Skip to content

Instantly share code, notes, and snippets.

@chrisjonesBSU

chrisjonesBSU/gmso-remove-particles.ipynb

Last active September 5, 2023 17:10
Show Gist options
  • Save chrisjonesBSU/cd2b5b8d4fda72b20e497a022195c95c to your computer and use it in GitHub Desktop.
Save chrisjonesBSU/cd2b5b8d4fda72b20e497a022195c95c to your computer and use it in GitHub Desktop.
Download ZIP
Removing particles in gmso
Display the source blob
Display the rendered blob
Raw
gmso-remove-particles.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 18,
"id": "09150dc0-25fd-4173-87f4-4a07044a279f",
"metadata": {},
"outputs": [],
"source": [
"import gmso\n",
"from gmso.external import from_mbuild, to_mbuild\n",
"import mbuild as mb"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f4f82e58-9b67-47b0-ab41-a47cce54bbbb",
"metadata": {},
"outputs": [],
"source": [
"_alkane = mb.load(\"CC\", smiles=True)\n",
"alkane = from_mbuild(_alkane)\n",
"alkane.identify_connections()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "4f50cfdb-3bfe-4e35-bb8c-f802b5999548",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"8\n",
"36\n"
]
}
],
"source": [
"print(alkane.n_sites)\n",
"print(alkane.n_connections)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "98a44ccf-4f3d-49a2-98f3-a4566ad79d29",
"metadata": {},
"outputs": [],
"source": [
"site_connections = alkane.get_connections_by_site(site=alkane.sites[-1])"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "2ed25304-731c-4446-93e6-7e9d7f5364e8",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'bonds': [<Bond Bond,\n",
" connection_members: (<Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6801252304>],\n",
" 'angles': [<Angle Angle,\n",
" connection_members: (<Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814649936>,\n",
" <Angle Angle,\n",
" connection_members: (<Atom H,\n",
" position: [ 0.10994617 -0.09535855 -0.05134287] nm,\n",
" label: None,\n",
" id: 6814635280>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814650256>,\n",
" <Angle Angle,\n",
" connection_members: (<Atom H,\n",
" position: [ 0.11407807 0.08535636 -0.0593128 ] nm,\n",
" label: None,\n",
" id: 6814635792>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814649104>],\n",
" 'dihedrals': [<Dihedral Dihedral,\n",
" connection_members: (<Atom H,\n",
" position: [-0.11407801 -0.08535597 0.05931338] nm,\n",
" label: None,\n",
" id: 6801801168>, <Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6801886672>,\n",
" <Dihedral Dihedral,\n",
" connection_members: (<Atom H,\n",
" position: [-0.10994615 0.09535899 0.05134223] nm,\n",
" label: None,\n",
" id: 6814634192>, <Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814650960>,\n",
" <Dihedral Dihedral,\n",
" connection_members: (<Atom H,\n",
" position: [-0.11654095 -0.00179734 -0.10115584] nm,\n",
" label: None,\n",
" id: 6814634320>, <Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814649744>],\n",
" 'impropers': [<Improper Improper,\n",
" connection_members: (<Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom H,\n",
" position: [ 0.10994617 -0.09535855 -0.05134287] nm,\n",
" label: None,\n",
" id: 6814635280>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814651280>,\n",
" <Improper Improper,\n",
" connection_members: (<Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom H,\n",
" position: [ 0.11407807 0.08535636 -0.0593128 ] nm,\n",
" label: None,\n",
" id: 6814635792>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814651344>,\n",
" <Improper Improper,\n",
" connection_members: (<Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>, <Atom H,\n",
" position: [ 0.10994617 -0.09535855 -0.05134287] nm,\n",
" label: None,\n",
" id: 6814635280>, <Atom H,\n",
" position: [ 0.11407807 0.08535636 -0.0593128 ] nm,\n",
" label: None,\n",
" id: 6814635792>, <Atom H,\n",
" position: [0.11654089 0.00179655 0.10115589] nm,\n",
" label: None,\n",
" id: 6814636304>),\n",
" potential: None,\n",
" id: 6814651408>]}"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"site_connections"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "d6bf5a34-643a-4018-9384-056bed9b1860",
"metadata": {},
"outputs": [],
"source": [
"# Get list of hydrogen sites, remove their connections and then remove the particle\n",
"hydrogen_sites = [site for site in alkane.sites if site.element.atomic_number == 1]\n",
"\n",
"for h in hydrogen_sites:\n",
" site_conn_dict = alkane.get_connections_by_site(h)\n",
" for conn_type in site_conn_dict:\n",
" for conn in site_conn_dict[conn_type]:\n",
" alkane.remove_connection(conn)\n",
" alkane.remove_site(h)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "c6032b27-adbb-46a1-be97-213e050e6970",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2\n",
"1\n"
]
}
],
"source": [
"print(alkane.n_sites)\n",
"print(alkane.n_connections)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "181da5e9-742c-4cbe-be29-6bc5e947c573",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"IndexedSet([<Bond Bond,\n",
" connection_members: (<Atom C,\n",
" position: [-0.07590747 0.00182889 0.00211742] nm,\n",
" label: None,\n",
" id: 6814633744>, <Atom C,\n",
" position: [ 0.07590746 -0.00182894 -0.00211742] nm,\n",
" label: None,\n",
" id: 6801883984>),\n",
" potential: None,\n",
" id: 6814635216>])"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"alkane.connections"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "a3030725-dc82-42a1-a8ad-9a8610445613",
"metadata": {},
"outputs": [],
"source": [
"alkane_ua = to_mbuild(alkane)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "ce76fd9a-1432-40ad-9b84-f2fab7a8072c",
"metadata": {},
"outputs": [
{
"data": {
"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_1693933652754884\" style=\"position: relative; width: 640px; height: 480px\">\n <p id=\"3dmolwarning_1693933652754884\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>\n <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n return new Promise((resolve, reject) => {\n //this is to ignore the existence of requirejs amd\n var savedexports, savedmodule;\n if (typeof exports !== 'undefined') savedexports = exports;\n else exports = {}\n if (typeof module !== 'undefined') savedmodule = module;\n else module = {}\n\n var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\n exports = savedexports;\n module = savedmodule;\n resolve();\n };\n var firstScriptTag = document.getElementsByTagName('script')[0];\n firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.js');\n}\n\nvar viewer_1693933652754884 = null;\nvar warn = document.getElementById(\"3dmolwarning_1693933652754884\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_1693933652754884 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1693933652754884\"),{backgroundColor:\"white\"});\nviewer_1693933652754884.zoomTo();\n\tviewer_1693933652754884.addModel(\"@<TRIPOS>MOLECULE\\nCompound\\n2 1 1 0 1\\nSMALL\\nNO_CHARGES\\n@<TRIPOS>CRYSIN\\n 6.5182 6.0000 6.0000 90.0000 90.0000 90.0000 1 1\\n@<TRIPOS>ATOM\\n 1 C -0.7591 0.0183 0.0212 C 1 Compound\\n 2 C 0.7591 -0.0183 -0.0212 C 1 Compound\\n@<TRIPOS>BOND\\n 1 1 2 1\\n@<TRIPOS>SUBSTRUCTURE\\n 1 Compound 1 RESIDUE 0 **** ROOT 0\\n\",\"mol2\");\n\tviewer_1693933652754884.setStyle({\"stick\": {\"radius\": 0.2, \"color\": \"grey\"}, \"sphere\": {\"scale\": 0.3, \"colorscheme\": {}}});\n\tviewer_1693933652754884.zoomTo();\nviewer_1693933652754884.render();\n});\n</script>",
"text/html": [
"<div id=\"3dmolviewer_1693933652754884\" style=\"position: relative; width: 640px; height: 480px\">\n",
" <p id=\"3dmolwarning_1693933652754884\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension: <br>\n",
" <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var loadScriptAsync = function(uri){\n",
" return new Promise((resolve, reject) => {\n",
" //this is to ignore the existence of requirejs amd\n",
" var savedexports, savedmodule;\n",
" if (typeof exports !== 'undefined') savedexports = exports;\n",
" else exports = {}\n",
" if (typeof module !== 'undefined') savedmodule = module;\n",
" else module = {}\n",
"\n",
" var tag = document.createElement('script');\n",
" tag.src = uri;\n",
" tag.async = true;\n",
" tag.onload = () => {\n",
" exports = savedexports;\n",
" module = savedmodule;\n",
" resolve();\n",
" };\n",
" var firstScriptTag = document.getElementsByTagName('script')[0];\n",
" firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
"});\n",
"};\n",
"\n",
"if(typeof $3Dmolpromise === 'undefined') {\n",
"$3Dmolpromise = null;\n",
" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.js');\n",
"}\n",
"\n",
"var viewer_1693933652754884 = null;\n",
"var warn = document.getElementById(\"3dmolwarning_1693933652754884\");\n",
"if(warn) {\n",
" warn.parentNode.removeChild(warn);\n",
"}\n",
"$3Dmolpromise.then(function() {\n",
"viewer_1693933652754884 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1693933652754884\"),{backgroundColor:\"white\"});\n",
"viewer_1693933652754884.zoomTo();\n",
"\tviewer_1693933652754884.addModel(\"@<TRIPOS>MOLECULE\\nCompound\\n2 1 1 0 1\\nSMALL\\nNO_CHARGES\\n@<TRIPOS>CRYSIN\\n 6.5182 6.0000 6.0000 90.0000 90.0000 90.0000 1 1\\n@<TRIPOS>ATOM\\n 1 C -0.7591 0.0183 0.0212 C 1 Compound\\n 2 C 0.7591 -0.0183 -0.0212 C 1 Compound\\n@<TRIPOS>BOND\\n 1 1 2 1\\n@<TRIPOS>SUBSTRUCTURE\\n 1 Compound 1 RESIDUE 0 **** ROOT 0\\n\",\"mol2\");\n",
"\tviewer_1693933652754884.setStyle({\"stick\": {\"radius\": 0.2, \"color\": \"grey\"}, \"sphere\": {\"scale\": 0.3, \"colorscheme\": {}}});\n",
"\tviewer_1693933652754884.zoomTo();\n",
"viewer_1693933652754884.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/plain": [
"<py3Dmol.view at 0x196398790>"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"alkane_ua.visualize()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.4"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment