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caf074a
Initial check-in of CoRE-MOF notebook
bardwell-ccdc 9c21b76
Correct whitespace
bardwell-ccdc a0edafa
Improved readme
bardwell-ccdc ac313ca
Corrected grammar
bardwell-ccdc ea7573f
Added PACMAN requirement
bardwell-ccdc 25bb906
Corrected typo NO_JIRA
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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. | ||
| list_coremof_csd_unmodified_20250227.json: a list of structures of CSD-unmodified dataset. | ||
| 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) |
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notebooks/CoRE-MOF/download_unmodified_MOFs_from_CSD.ipynb
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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "43d1d18f-6770-4d51-acdc-b6abeefb20e1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## get list of CoRE MOF - CSD - unmodified" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 14, | ||
| "id": "f2ffddd5-373d-4569-ad30-6227c7fe746e", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import json" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 16, | ||
| "id": "0c5aff3d-56fc-47b6-8644-61dbfb9c67c5", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "with open(\"./list_coremof_csd_unmodified_20250227.json\", \"r\") as f:\n", | ||
| " csd_unmodified = json.load(f)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "8c3447f3-9938-48d4-a8b8-939ac3ce7f40", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### there are two subset (CR & NCR)\n", | ||
| "\n", | ||
| "```python\n", | ||
| " CSD Unmodified Dataset # (N = 12,261)\n", | ||
| " │\n", | ||
| " ├── CR # computation-ready (N = 4,703)\n", | ||
| " │ │\n", | ||
| " │ ├── ASR # all solvent removed (N = 1,894)\n", | ||
| " │ ├── FSR # free solvent removed (N = 2,657)\n", | ||
| " │ └── Ion # with ion (N = 152)\n", | ||
| " │\n", | ||
| " └── NCR # not computation-ready (N = 7,558)\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 36, | ||
| "id": "55deb24d-8d13-441f-acd6-bca911ee75ae", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "dict_keys(['CR', 'NCR'])" | ||
| ] | ||
| }, | ||
| "execution_count": 36, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "csd_unmodified.keys()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 38, | ||
| "id": "0936cfd5-bb33-4e14-9de4-30282bd7d40a", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "dict_keys(['ASR', 'FSR', 'ION'])" | ||
| ] | ||
| }, | ||
| "execution_count": 38, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "csd_unmodified[\"CR\"].keys()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "1333bfb5-811e-480b-96e2-1b822449a2a6", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "**Note that the refcode in the CoRE MOF DB has an additional string ending such as “_ASR_pacman”.**" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "4a9fc947-3205-46d4-83a2-5fed8176d900", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "**For CR subset, there are CoRE MOF ID and REFCODE.**\n", | ||
| "**For NCR subset, there is only REFCODE.**" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 60, | ||
| "id": "73643f82-05ca-4905-8699-1e717aa16f2c", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "ABUXUT_ASR_pacman\n", | ||
| "2016[Cu][nan]3[ASR]1\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# example for CR\n", | ||
| "print(csd_unmodified[\"CR\"][\"ASR\"][1][0])\n", | ||
| "print(csd_unmodified[\"CR\"][\"ASR\"][1][1])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 64, | ||
| "id": "ec0e0fd1-e20f-4459-bcc0-3ddcca5cd9d8", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "ABECIX_FSR_pacman\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# example for NCR\n", | ||
| "print(csd_unmodified[\"NCR\"][0])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "a847770f-4dac-4888-a469-f050e330d959", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## download original CIFs from CSD\n", | ||
| "you need install [*CSD python API*](https://downloads.ccdc.cam.ac.uk/documentation/API/installation_notes.html) and activate the licence first." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "ae5f4c8c-2266-4638-b47c-aeb3ad293f30", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "and install [CoREMOF_tools](https://coremof-tools.readthedocs.io/en/latest/index.html) by `pip install CoREMOF-tools`" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 70, | ||
| "id": "91208e59-7bf6-4812-89b6-13943ba35a99", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from CoREMOF.structure import download_from_CSD" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 74, | ||
| "id": "be948ea1-8a5e-4a72-be5e-7a8c0059043f", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "### download ASR structure\n", | ||
| "\n", | ||
| "for refcodes in csd_unmodified[\"CR\"][\"ASR\"][:10]: # test for 10 structures\n", | ||
| " refcode = refcodes[0].replace(\"_ASR_pacman\", \"\")\n", | ||
| " download_from_CSD(refcode=refcode, output_folder=\"./structures/CR/ASR\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 76, | ||
| "id": "75e0c9d2-bdb2-424d-9158-29003a9fde16", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "### download FSR structure\n", | ||
| "\n", | ||
| "for refcodes in csd_unmodified[\"CR\"][\"FSR\"][:10]: # test for 10 structures\n", | ||
| " refcode = refcodes[0].replace(\"_FSR_pacman\", \"\")\n", | ||
| " download_from_CSD(refcode=refcode, output_folder=\"./structures/CR/FSR\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 78, | ||
| "id": "a0399d5e-2a57-4ede-b95e-0ba263fd4ae6", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "### download Ion structure\n", | ||
| "\n", | ||
| "for refcodes in csd_unmodified[\"CR\"][\"ION\"][:10]: # test for 10 structures\n", | ||
| " refcode = refcodes[0].replace(\"_ion_pacman\", \"\")\n", | ||
| " download_from_CSD(refcode=refcode, output_folder=\"./structures/CR/Ion\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 86, | ||
| "id": "691e839a-387b-44d9-88b2-2e27b44bee94", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "### download NCR structure\n", | ||
| "\n", | ||
| "for refcode in csd_unmodified[\"NCR\"][:10]: # test for 10 structures\n", | ||
| " refcode = refcode.split(\"_\")[0]\n", | ||
| " download_from_CSD(refcode=refcode, output_folder=\"./structures/NCR/\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "61e48f31-6cc1-4388-9095-b88270351ec1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### process the structures" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "b450249b-421c-429d-9f81-8cffd0611c0e", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "since solvent removal is not required, only make primitive cell and make P1 are needed." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 110, | ||
| "id": "5a5af1da-b1a5-4ea7-ab76-9c6a074f4497", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from CoREMOF.structure import make_primitive_p1" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 116, | ||
| "id": "1abd657b-4771-49e4-9bef-9bd2f1cb97eb", | ||
| "metadata": { | ||
| "scrolled": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "structure_pri = make_primitive_p1(filename=\"./structures/CR/ASR/\"+csd_unmodified[\"CR\"][\"ASR\"][0][0].split(\"_\")[0]+\".cif\") # ABAVOP " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "d0120d89-9667-45ea-b71a-aa19d6ab90fc", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "predict partial atom charge by [PACMAN Charge](https://pubs.acs.org/doi/10.1021/acs.jctc.4c00434)\n", | ||
| "install by `pip install pip install PACMAN-charge`" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "id": "001ba16b-c921-41bf-acb9-da36bdf6f8c6", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "CIF Name: ./structures/CR/ASR/ABAVOP.cif\n", | ||
| "Charge Type: DDEC6\n", | ||
| "Digits: 10\n", | ||
| "Atom Type: True\n", | ||
| "Neutral: True\n", | ||
| "Keep Connect: False\n", | ||
| "Compelete and save as ./structures/CR/ASR/ABAVOP_pacman.cif\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from PACMANCharge import pmcharge\n", | ||
| "pmcharge.predict(cif_file=\"./structures/CR/ASR/\"+csd_unmodified[\"CR\"][\"ASR\"][0][0].split(\"_\")[0]+\".cif\", # ABAVOP \n", | ||
| " charge_type=\"DDEC6\",\n", | ||
| " digits=10,\n", | ||
| " atom_type=True,neutral=True,\n", | ||
| " keep_connect=False)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "a7c0a0af-4549-405b-96df-7b4d56525b51", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "**if you want to use CoRE MOF ID, you can change REFCODE to CoRE MOF ID**" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 22, | ||
| "id": "4117005e-abde-4d54-bc4b-62a38c0758dd", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import os" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 26, | ||
| "id": "3069a5d1-4b34-45c4-9e78-ba8f5468a4ea", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "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", | ||
| "# ABAVOP_pacman.cif -> 2004[Co][rtl]3[ASR]2.cif" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "e294f9dd-d61e-4078-be4e-57b3c34b0846", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python [conda env:base] *", | ||
| "language": "python", | ||
| "name": "conda-base-py" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.5" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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Can you please add to the ReadMe some information about the dependency required, the Author. I can see there is some of this info in the Notebook itself, but it would be nice to have it in the ReadMe so folk can see it when they open the folder in github
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Look better? While you're here, I see sonarcloud found a problem that I don't really think is a problem, but no idea how to tell it that - any ideas?
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I agree its not an issue, we can formally accept it, but its not blocking merging now
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Aye, I've accepted the issue, as it does not apply to this.
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Doesn't the notebook need PACMANCharges? I'd just add it under a requirements header
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I've added in the requirement for PACMAN charge