This library contains code to work with mmCIF and PDB files.

// 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;
}

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:

• 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 if you want to build the testing code.

When building using MS Visual Studio, you will also need libzeep since MSVC does not yet provide a C++ template required by libcifpp.

This library uses cmake. The usual way of building and installing is to create a build directory and run cmake there.

On linux e.g. you would issue the following commands to build and install libcifpp in your $HOME/.local folder:

 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.

If you want to run the tests before installing, you should add -DENABLE_TESTING=ON to the first cmake command.