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

build_dict_cli tool

Overview

build_dict_cli is a command-line tool that serves as a preprocessor for modular mmCIF dictionaries. It resolves and combines dictionary components from multiple source files using include directives specified in categories such as pdbx_include_dictionary, pdbx_include_category, and pdbx_include_item.

Purpose

The tool allows dictionary maintainers to:

Combine multiple dictionary extensions (or combining extension with a parent dictionary) into a single comprehensive dictionary
Get dictionary version of the dictionary

Command-Line Arguments

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

Argument Details

--op: Specifies the operation to perform
- build: Generates a complete dictionary by processing includes
- get_version: Retrieves and outputs the version of the specified dictionary
--input_dict_path: Path to the dictionary generator file that contains include directives
--output_dict_path: Path where the combined output dictionary will be written
--cleanup: If specified, removes the include instruction categories from the final output

Creating a Generator File

A generator file is a special mmCIF dictionary file that primarily contains include directives. This file serves as the entry point for the dictionary build process.

Example Generator File

# mmcif_pdbx_v50-generator.dic

data_mmcif_pdbx.dic
#
loop_
_pdbx_include_dictionary.dictionary_id
_pdbx_include_dictionary.dictionary_locator
_pdbx_include_dictionary.include_mode
_pdbx_include_dictionary.dictionary_namespace_prefix
_pdbx_include_dictionary.dictionary_namespace_prefix_replace
mmcif_pdbx_v50.dic          mmcif_pdbx_v50.dic          extend . .
mmcif_investigation_fraghub_ext.dic      mmcif_investigation_fraghub_ext.dic  extend . .

Key Components in a Generator File

dictionary_id: Identifier for the dictionary to be included
dictionary_locator: File path to the dictionary (relative to the generator file)
include_mode: How to incorporate the dictionary (typically "extend")
dictionary_namespace_prefix: Namespace prefix for the included dictionary (use "." for none)
dictionary_namespace_prefix_replace: Replacement for the namespace prefix (use "." for none)

Usage Workflow

Prepare Dictionary Components:
- Create or obtain the dictionary files you want to combine
- Ensure all dictionary files are present in the same directory or specify the correct relative paths
Create a Generator File:
- Define a new mmCIF file with _pdbx_include_dictionary loop
- List all dictionaries to be included with their proper attributes

Run the Build Command:

build_dict_cli --op build --input_dict_path generator-file.dic --output_dict_path output-dictionary.dic

Verify the Output:
- The tool will combine all specified dictionaries into a single output file
- Check that all expected categories and items are present in the output

Example Use Case

To combine a base PDBx dictionary with a InvestigationCIF extension dictionary:

Ensure both dictionaries are available in your working directory:
```
mmcif_pdbx_v50.dic
mmcif_investigation_fraghub_ext.dic
```

Create a generator file (e.g., mmcif_pdbx_v50-generator-local.dic):

data_mmcif_pdbx.dic
#
loop_
_pdbx_include_dictionary.dictionary_id
_pdbx_include_dictionary.dictionary_locator
_pdbx_include_dictionary.include_mode
_pdbx_include_dictionary.dictionary_namespace_prefix
_pdbx_include_dictionary.dictionary_namespace_prefix_replace
mmcif_pdbx_v50.dic          mmcif_pdbx_v50.dic          extend . .
mmcif_investigation_fraghub_ext.dic      mmcif_investigation_fraghub_ext.dic  extend . .

Run the build command:

 build_dict_cli --op build --input_dict_path mmcif_pdbx_v50-generator-local.dic --output_dict_path ./mmcif_investigation_fraghub.dic

The tool will produce mmcif_investigation_fraghub.dic containing the combined content of both dictionaries.

Retrieving Dictionary Version

To get the version of a dictionary:

build_dict_cli --op get_version --input_dict_path mmcif_pdbx_v50.dic

This will output only the version number to stdout.

Metadata

Release files for mmcif 1.2.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mmcif 1.2.0
File	Size	Uploaded
mmcif-1.2.0.tar.gz	1.1 MB	Sep 30, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for mmcif 1.2.0
File	Interpreter	ABI	Platform	Reset
mmcif-1.2.0-cp314-cp314t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 623.0 kB Sep 30, 2026	CPython 3.14	CPython 3.14 free-threading	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
mmcif-1.2.0-cp314-cp314t-macosx_11_0_arm64.whl 534.7 kB Sep 30, 2026	CPython 3.14	CPython 3.14 free-threading	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp314-cp314t-macosx_10_15_x86_64.whl 569.7 kB Sep 30, 2026	CPython 3.14	CPython 3.14 free-threading	macOS 10.15+ x86-64	Details
mmcif-1.2.0-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 616.9 kB Sep 30, 2026	CPython 3.14	CPython 3.14	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
mmcif-1.2.0-cp314-cp314-macosx_11_0_arm64.whl 512.4 kB Sep 30, 2026	CPython 3.14	CPython 3.14	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp314-cp314-macosx_10_15_x86_64.whl 552.9 kB Sep 30, 2026	CPython 3.14	CPython 3.14	macOS 10.15+ x86-64	Details
mmcif-1.2.0-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 616.4 kB Sep 30, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
mmcif-1.2.0-cp313-cp313-macosx_11_0_arm64.whl 511.2 kB Sep 30, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp313-cp313-macosx_10_13_x86_64.whl 552.6 kB Sep 30, 2026	CPython 3.13	CPython 3.13	macOS 10.13+ x86-64	Details
mmcif-1.2.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 616.4 kB Sep 30, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
mmcif-1.2.0-cp312-cp312-macosx_11_0_arm64.whl 511.1 kB Sep 30, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp312-cp312-macosx_10_13_x86_64.whl 552.6 kB Sep 30, 2026	CPython 3.12	CPython 3.12	macOS 10.13+ x86-64	Details
mmcif-1.2.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 616.6 kB Sep 30, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
mmcif-1.2.0-cp311-cp311-macosx_11_0_arm64.whl 510.7 kB Sep 30, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp311-cp311-macosx_10_9_x86_64.whl 547.8 kB Sep 30, 2026	CPython 3.11	CPython 3.11	macOS 10.9+ x86-64	Details
mmcif-1.2.0-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 615.5 kB Sep 30, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
mmcif-1.2.0-cp310-cp310-macosx_11_0_arm64.whl 509.5 kB Sep 30, 2026	CPython 3.10	CPython 3.10	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl 546.3 kB Sep 30, 2026	CPython 3.10	CPython 3.10	macOS 10.9+ x86-64	Details
mmcif-1.2.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 646.1 kB Sep 30, 2026	CPython 3.9	CPython 3.9	Linux glibc 2.17+ x86-64	Details
mmcif-1.2.0-cp39-cp39-macosx_11_0_arm64.whl 509.5 kB Sep 30, 2026	CPython 3.9	CPython 3.9	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp39-cp39-macosx_10_9_x86_64.whl 546.3 kB Sep 30, 2026	CPython 3.9	CPython 3.9	macOS 10.9+ x86-64	Details
mmcif-1.2.0-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl 645.1 kB Sep 30, 2026	CPython 3.8	CPython 3.8	Linux glibc 2.17+ x86-64	Details
mmcif-1.2.0-cp38-cp38-macosx_11_0_arm64.whl 509.2 kB Sep 30, 2026	CPython 3.8	CPython 3.8	macOS 11.0+ ARM64	Details
mmcif-1.2.0-cp38-cp38-macosx_10_9_x86_64.whl 545.9 kB Sep 30, 2026	CPython 3.8	CPython 3.8	macOS 10.9+ x86-64	Details

Total release size: 14.6 MB

Release files / mmcif-1.2.0.tar.gz

Download URL	mmcif-1.2.0.tar.gz
Size	1.1 MB
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Download URL	mmcif-1.2.0-cp314-cp314t-macosx_11_0_arm64.whl
Size	534.7 kB
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Download URL	mmcif-1.2.0-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / mmcif-1.2.0-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

Download URL	mmcif-1.2.0-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / mmcif-1.2.0-cp313-cp313-macosx_11_0_arm64.whl

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Size	511.2 kB
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Release files / mmcif-1.2.0-cp313-cp313-macosx_10_13_x86_64.whl

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Release files / mmcif-1.2.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

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Release files / mmcif-1.2.0-cp310-cp310-macosx_11_0_arm64.whl

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Size	509.5 kB
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / mmcif-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl

Download URL	mmcif-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / mmcif-1.2.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl

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Size	646.1 kB
Tags	CPython 3.9 Linux glibc 2.17+ x86-64
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / mmcif-1.2.0-cp39-cp39-macosx_11_0_arm64.whl

Download URL	mmcif-1.2.0-cp39-cp39-macosx_11_0_arm64.whl
Size	509.5 kB
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / mmcif-1.2.0-cp39-cp39-macosx_10_9_x86_64.whl

Download URL	mmcif-1.2.0-cp39-cp39-macosx_10_9_x86_64.whl
Size	546.3 kB
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Upload date	Sep 30, 2026
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Release files / mmcif-1.2.0-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl

Download URL	mmcif-1.2.0-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
Size	645.1 kB
Tags	CPython 3.8 Linux glibc 2.17+ x86-64
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / mmcif-1.2.0-cp38-cp38-macosx_11_0_arm64.whl

Download URL	mmcif-1.2.0-cp38-cp38-macosx_11_0_arm64.whl
Size	509.2 kB
Tags	CPython 3.8 macOS 11.0+ ARM64
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`

Release files / mmcif-1.2.0-cp38-cp38-macosx_10_9_x86_64.whl

Download URL	mmcif-1.2.0-cp38-cp38-macosx_10_9_x86_64.whl
Size	545.9 kB
Tags	CPython 3.8 macOS 10.9+ x86-64
SHA-256 checksum How to use checksums	`29ac9c43df7a6274e3ec4f8f42be7b77b3f449ea06981ad53bfe6c06e13d7e30`
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Upload date	Sep 30, 2026
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Uploaded via	`twine/7.0.0 CPython/3.14.7`