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Merge pull request #75 from ccdc-opensource/CoRE-MOF
Initial check-in of CoRE-MOF notebook
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‎notebooks/CoRE-MOF/README.md

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# CoRE-MOF
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## Introduction
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This package contains shared functionality that is used to export entries used by CoRE-MOF
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download_unmodified_MOFs_from_CSD.ipynb: a script for downloading structures of CSD-unmodified dataset.
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list_coremof_csd_unmodified_20250227.json: a list of structures of CSD-unmodified dataset.
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structures: an successful case by using the script.
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## Requirements
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[CoRE-MOF tools](https://coremof-tools.readthedocs.io/en/latest/index.html), [PACMAN Charge](https://pubs.acs.org/doi/10.1021/acs.jctc.4c00434), CSD Python API
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## Licensing Requirements
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CSD-Core or better
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## Authors
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[CoRE-MOF](https://coremof-tools.readthedocs.io/en/latest/index.html)

‎notebooks/CoRE-MOF/download_unmodified_MOFs_from_CSD.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "43d1d18f-6770-4d51-acdc-b6abeefb20e1",
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"metadata": {},
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"source": [
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"## get list of CoRE MOF - CSD - unmodified"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 14,
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"id": "f2ffddd5-373d-4569-ad30-6227c7fe746e",
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"metadata": {},
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"outputs": [],
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"source": [
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"import json"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 16,
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"id": "0c5aff3d-56fc-47b6-8644-61dbfb9c67c5",
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"metadata": {},
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"outputs": [],
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"source": [
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"with open(\"./list_coremof_csd_unmodified_20250227.json\", \"r\") as f:\n",
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" csd_unmodified = json.load(f)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "8c3447f3-9938-48d4-a8b8-939ac3ce7f40",
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"metadata": {},
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"source": [
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"### there are two subset (CR & NCR)\n",
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"\n",
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"```python\n",
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" CSD Unmodified Dataset # (N = 12,261)\n",
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" │\n",
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" ├── CR # computation-ready (N = 4,703)\n",
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" │ │\n",
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" │ ├── ASR # all solvent removed (N = 1,894)\n",
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" │ ├── FSR # free solvent removed (N = 2,657)\n",
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" │ └── Ion # with ion (N = 152)\n",
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" │\n",
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" └── NCR # not computation-ready (N = 7,558)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 36,
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"id": "55deb24d-8d13-441f-acd6-bca911ee75ae",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"dict_keys(['CR', 'NCR'])"
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]
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},
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"execution_count": 36,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"csd_unmodified.keys()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 38,
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"id": "0936cfd5-bb33-4e14-9de4-30282bd7d40a",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"dict_keys(['ASR', 'FSR', 'ION'])"
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]
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},
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"execution_count": 38,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"csd_unmodified[\"CR\"].keys()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1333bfb5-811e-480b-96e2-1b822449a2a6",
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"metadata": {},
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"source": [
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"**Note that the refcode in the CoRE MOF DB has an additional string ending such as “_ASR_pacman”.**"
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]
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},
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{
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"cell_type": "markdown",
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"id": "4a9fc947-3205-46d4-83a2-5fed8176d900",
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"metadata": {},
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"source": [
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"**For CR subset, there are CoRE MOF ID and REFCODE.**\n",
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"**For NCR subset, there is only REFCODE.**"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 60,
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"id": "73643f82-05ca-4905-8699-1e717aa16f2c",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ABUXUT_ASR_pacman\n",
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"2016[Cu][nan]3[ASR]1\n"
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]
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}
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],
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"source": [
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"# example for CR\n",
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"print(csd_unmodified[\"CR\"][\"ASR\"][1][0])\n",
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"print(csd_unmodified[\"CR\"][\"ASR\"][1][1])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 64,
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"id": "ec0e0fd1-e20f-4459-bcc0-3ddcca5cd9d8",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"ABECIX_FSR_pacman\n"
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]
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}
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],
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"source": [
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"# example for NCR\n",
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"print(csd_unmodified[\"NCR\"][0])"
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]
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},
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{
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"cell_type": "markdown",
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"id": "a847770f-4dac-4888-a469-f050e330d959",
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"metadata": {},
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"source": [
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"## download original CIFs from CSD\n",
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"you need install [*CSD python API*](https://downloads.ccdc.cam.ac.uk/documentation/API/installation_notes.html) and activate the licence first."
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]
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},
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{
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"cell_type": "markdown",
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"id": "ae5f4c8c-2266-4638-b47c-aeb3ad293f30",
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"metadata": {},
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"source": [
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"and install [CoREMOF_tools](https://coremof-tools.readthedocs.io/en/latest/index.html) by `pip install CoREMOF-tools`"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 70,
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"id": "91208e59-7bf6-4812-89b6-13943ba35a99",
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"metadata": {},
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"outputs": [],
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"source": [
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"from CoREMOF.structure import download_from_CSD"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 74,
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"id": "be948ea1-8a5e-4a72-be5e-7a8c0059043f",
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"metadata": {},
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"outputs": [],
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"source": [
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"### download ASR structure\n",
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"\n",
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"for refcodes in csd_unmodified[\"CR\"][\"ASR\"][:10]: # test for 10 structures\n",
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" refcode = refcodes[0].replace(\"_ASR_pacman\", \"\")\n",
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" download_from_CSD(refcode=refcode, output_folder=\"./structures/CR/ASR\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 76,
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"id": "75e0c9d2-bdb2-424d-9158-29003a9fde16",
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"metadata": {},
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"outputs": [],
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"source": [
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"### download FSR structure\n",
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"\n",
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"for refcodes in csd_unmodified[\"CR\"][\"FSR\"][:10]: # test for 10 structures\n",
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" refcode = refcodes[0].replace(\"_FSR_pacman\", \"\")\n",
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" download_from_CSD(refcode=refcode, output_folder=\"./structures/CR/FSR\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 78,
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"id": "a0399d5e-2a57-4ede-b95e-0ba263fd4ae6",
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"metadata": {},
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"outputs": [],
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"source": [
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"### download Ion structure\n",
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"\n",
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"for refcodes in csd_unmodified[\"CR\"][\"ION\"][:10]: # test for 10 structures\n",
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" refcode = refcodes[0].replace(\"_ion_pacman\", \"\")\n",
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" download_from_CSD(refcode=refcode, output_folder=\"./structures/CR/Ion\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 86,
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"id": "691e839a-387b-44d9-88b2-2e27b44bee94",
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"metadata": {},
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"outputs": [],
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"source": [
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"### download NCR structure\n",
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"\n",
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"for refcode in csd_unmodified[\"NCR\"][:10]: # test for 10 structures\n",
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" refcode = refcode.split(\"_\")[0]\n",
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" download_from_CSD(refcode=refcode, output_folder=\"./structures/NCR/\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "61e48f31-6cc1-4388-9095-b88270351ec1",
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"metadata": {},
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"source": [
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"### process the structures"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b450249b-421c-429d-9f81-8cffd0611c0e",
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"metadata": {},
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"source": [
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"since solvent removal is not required, only make primitive cell and make P1 are needed."
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]
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},
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{
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"cell_type": "code",
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"execution_count": 110,
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"id": "5a5af1da-b1a5-4ea7-ab76-9c6a074f4497",
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"metadata": {},
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"outputs": [],
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"source": [
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"from CoREMOF.structure import make_primitive_p1"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 116,
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"id": "1abd657b-4771-49e4-9bef-9bd2f1cb97eb",
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"metadata": {
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"scrolled": true
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},
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"outputs": [],
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"source": [
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"structure_pri = make_primitive_p1(filename=\"./structures/CR/ASR/\"+csd_unmodified[\"CR\"][\"ASR\"][0][0].split(\"_\")[0]+\".cif\") # ABAVOP "
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]
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},
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{
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"cell_type": "markdown",
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"id": "d0120d89-9667-45ea-b71a-aa19d6ab90fc",
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"metadata": {},
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"source": [
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"predict partial atom charge by [PACMAN Charge](https://pubs.acs.org/doi/10.1021/acs.jctc.4c00434)\n",
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"install by `pip install pip install PACMAN-charge`"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 18,
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"id": "001ba16b-c921-41bf-acb9-da36bdf6f8c6",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"CIF Name: ./structures/CR/ASR/ABAVOP.cif\n",
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"Charge Type: DDEC6\n",
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"Digits: 10\n",
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"Atom Type: True\n",
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"Neutral: True\n",
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"Keep Connect: False\n",
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"Compelete and save as ./structures/CR/ASR/ABAVOP_pacman.cif\n"
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]
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}
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],
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"source": [
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"from PACMANCharge import pmcharge\n",
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"pmcharge.predict(cif_file=\"./structures/CR/ASR/\"+csd_unmodified[\"CR\"][\"ASR\"][0][0].split(\"_\")[0]+\".cif\", # ABAVOP \n",
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" charge_type=\"DDEC6\",\n",
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" digits=10,\n",
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" atom_type=True,neutral=True,\n",
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" keep_connect=False)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "a7c0a0af-4549-405b-96df-7b4d56525b51",
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"metadata": {},
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"source": [
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"**if you want to use CoRE MOF ID, you can change REFCODE to CoRE MOF ID**"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 22,
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"id": "4117005e-abde-4d54-bc4b-62a38c0758dd",
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"metadata": {},
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"outputs": [],
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"source": [
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"import os"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 26,
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"id": "3069a5d1-4b34-45c4-9e78-ba8f5468a4ea",
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"metadata": {},
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"outputs": [],
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"source": [
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"os.rename(\"./structures/CR/ASR/\"+csd_unmodified[\"CR\"][\"ASR\"][0][0].split(\"_\")[0]+\"_pacman.cif\", \"./structures/CR/ASR/\" + csd_unmodified[\"CR\"][\"ASR\"][0][1]+\".cif\") \n",
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"# ABAVOP_pacman.cif -> 2004[Co][rtl]3[ASR]2.cif"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "e294f9dd-d61e-4078-be4e-57b3c34b0846",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python [conda env:base] *",
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"language": "python",
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"name": "conda-base-py"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.5"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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