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Update our Jupyter Notebooks #884

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2df97ca
ipython: fix parser import in 1D torsion scan
alongd May 7, 2026
c3b627f
ipython: drop rmgdb usage in TS Guesses
alongd May 7, 2026
cbad4c9
ipython: use perceive_molecule_from_xyz in external symmetry
alongd May 7, 2026
443cd83
ipython: use perceive_molecule_from_xyz in xyz_to_smiles
alongd May 7, 2026
3508b73
ipython: use perceive_molecule_from_xyz in Plot xyz
alongd May 7, 2026
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118 changes: 7 additions & 111 deletions ipython/Tools/External symmetry and optical isomers.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -19,24 +19,10 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"RDKit WARNING: [13:53:02] Enabling RDKit 2019.09.3 jupyter extensions\n"
]
}
],
"source": [
"from arc.molecule import Molecule\n",
"from arc.species import ARCSpecies\n",
"from IPython.display import display\n",
"from arc.plotter import show_sticks\n",
"from arc.species.converter import molecules_from_xyz, check_xyz_dict"
]
"outputs": [],
"source": "from arc.molecule import Molecule\nfrom arc.species import ARCSpecies\nfrom IPython.display import display\nfrom arc.plotter import show_sticks\nfrom arc.species.converter import check_xyz_dict\nfrom arc.species.perceive import perceive_molecule_from_xyz"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -90,100 +76,10 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING:pint.util:Could not resolve planks_constant: UndefinedUnitError()\n",
"WARNING:pint.util:Could not resolve plank_constant: UndefinedUnitError()\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"SMILES: [O]OC(c1cc(ccc1OC)C(C)C)NC(C)C\n",
"External symmetry: 1\n",
"Optical isomers: 2\n"
]
},
{
"data": {
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MgSQS/Pe/4Xjw3dzc7O7uvnTpUtQP7LEMdu7ceUZ76oUWg2j58OHDZ4m8L57vDw8PR0RE5Obm6vPAHgsgKSlJz8IEBANfK3jZfN90HjhoRGJiYl5UxDIjsH9eNJ/Pl8vlY4sZ1taCFSvAwMBz08Tdu8GTJ88FqNZNa2traGio/veDsZ+TMJnMPXv2jB0iVjPf14ewsDBMbuyjzI+dhrKyMqVSOXYVQzPf15bTEuf7pgD243LRokWxsbFjb6xmvm8KYD8un8PJCeTkgP37gYsLSEwEQiHIzAQkEhhfGtgGhmAf+0xBYSE4ehTcvw9cXcGGDeCzzwCOOXzWAy5a2sAFE77nZWOG2LS0HP4PTxvULK95WTgAAAAASUVORK5CYII=\n",
"text/plain": [
"Molecule(smiles=\"[O]OC(c1cc(ccc1OC)C(C)C)NC(C)C\")"
]
},
"metadata": {},
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"$3Dmolpromise.then(function() {\n",
"viewer_15931954791471632 = $3Dmol.createViewer($(\"#3dmolviewer_15931954791471632\"),{backgroundColor:\"white\"});\n",
"\tviewer_15931954791471632.addModel(\"\\n RDKit 3D\\n\\n 40 40 0 0 0 0 0 0 0 0999 V2000\\n -1.2234 2.3879 -0.3134 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1480 -0.1944 2.3919 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.2458 -0.4645 3.0320 O 0 0 0 0 0 1 0 0 0 0 0 0\\n -1.7224 -1.4210 0.4870 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.4775 -0.8093 -0.0681 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8681 -1.5928 -0.9629 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3923 -0.0964 0.9409 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8991 -1.0677 1.3827 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2789 -2.1263 -0.8273 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.2076 -3.0540 -1.2315 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.8957 -0.6518 -1.6013 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2112 3.6664 -0.9107 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2407 0.0642 -0.1407 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.1181 0.4201 0.3389 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.0655 1.6772 -0.2774 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0265 -0.3608 0.3959 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2687 1.3137 -0.7474 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1360 2.1193 -0.8224 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2890 -0.2602 -0.5594 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8888 -1.3820 -1.4044 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.2001 0.6353 0.8529 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8237 -1.6513 1.4178 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0633 -0.1294 1.9182 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1290 -1.6289 1.9207 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0030 -1.9430 -1.8689 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.1963 -2.7220 -0.8140 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4858 -2.7261 -0.3701 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1825 -3.3114 -0.8023 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.2564 -3.2473 -2.3058 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.4556 -3.7105 -0.7894 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.6229 0.3977 -1.4624 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.8865 -0.8091 -1.1605 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9707 -0.8388 -2.6762 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.2250 4.0514 -0.8151 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5186 4.3405 -0.3952 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.9445 3.6090 -1.9718 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.5758 -1.7118 0.9554 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.9441 -1.3333 0.8707 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2057 3.0841 -1.3071 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1963 1.6777 -1.1788 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 12 1 0\\n 1 15 1 0\\n 2 7 1 0\\n 2 3 1 0\\n 4 6 1 0\\n 4 7 1 0\\n 4 37 1 0\\n 5 8 1 0\\n 5 9 1 0\\n 5 13 1 0\\n 5 19 1 0\\n 6 10 1 0\\n 6 11 1 0\\n 6 20 1 0\\n 7 14 1 0\\n 7 21 1 0\\n 8 22 1 0\\n 8 23 1 0\\n 8 24 1 0\\n 9 25 1 0\\n 9 26 1 0\\n 9 27 1 0\\n 10 28 1 0\\n 10 29 1 0\\n 10 30 1 0\\n 11 31 1 0\\n 11 32 1 0\\n 11 33 1 0\\n 12 34 1 0\\n 12 35 1 0\\n 12 36 1 0\\n 13 17 2 0\\n 13 16 1 0\\n 14 16 2 0\\n 14 15 1 0\\n 15 18 2 0\\n 16 38 1 0\\n 17 18 1 0\\n 17 40 1 0\\n 18 39 1 0\\nM RAD 1 3 2\\nM END\\n\",\"sdf\");\n",
"\tviewer_15931954791471632.setStyle({\"stick\": {}});\n",
"\tviewer_15931954791471632.zoomTo();\n",
"viewer_15931954791471632.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"\n",
"if smiles is None:\n",
" mol = molecules_from_xyz(check_xyz_dict(xyz))[1]\n",
" smiles = mol.to_smiles()\n",
"\n",
"rmg_mol = Molecule(smiles=smiles)\n",
"arc_spc = ARCSpecies(label='test', smiles=smiles, xyz=xyz)\n",
"arc_spc.determine_symmetry()\n",
"\n",
"print('SMILES: ', smiles)\n",
"print('External symmetry: ', arc_spc.external_symmetry)\n",
"print('Optical isomers: ', arc_spc.optical_isomers)\n",
"\n",
"display(rmg_mol)\n",
"success = show_sticks(xyz=xyz)"
]
"outputs": [],
"source": "\nif smiles is None:\n mol = perceive_molecule_from_xyz(check_xyz_dict(xyz))\n smiles = mol.to_smiles()\n\nrmg_mol = Molecule(smiles=smiles)\narc_spc = ARCSpecies(label='test', smiles=smiles, xyz=xyz)\narc_spc.determine_symmetry()\n\nprint('SMILES: ', smiles)\nprint('External symmetry: ', arc_spc.external_symmetry)\nprint('Optical isomers: ', arc_spc.optical_isomers)\n\ndisplay(rmg_mol)\nsuccess = show_sticks(xyz=xyz)"
},
{
"cell_type": "code",
Expand Down Expand Up @@ -214,4 +110,4 @@
},
"nbformat": 4,
"nbformat_minor": 2
}
}
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