mmCIF Core Access Library

Introduction

This module includes a native Python mmCIF API for data files and dictionaries along with pybind11 wrappers for the PDB C++ Core mmCIF Library.

Installation

Download the library source software from the project repository:

git clone  --recurse-submodules  https://github.com/rcsb/py-mmcif.git

Optionally, run test suite using the Tox test runner. The C++ library bindings have been tested on Centos 7/Ubuntu 20.04 Linux with GCC/G++ > 4.8.5 and MacOS (10.15) with > clang-900.0.39.2 using Python versions 2.7.18 and 3.9.4.

tox

Installation is via the program pip.

pip install mmcif

or from the local repository:

pip install .

To generate API documentation using Sphinx:

cd scripts
# Check Sphinx dependencies in the introductory comments to the following script.
./initdocs.sh

A command-line script is provided as a preprocessor for modular dictionaries that include definition and data content using categories pdbx_include_dictionary, pdbx_include_category and pdbx_include_item.

build_dict_cli --help
usage: build_dict_cli [-h] --op OP --input_dict_path INPUT_DICT_PATH [--output_dict_path OUTPUT_DICT_PATH] [--cleanup]

optional arguments:
  -h, --help            show this help message and exit
  --op OP               Operation (build | get_version)
  --input_dict_path INPUT_DICT_PATH
                        Path to dictionary generator file
  --output_dict_path OUTPUT_DICT_PATH
                        Path to output dictionary text file
  --cleanup             Remove include instruction categories after processing
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