CHECK_EQUAL(bH.size(), 2);
// BOOST_CHECK_EQUAL(bH.size(), 2);
std::vector<cif::row_initializer> ai[2];
// std::vector<cif::row_initializer> ai[2];
auto &db = s.get_datablock();
auto &as = db["atom_site"];
// auto &db = s.get_datablock();
// auto &as = db["atom_site"];
for (size_t i = 0; i < 2; ++i)
{
for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
/*auto &ri = */ai[i].emplace_back(r);
}
// for (size_t i = 0; i < 2; ++i)
// {
// for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
// /*auto &ri = */ai[i].emplace_back(r);
// }
s.remove_branch(bH);
// s.remove_branch(bH);
BOOST_CHECK(file.is_valid());
// BOOST_CHECK(file.is_valid());
auto &bN = s.create_branch(ai[0]);
s.extend_branch(bN.get_asym_id(), ai[1], 1, "O4");
// auto &bN = s.create_branch(ai[0]);
// s.extend_branch(bN.get_asym_id(), ai[1], 1, "O4");
BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose");
BOOST_CHECK_EQUAL(bN.size(), 2);
// BOOST_CHECK_EQUAL(bN.name(), "2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose");
// BOOST_CHECK_EQUAL(bN.size(), 2);
BOOST_CHECK(file.is_valid());
// BOOST_CHECK(file.is_valid());
file.save(gTestDir / "test-create_sugar_2.cif");
// file.save(gTestDir / "test-create_sugar_2.cif");
BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));
}
// BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));
// }
// --------------------------------------------------------------------
......
test/unit-3d-test.cpp
......@@ -93,13 +93,13 @@ BOOST_AUTO_TEST_CASE(t1)
const auto &&[angle0, axis0] = cif::quaternion_to_angle_axis(q);
std::vector<cif::point> p1{
{ 16.979, 13.301, 44.555 },
{ 18.150, 13.525, 43.680 },
{ 18.656, 14.966, 43.784 },
{ 17.890, 15.889, 44.078 },
{ 17.678, 13.270, 42.255 },
{ 16.248, 13.734, 42.347 },
{ 15.762, 13.216, 43.724 }
{ 16.979f, 13.301f, 44.555f },
{ 18.150f, 13.525f, 43.680f },
{ 18.656f, 14.966f, 43.784f },
{ 17.890f, 15.889f, 44.078f },
{ 17.678f, 13.270f, 42.255f },
{ 16.248f, 13.734f, 42.347f },
{ 15.762f, 13.216f, 43.724f }
};
auto p2 = p1;
......@@ -120,7 +120,7 @@ BOOST_AUTO_TEST_CASE(t1)
for (auto &p : p1)
p.rotate(q2);
float rmsd = cif::RMSd(p1, p2);
auto rmsd = cif::RMSd(p1, p2);
BOOST_TEST(rmsd < 1e-5);
......@@ -175,27 +175,27 @@ BOOST_AUTO_TEST_CASE(dh_q_1)
float angle;
cif::point pts[4];
} tests[] = {
{ -97.5,
{ { 68.8649979, -7.34800005, 54.3769989 },
{ 68.1350021, -8.18700027, 53.6489983 },
{ 68.7760239, -9.07335377, 52.7140236 },
{ 68.9000015, -10.3944235, 53.2217026 } } },
{ 80.3,
{ { 0.304512024, 0.531184196, 2.25860214 },
{ 0.956512451, 0.0321846008, 1.07460022 },
{ -97.5f,
{ { 68.8649979f, -7.34800005f, 54.3769989f },
{ 68.1350021f, -8.18700027f, 53.6489983f },
{ 68.7760239f, -9.07335377f, 52.7140236f },
{ 68.9000015f, -10.3944235f, 53.2217026f } } },
{ 80.3f,
{ { 0.304512024f, 0.531184196f, 2.25860214f },
{ 0.956512451f, 0.0321846008f, 1.07460022f },
{ 0, 0, 0 },
{ 0.21336633, -1.09552193, -0.878999829 } } },
{ -97.5,
{ { 0.088973999, 1.72535372, 1.66297531 },
{ -0.641021729, 0.886353493, 0.93497467 },
{ 0.21336633f, -1.09552193f, -0.878999829f } } },
{ -97.5f,
{ { 0.088973999f, 1.72535372f, 1.66297531f },
{ -0.641021729f, 0.886353493f, 0.93497467f },
{ 0, 0, 0 },
{ 1.29433727, -0.395142615, 0.432300746 } } },
{ -97.5,
{ 1.29433727f, -0.395142615f, 0.432300746f } } },
{ -97.5f,
{
{ 0.088973999, 1.72535372, 1.66297531 },
{ -0.641021729, 0.886353493, 0.93497467 },
{ 0.088973999f, 1.72535372f, 1.66297531f },
{ -0.641021729f, 0.886353493f, 0.93497467f },
{ 0, 0, 0 },
{ 1.33983064, 0.384027064, -0.275154471 },
{ 1.33983064f, 0.384027064f, -0.275154471f },
} }
};
......
test/unit-v2-test.cpp
......@@ -78,23 +78,23 @@ bool init_unit_test()
BOOST_AUTO_TEST_CASE(cc_1)
{
std::tuple<std::string_view, float, char> tests[] = {
{ "1.0", 1.0, 0 },
{ "1.0e10", 1.0e10, 0 },
{ "-1.1e10", -1.1e10, 0 },
{ "-.2e11", -.2e11, 0 },
{ "1.3e-10", 1.3e-10, 0 },
{ "1.0 ", 1.0, ' ' },
{ "1.0e10 ", 1.0e10, ' ' },
{ "-1.1e10 ", -1.1e10, ' ' },
{ "-.2e11 ", -.2e11, ' ' },
{ "1.3e-10 ", 1.3e-10, ' ' },
{ "3.0", 3.0, 0 },
{ "3.0 ", 3.0, ' ' },
{ "3.000000", 3.0, 0 },
{ "3.000000 ", 3.0, ' ' },
{ "1.0", 1.0f, 0 },
{ "1.0e10", 1.0e10f, 0 },
{ "-1.1e10", -1.1e10f, 0 },
{ "-.2e11", -.2e11f, 0 },
{ "1.3e-10", 1.3e-10f, 0 },
{ "1.0 ", 1.0f, ' ' },
{ "1.0e10 ", 1.0e10f, ' ' },
{ "-1.1e10 ", -1.1e10f, ' ' },
{ "-.2e11 ", -.2e11f, ' ' },
{ "1.3e-10 ", 1.3e-10f, ' ' },
{ "3.0", 3.0f, 0 },
{ "3.0 ", 3.0f, ' ' },
{ "3.000000", 3.0f, 0 },
{ "3.000000 ", 3.0f, ' ' },
};
for (const auto &[txt, val, ch] : tests)
......@@ -112,7 +112,7 @@ BOOST_AUTO_TEST_CASE(cc_1)
BOOST_AUTO_TEST_CASE(cc_2)
{
std::tuple<float, int, std::string_view> tests[] = {
{ 1.1, 1, "1.1" }
{ 1.1f, 1, "1.1" }
};
for (const auto &[val, prec, test] : tests)
......@@ -131,7 +131,7 @@ BOOST_AUTO_TEST_CASE(item_1)
using namespace cif;
item i1("1", "1");
item i2("2", 2.0);
item i2("2", 2.0f);
item i3("3", '3');
item ci1(i1);
......@@ -163,23 +163,23 @@ BOOST_AUTO_TEST_CASE(r_1)
c.emplace({
{ "f-1", 1 },
{ "f-2", "two" },
{ "f-3", 3.0, 3 },
{ "f-3", 3.0f, 3 },
});
auto row = c.front();
BOOST_CHECK_EQUAL(row["f-1"].compare(1), 0);
BOOST_CHECK_EQUAL(row["f-2"].compare("two"), 0);
BOOST_CHECK_EQUAL(row["f-3"].compare(3.0), 0); // This fails when running in valgrind... sigh
BOOST_CHECK_EQUAL(row["f-3"].compare(3.0f), 0); // This fails when running in valgrind... sigh
const auto &[f1, f2, f3] = row.get<int, std::string, float>("f-1", "f-2", "f-3");
BOOST_CHECK_EQUAL(f1, 1);
BOOST_CHECK_EQUAL(f2, "two");
BOOST_CHECK_EQUAL(f3, 3.0); // This fails when running in valgrind... sigh
BOOST_CHECK_EQUAL(f3, 3.0f); // This fails when running in valgrind... sigh
BOOST_CHECK_EQUAL(row.get<int>("f-1"), 1);
BOOST_CHECK_EQUAL(row.get<std::string>("f-2"), "two");
BOOST_CHECK_EQUAL(row.get<float>("f-3"), 3.0);
BOOST_CHECK_EQUAL(row.get<float>("f-3"), 3.0f);
int f_1;
std::string f_2;
......@@ -189,7 +189,7 @@ BOOST_AUTO_TEST_CASE(r_1)
BOOST_CHECK_EQUAL(f_1, 1);
BOOST_CHECK_EQUAL(f_2, "two");
BOOST_CHECK_EQUAL(f_3, 3.0); // This fails when running in valgrind... sigh
BOOST_CHECK_EQUAL(f_3, 3.0f); // This fails when running in valgrind... sigh
}
BOOST_AUTO_TEST_CASE(r_2)
......@@ -486,14 +486,14 @@ _test.value
BOOST_CHECK_EQUAL(++n, 1);
BOOST_CHECK_EQUAL(r["id"].as<int>(), 1);
BOOST_CHECK_EQUAL(r["name"].as<std::string>(), "aap");
BOOST_CHECK_EQUAL(r["value"].as<float>(), 1.0);
BOOST_CHECK_EQUAL(r["value"].as<float>(), 1.0f);
}
auto t = test.find(cif::key("id") == 1);
BOOST_CHECK(not t.empty());
BOOST_CHECK_EQUAL(t.front()["name"].as<std::string>(), "aap");
auto t2 = test.find(cif::key("value") == 1.2);
auto t2 = test.find(cif::key("value") == 1.2f);
BOOST_CHECK(not t2.empty());
BOOST_CHECK_EQUAL(t2.front()["name"].as<std::string>(), "mies");
}
......
tools/update-libcifpp-data.in
......@@ -2,7 +2,10 @@
set -e
if [ "$EUID" -ne 0 ]
# Get the effective UID, but do so in a compatible way (we may be running dash)
euid=${EUID:-$(id -u)}
if [ "${euid}" -ne 0 ] ; then
then echo "Please run as root"
exit
fi
......
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