// A simple program counting residues with an OXT atom

#include <filesystem>
#include <iostream>

#include <cif++.hpp>

namespace fs = std::filesystem;

int main(int argc, char *argv[])
{
    if (argc != 2)
        exit(1);

    // Read file, can be PDB or mmCIF and can even be compressed with gzip.
    cif::file file = cif::pdb::read(argv[1]);

    if (file.empty())
    {
        std::cerr << "Empty file" << std::endl;
        exit(1);
    }

    // Take the first datablock in the file
    auto &db = file.front();

    // Use the atom_site category
    auto &atom_site = db["atom_site"];

    // Count the atoms with atom-id "OXT"
    auto n = atom_site.count(cif::key("label_atom_id") == "OXT");

    std::cout << "File contains " << atom_site.size() << " atoms of which "
              << n << (n == 1 ? " is" : " are") << " OXT" << std::endl
              << "residues with an OXT are:" << std::endl;

    // Loop over all atoms with atom-id "OXT" and print out some info.
    // That info is extracted using structured binding in C++
    for (const auto &[asym, comp, seqnr] :
            atom_site.find<std::string, std::string, int>(
                cif::key("label_atom_id") == "OXT",
                "label_asym_id", "label_comp_id", "label_seq_id"))
    {
        std::cout << asym << ' ' << comp << ' ' << seqnr << std::endl;
    }

    return 0;
}

Installation

You might be able to use libcifpp from a package manager used by your OS distribution. But most likely this package will be out-of-date. Therefore it is recommended to build libcifpp from code. It is not hard to do.

Requirements

The code for this library was written in C++17. You therefore need a recent compiler to build it. For the development gcc 9.4 and clang 9.0 have been used as well as MSVC version 2019.

Other requirements are:

cmake A build tool.
mrc, a resource compiler that allows including data files into the executable making them easier to install. Strictly speaking this is optional, but at the expense of functionality.
libeigen, a library to do amongst others matrix calculations. This usually can be installed using your package manager, in Debian/Ubuntu it is called libeigen3-dev
zlib, the development version of this library. On Debian/Ubuntu this is the package zlib1g-dev.
boost.

The Boost libraries are only needed in case you want to build the test code or if you are using GCC. That last condition is due to a long standing bug in the implementation of std::regex. It simply crashes on the regular expressions used in the mmcif_pdbx dictionary and so we use the boost regex implementation instead.

Building

Building the code is as simple as typing:

 git clone https://github.com/PDB-REDO/libcifpp.git --recurse-submodules
 cd libcifpp
 cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$HOME/.local -DCMAKE_BUILD_TYPE=Release
 cmake --build build
 cmake --install build

This checks out the source code from github, creates a new directory where cmake stores its files. Run a configure, build the code and then it installs the library and auxiliary files.

Tests are created by default, and to test the code you can run:

 cmake --build build
 ctest --test-dir build