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libcifpp
Commit 9d155412 by Maarten L. Hekkelman
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include cstring for gnu c++ 12

parent 35c99564
Showing with 78 additions and 78 deletions
include/cif++/Cif++.hpp
/*- /*-
* SPDX-License-Identifier: BSD-2-Clause * SPDX-License-Identifier: BSD-2-Clause
* *
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
* *
* Redistribution and use in source and binary forms, with or without * Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met: * modification, are permitted provided that the following conditions are met:
* *
* 1. Redistributions of source code must retain the above copyright notice, this * 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer * list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice, * 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation * this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution. * and/or other materials provided with the distribution.
* *
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND * 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 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
...@@ -26,82 +26,82 @@ ...@@ -26,82 +26,82 @@
#pragma once #pragma once
#include <string>
#include <array> #include <array>
#include <cstring>
#include <functional> #include <functional>
#include <iomanip>
#include <iostream> #include <iostream>
#include <list> #include <list>
#include <optional> #include <optional>
#include <regex> #include <regex>
#include <set> #include <set>
#include <sstream>
#include <iomanip>
#include <shared_mutex> #include <shared_mutex>
#include <sstream>
#include <string>
#include <boost/format.hpp> #include <boost/format.hpp>
#include "cif++/CifUtils.hpp" #include "cif++/CifUtils.hpp"
/* /*
Simple C++ interface to CIF files. Simple C++ interface to CIF files.
Assumptions: a file contains one or more datablocks modelled by the class datablock. Assumptions: a file contains one or more datablocks modelled by the class datablock.
Each datablock contains categories. These map to the original tables used to fill Each datablock contains categories. These map to the original tables used to fill
the mmCIF file. Each Category can contain multiple Items, the columns in the table. the mmCIF file. Each Category can contain multiple Items, the columns in the table.
Values are stored as character strings internally. Values are stored as character strings internally.
Synopsis: Synopsis:
// create a cif file // create a cif file
cif::datablock e("1MVE"); cif::datablock e("1MVE");
e.append(cif::Category{"_entry", { "id", "1MVE" } }); e.append(cif::Category{"_entry", { "id", "1MVE" } });
cif::Category atomSite("atom_site"); cif::Category atomSite("atom_site");
size_t nr{}; size_t nr{};
for (auto& myAtom: atoms) for (auto& myAtom: atoms)
{ {
atomSite.push_back({ atomSite.push_back({
{ "group_PDB", "ATOM" }, { "group_PDB", "ATOM" },
{ "id", ++nr }, { "id", ++nr },
{ "type_symbol", myAtom.type.str() }, { "type_symbol", myAtom.type.str() },
... ...
}); });
} }
e.append(move(atomSite)); e.append(move(atomSite));
cif::File f; cif::File f;
f.append(e); f.append(e);
ofstream os("1mve.cif"); ofstream os("1mve.cif");
f.write(os); f.write(os);
// read // read
f.read(ifstream{"1mve.cif"}); f.read(ifstream{"1mve.cif"});
auto& e = f.firstDatablock(); auto& e = f.firstDatablock();
cout << "ID of datablock: " << e.id() << endl; cout << "ID of datablock: " << e.id() << endl;
auto& atoms = e["atom_site"]; auto& atoms = e["atom_site"];
for (auto& atom: atoms) for (auto& atom: atoms)
{ {
cout << atom["group_PDB"] << ", " cout << atom["group_PDB"] << ", "
<< atom["id"] << ", " << atom["id"] << ", "
... ...
float x, y, z; float x, y, z;
cif::tie(x, y, z) = atom.get("Cartn_x", "Cartn_y", "Cartn_z"); cif::tie(x, y, z) = atom.get("Cartn_x", "Cartn_y", "Cartn_z");
... ...
} }
Another way of querying a Category is by using this construct: Another way of querying a Category is by using this construct:
auto cat& = e["atom_site"]; auto cat& = e["atom_site"];
auto Rows = cat.find(Key("label_asym_id") == "A" and Key("label_seq_id") == 1); auto Rows = cat.find(Key("label_asym_id") == "A" and Key("label_seq_id") == 1);
*/ */
...@@ -147,12 +147,12 @@ class Item ...@@ -147,12 +147,12 @@ class Item
Item(std::string_view name, char value) Item(std::string_view name, char value)
: mName(name) : mName(name)
, mValue({ value }) , mValue({value})
{ {
} }
template<typename T, std::enable_if_t<std::is_floating_point_v<T>, int> = 0> template <typename T, std::enable_if_t<std::is_floating_point_v<T>, int> = 0>
Item(std::string_view name, const T& value, const char *fmt) Item(std::string_view name, const T &value, const char *fmt)
: mName(name) : mName(name)
, mValue((boost::format(fmt) % value).str()) , mValue((boost::format(fmt) % value).str())
{ {
...@@ -284,10 +284,10 @@ class Datablock ...@@ -284,10 +284,10 @@ class Datablock
friend bool operator==(const Datablock &lhs, const Datablock &rhs); friend bool operator==(const Datablock &lhs, const Datablock &rhs);
friend std::ostream& operator<<(std::ostream &os, const Datablock &data); friend std::ostream &operator<<(std::ostream &os, const Datablock &data);
private: private:
CategoryList mCategories; // LRU CategoryList mCategories; // LRU
mutable std::shared_mutex mLock; mutable std::shared_mutex mLock;
std::string mName; std::string mName;
const Validator *mValidator; const Validator *mValidator;
...@@ -1636,7 +1636,7 @@ class conditional_iterator_proxy ...@@ -1636,7 +1636,7 @@ class conditional_iterator_proxy
using iterator = conditional_iterator_impl; using iterator = conditional_iterator_impl;
using reference = typename iterator::reference; using reference = typename iterator::reference;
template<typename... Ns> template <typename... Ns>
conditional_iterator_proxy(CategoryType &cat, row_iterator pos, Condition &&cond, Ns... names); conditional_iterator_proxy(CategoryType &cat, row_iterator pos, Condition &&cond, Ns... names);
conditional_iterator_proxy(conditional_iterator_proxy &&p); conditional_iterator_proxy(conditional_iterator_proxy &&p);
...@@ -1910,7 +1910,7 @@ class Category ...@@ -1910,7 +1910,7 @@ class Category
conditional_iterator_proxy<const Category> find(const_iterator pos, Condition &&cond) const conditional_iterator_proxy<const Category> find(const_iterator pos, Condition &&cond) const
{ {
return conditional_iterator_proxy<const Category>{const_cast<Category&>(*this), pos, std::forward<Condition>(cond)}; return conditional_iterator_proxy<const Category>{const_cast<Category &>(*this), pos, std::forward<Condition>(cond)};
} }
template <typename... Ts, typename... Ns> template <typename... Ts, typename... Ns>
...@@ -1931,14 +1931,14 @@ class Category ...@@ -1931,14 +1931,14 @@ class Category
conditional_iterator_proxy<Category, Ts...> find(const_iterator pos, Condition &&cond, Ns... names) conditional_iterator_proxy<Category, Ts...> find(const_iterator pos, Condition &&cond, Ns... names)
{ {
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return"); static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
return {*this, pos, std::forward<Condition>(cond), std::forward<Ns>(names)... }; return {*this, pos, std::forward<Condition>(cond), std::forward<Ns>(names)...};
} }
template <typename... Ts, typename... Ns> template <typename... Ts, typename... Ns>
conditional_iterator_proxy<const Category, Ts...> find(const_iterator pos, Condition &&cond, Ns... names) const conditional_iterator_proxy<const Category, Ts...> find(const_iterator pos, Condition &&cond, Ns... names) const
{ {
static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return"); static_assert(sizeof...(Ts) == sizeof...(Ns), "The number of column titles should be equal to the number of types to return");
return {*this, pos, std::forward<Condition>(cond), std::forward<Ns>(names)... }; return {*this, pos, std::forward<Condition>(cond), std::forward<Ns>(names)...};
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1981,13 +1981,13 @@ class Category ...@@ -1981,13 +1981,13 @@ class Category
} }
template <typename T> template <typename T>
T find1(Condition &&cond, const char* column) const T find1(Condition &&cond, const char *column) const
{ {
return find1<T>(cbegin(), std::forward<Condition>(cond), column); return find1<T>(cbegin(), std::forward<Condition>(cond), column);
} }
template <typename T> template <typename T>
T find1(const_iterator pos, Condition &&cond, const char* column) const T find1(const_iterator pos, Condition &&cond, const char *column) const
{ {
auto h = find<T>(pos, std::forward<Condition>(cond), column); auto h = find<T>(pos, std::forward<Condition>(cond), column);
...@@ -2237,7 +2237,7 @@ class File ...@@ -2237,7 +2237,7 @@ class File
append(new Datablock(name)); append(new Datablock(name));
return back(); return back();
} }
Datablock *get(std::string_view name) const; Datablock *get(std::string_view name) const;
Datablock &operator[](std::string_view name); Datablock &operator[](std::string_view name);
......
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