# mmcif-gen
A versatile command-line tool for generating any mmCIF files from various data sources. This tool can be to create:
1. Metadata mmcif files (To capture experimental metadata from different facilities)
2. Investigation mmcif files (like: https://ftp.ebi.ac.uk/pub/databases/msd/fragment_screening/investigations/)
The tool has transformational mapping to convert data as it is stored at various facilities to corresponding catgories and items in mmcif format.
## Installation
Install directly from PyPI:
```bash
pip install mmcif-gen
```
## Usage
The tool provides two main commands:
1. `fetch-facility-json`: Fetch facility-specific JSON configuration files
2. `make-mmcif`: Generate mmCIF files using the configurations
### Fetching Facility JSON Files
The JSON operations files determine how the data would be mapped from the original source and translated into mmCIF format.
These files can be written, but can also be fetched from the github repository using simple commands.
```bash
# Fetch configuration for a specific facility
mmcif-gen fetch-facility-json dls-metadata
# Specify custom output directory
mmcif-gen fetch-facility-json dls-metadata -o ./mapping_operations
```
### Generating metadata mmCIF Files
Currently the valid facilities to generate mmcif files for are `pdbe`, `maxiv`, `dls`, and `xchem`.
The general syntax for generating mmCIF files is:
```bash
mmcif-gen make-mmcif <facility> [options]
```
Each facility has its own set of required parameters, which can be checked by running the command with the `--help` flag.
```
mmcif-gen make-mmcif pdbe --help
```
#### Example Usage
#### DLS (Diamond Light Source)
```bash
# Using metadata configuration
mmcif-gen make-mmcif dls --json dls_metadata.json --output-folder ./out --id id_1234 --dls-json metadata-from-isypb.json
```
### Working with Investigation Files
Investigation files are a specialized type of mmCIF file that capture metadata across multiple experiments.
Investigation files are created in a very similar way:
#### PDBe
```bash
# Using model folder
mmcif-gen make-mmcif pdbe --json pdbe_investigation.json --model-folder ./models --output-folder ./out --id I_1234
# Using PDB IDs
mmcif-gen make-mmcif pdbe --json pdbe_investigation.json --pdb-ids 6dmn 6dpp 6do8 --output-folder ./out
# Using CSV input
mmcif-gen make-mmcif pdbe --json pdbe_investigation.json --csv-file groups.csv --output-folder ./out
```
#### MAX IV
```bash
# Using SQLite database
mmcif-gen make-mmcif maxiv --json maxiv_investigation.json --sqlite fragmax.sqlite --output-folder ./out --id I_5678
```
#### XChem
```bash
# Using SQLite database with additional information
mmcif-gen make-mmcif xchem --json xchem_investigation.json --sqlite soakdb.sqlite --txt ./metadata --deposit ./deposit --output-folder ./out
```
## Data Enrichment
For investigation files that need enrichment with additional data (e.g., ground state information):
```bash
# Using the miss_importer utility
python miss_importer.py --investigation-file inv.cif --sf-file structure.sf --pdb-id 1ABC
```
## Operation JSON Files
The tool uses JSON configuration files to define how data should be transformed into mmCIF format. These files can be:
1. Fetched files using the `fetch-facility-json` command
2. Modified versions of official configurations
### Configuration File Structure
```json
{
"source_category" : "_audit_author",
"source_items" : ["name"],
"target_category" : "_audit_author",
"target_items" : "_same",
"operation" : "distinct_union",
"operation_parameters" :{
"primary_parameters" : ["name"]
}
}
```
Refer to existing JSON files in the `operations/` directory for examples.
## Development
### Project Structure
```
mmcif-gen/
├── facilities/ # Facility-specific implementations
│ ├── pdbe.py
│ ├── maxiv.py
│ └── ...
├── operations/ # JSON configuration files
│ ├── dls/
│ ├── maxiv/
│ └── ...
├── tests/ # Test cases
├── setup.py # Package configuration
└── README.md # Documentation
```
### Running Tests
```bash
python -m unittest discover -s tests
```
## Contributing
Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
## Support
For issues and questions, please use the [GitHub issue tracker](https://github.com/PDBeurope/Investigations/issues).
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"description": "# mmcif-gen\n\nA versatile command-line tool for generating any mmCIF files from various data sources. This tool can be to create:\n\n1. Metadata mmcif files (To capture experimental metadata from different facilities)\n2. Investigation mmcif files (like: https://ftp.ebi.ac.uk/pub/databases/msd/fragment_screening/investigations/)\n\nThe tool has transformational mapping to convert data as it is stored at various facilities to corresponding catgories and items in mmcif format.\n\n## Installation\n\nInstall directly from PyPI:\n\n```bash\npip install mmcif-gen\n```\n\n## Usage\n\nThe tool provides two main commands:\n\n1. `fetch-facility-json`: Fetch facility-specific JSON configuration files\n2. `make-mmcif`: Generate mmCIF files using the configurations\n\n### Fetching Facility JSON Files\n\nThe JSON operations files determine how the data would be mapped from the original source and translated into mmCIF format.\n\nThese files can be written, but can also be fetched from the github repository using simple commands.\n\n```bash\n# Fetch configuration for a specific facility\nmmcif-gen fetch-facility-json dls-metadata\n\n# Specify custom output directory\nmmcif-gen fetch-facility-json dls-metadata -o ./mapping_operations\n```\n\n### Generating metadata mmCIF Files\n\nCurrently the valid facilities to generate mmcif files for are `pdbe`, `maxiv`, `dls`, and `xchem`.\n\nThe general syntax for generating mmCIF files is:\n\n```bash\nmmcif-gen make-mmcif <facility> [options]\n```\n\nEach facility has its own set of required parameters, which can be checked by running the command with the `--help` flag.\n\n\n```\nmmcif-gen make-mmcif pdbe --help\n```\n#### Example Usage\n\n#### DLS (Diamond Light Source)\n\n```bash\n# Using metadata configuration\nmmcif-gen make-mmcif dls --json dls_metadata.json --output-folder ./out --id id_1234 --dls-json metadata-from-isypb.json\n```\n### Working with Investigation Files\n\nInvestigation files are a specialized type of mmCIF file that capture metadata across multiple experiments.\n\nInvestigation files are created in a very similar way:\n\n#### PDBe\n\n```bash\n# Using model folder\nmmcif-gen make-mmcif pdbe --json pdbe_investigation.json --model-folder ./models --output-folder ./out --id I_1234\n\n# Using PDB IDs\nmmcif-gen make-mmcif pdbe --json pdbe_investigation.json --pdb-ids 6dmn 6dpp 6do8 --output-folder ./out\n\n# Using CSV input\nmmcif-gen make-mmcif pdbe --json pdbe_investigation.json --csv-file groups.csv --output-folder ./out\n```\n\n#### MAX IV\n\n```bash\n# Using SQLite database\nmmcif-gen make-mmcif maxiv --json maxiv_investigation.json --sqlite fragmax.sqlite --output-folder ./out --id I_5678\n```\n\n#### XChem\n\n```bash\n# Using SQLite database with additional information\nmmcif-gen make-mmcif xchem --json xchem_investigation.json --sqlite soakdb.sqlite --txt ./metadata --deposit ./deposit --output-folder ./out\n```\n\n\n## Data Enrichment\n\nFor investigation files that need enrichment with additional data (e.g., ground state information):\n\n```bash\n# Using the miss_importer utility\npython miss_importer.py --investigation-file inv.cif --sf-file structure.sf --pdb-id 1ABC\n```\n\n## Operation JSON Files\n\nThe tool uses JSON configuration files to define how data should be transformed into mmCIF format. These files can be:\n\n1. Fetched files using the `fetch-facility-json` command\n2. Modified versions of official configurations\n\n### Configuration File Structure\n\n```json\n {\n \"source_category\" : \"_audit_author\",\n \"source_items\" : [\"name\"],\n \"target_category\" : \"_audit_author\",\n \"target_items\" : \"_same\",\n \"operation\" : \"distinct_union\",\n \"operation_parameters\" :{\n \"primary_parameters\" : [\"name\"]\n }\n }\n```\n\nRefer to existing JSON files in the `operations/` directory for examples.\n\n\n## Development\n\n### Project Structure\n\n```\nmmcif-gen/\n\u251c\u2500\u2500 facilities/ # Facility-specific implementations\n\u2502 \u251c\u2500\u2500 pdbe.py\n\u2502 \u251c\u2500\u2500 maxiv.py\n\u2502 \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 operations/ # JSON configuration files\n\u2502 \u251c\u2500\u2500 dls/\n\u2502 \u251c\u2500\u2500 maxiv/\n\u2502 \u2514\u2500\u2500 ...\n\u251c\u2500\u2500 tests/ # Test cases\n\u251c\u2500\u2500 setup.py # Package configuration\n\u2514\u2500\u2500 README.md # Documentation\n```\n\n### Running Tests\n\n```bash\npython -m unittest discover -s tests\n```\n\n## Contributing\n\nContributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.\n\n\n## Support\n\nFor issues and questions, please use the [GitHub issue tracker](https://github.com/PDBeurope/Investigations/issues).\n",
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