CIF Cleaner is an interactive and codeless program for sorting,
pre-processing, and parsing CIF (Crystallographic Information File) files. It
extracts information from .cif files in a folder containing such files.
CIF Cleaner is built using the cifkit package:
https://github.com/bobleesj/cifkit.
In high-throughput analysis, we extract .cif files from databases, sorting
them based on specific attributes. CIF Cleaner was developed to streamline
this process by utilizing interactive prompts.
This tool is used by undergraduate and graduate researchers in the Oliynyk research group at CUNY Hunter College.
Open your terminal or command-line interface:
- Clone the repository and enter the directory:
git clone https://github.com/bobleesj/cif-cleaner.git
cd cif-cleaner- Install dependencies from the requirements.txt file:
pip install -r requirements.txtRun the program:
python main.pyThe program automatically detects folders containing .cif files at the project level.
Welcome! Please choose an option to proceed:
[1] Move files based on unsupported format after pre-formatting
[2] Move files based on unreasonable distance
[3] Move files based on supercell atom count
[4] Move files based on tags
[5] Move files based on composition type
[6] Move files based on elements
[7] Move files based on coordination number
[8] Copy files based on atomic occupancy and mixing
[9] Get file info in the folder
Enter your choice (1-9): 6
You have chosen: Get file info in the folder
Available folders containing CIF files:
1. elements CIF, 1787 files
2. binary R-X CIF, 3757 files
3. binary R-M CIF, 5510 files
4. binary M-X CIF, 2026 files
5. 20240706_test, 28 files
6. ternary R-M-X CIF, 11418 files
Enter the number corresponding to the folder containing .cif files: 1
| Option | Description | User input |
|---|---|---|
| 1 | Standardize and relocate .cif files that do not comply with the expected format | - |
| 2 | Move .cif by minimum distance threshold | Min distance (e.g., 2.0 Å) |
| 3 | Move .cif by supercell size | Min and max atom count |
| 4 | Move .cif by tags | - |
| 5 | Move .cif by composition type i.g. binary, ternary, etc. | - |
| 6 | Move .cif by input elements, matching or containing | Elements (e.g., Er Co) |
| 7 | Move .cif by input coordination numbers, matching or containing | Coordination numbers (e.g., 12 16) |
| 8 | Copy .cif by atomic mixing, i.g. full occupancy, atomic mixing, etc. | - |
| 9 | Get information from .cif files and save .csv | - |
For Option [2], the following histogram is saved in the folder. You need to enter the threshold distance. Any files below this threshold will be moved to a separate folder.
Enter the threshold distance (unit in Å): 2
A folder called min_dist_below_2.0 is created, and files with the minimum
atomic distance below 2.0 Å are moved.
A supercell is generated by applying a ±1 shift from the unit cell
The program prompts you to enter the minimum and maximum supercell atom count:
Enter the min number of atoms in the supercell: 300
Enter the max number of atoms in the supercell: 500
A folder called supercell_above_300_below_500 will be created with files that
meet the criteria.
A .csv is generated containing containing information for each .cif file in
the selected folder.
| Filename | Formula | Structure | Tag | Supercell atom count | Site mixing type | Composition type | Min distance (Å) | Processing time (s) |
|---|---|---|---|---|---|---|---|---|
| 300237 | LaPtSb | CaIn2 | 423 | full_occupancy_atomic_mixing | 3 | 2.727 | 0.301 | |
| 301710 | YFeSi3 | Ce(Ni0.59Sb0.41)4 | 558 | full_occupancy_atomic_mixing | 3 | 2.293 | 0.329 | |
| 1955459 | PrNi0.48Si1.48 | AlB2 | 267 | deficiency_atomic_mixing | 3 | 2.328 | 0.181 | |
| 1949113 | Ce2.11Pd1.92In0.89 | Mo2FeB2 | 437 | deficiency_atomic_mixing | 3 | 2.431 | 0.254 | |
| 301188 | Yb0.5Co3Ge3 | Y0.5Co3Ge3 | 323 | deficiency_without_atomic_mixing | 3 | 1.2 | 0.183 | |
| 1942974 | Dy0.0011Fe0.8291Ga0.1698 | W | 162 | full_occupancy_atomic_mixing | 3 | 2.514 | 0.032 | |
| 1940621 | LuPd0.5Si1.5 | AlB2 | 267 | deficiency_atomic_mixing | 3 | 2.325 | 0.186 | |
| 1200981 | Ni3Sn2 | Ni3Sn2 | rt | 594 | full_occupancy | 2 | 2.503 | 0.317 |
| 301180 | Lu0.5Co3Ge3 | Y0.5Co3Ge3 | 323 | deficiency_without_atomic_mixing | 3 | 1.197 | 0.187 |
In addition to CIF Cleaner, there are other interactive tools available that
allow you to extract geometric features and visualize bonding patterns from
.cif files. I invite you to explore these tools to enhance your analysis:
- Cif Bond Analyzer (CBA): conduct bonding, coordination, and site analysis. https://github.com/bobleesj/structure-analyzer-featurizer
- Structure Analysis/Featurizer (SAF): extract ML features for binary and ternary compounds. https://github.com/bobleesj/cif-bond-analyzer
the repository and recommend it to your colleagues who might find this repository helpful.
the repository and request a pull request for any changes.
- If you have any questions or have any suggestions, feel free to reach out to Sangjoon Bob Lee (@bobleesj) for any questions.
- 20240709: implement
cifkiv1.0.2, preprocess for option 1 only (#24) - 20240708: integreated CI tests for all options
- 20240705: integrated
cikift, refactored code and prompts - 20240303: added GitHub CI integration