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greglandrum/Non-tetrahedral stereo.ipynb

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Non-tetrahedral stereo.ipynb
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Non-tetrahedral stereo.ipynb
{
"cells": [
{
"metadata": {
"trusted": true
},
"id": "treated-somewhere",
"cell_type": "code",
"source": "from rdkit import Chem\nfrom rdkit.Chem import Draw\nfrom rdkit.Chem.Draw import IPythonConsole\nIPythonConsole.ipython_useSVG = True\nIPythonConsole.drawOptions.prepareMolsBeforeDrawing = False\nfrom rdkit.Chem import rdDepictor\nfrom rdkit.Chem import rdDistGeom",
"execution_count": 8,
"outputs": []
},
{
"metadata": {},
"id": "invisible-thursday",
"cell_type": "markdown",
"source": "dev/nontetrahedral_stereo branch\n\nCommit: c78a8f7a2"
},
{
"metadata": {},
"id": "wooden-husband",
"cell_type": "markdown",
"source": "# 2D\n\nWithout wedging you can't tell if these are correct, but at least you can see that they could be correct"
},
{
"metadata": {},
"id": "oriental-forest",
"cell_type": "markdown",
"source": "## SP"
},
{
"metadata": {
"trusted": true
},
"id": "southwest-narrative",
"cell_type": "code",
"source": "Draw.MolsToGridImage([Chem.MolFromSmiles(x) for x in \n ('C[Pt@SP1](F)(Cl)[H]','C[Pt@SP2](F)(Cl)[H]','C[Pt@SP3](F)(Cl)[H]')])",
"execution_count": 3,
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": "[06:36:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:36:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:36:19] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n"
},
{
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"text/plain": "<IPython.core.display.SVG object>"
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {},
"id": "devoted-beaver",
"cell_type": "markdown",
"source": "## TB\nThese should be re-oriented so that the axial ligands are vertical, not horizontal"
},
{
"metadata": {
"trusted": true
},
"id": "hungarian-height",
"cell_type": "code",
"source": "ms = [Chem.MolFromSmiles(x) for x in \n ('S[As@TB1](F)(Cl)(Br)N','S[As@TB3](F)(Cl)(Br)N','S[As@TB15](F)(Cl)(Br)N')]\nfor m in ms:\n rdDepictor.Compute2DCoords(m,canonOrient=False)\nDraw.MolsToGridImage(ms)",
"execution_count": 9,
"outputs": [
{
"data": {
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"text/plain": "<IPython.core.display.SVG object>"
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {},
"id": "administrative-instrument",
"cell_type": "markdown",
"source": "## OH"
},
{
"metadata": {
"trusted": true
},
"id": "occupied-monster",
"cell_type": "code",
"source": "ms = [Chem.MolFromSmiles(x) for x in \n ('O[Co@OH1](Cl)(C)(N)(F)P','O[Co@OH3](Cl)(C)(N)(F)P','O[Co@OH27](Cl)(C)(N)(F)P')]\nfor m in ms:\n rdDepictor.Compute2DCoords(m,canonOrient=False)\nDraw.MolsToGridImage(ms)",
"execution_count": 11,
"outputs": [
{
"data": {
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"text/plain": "<IPython.core.display.SVG object>"
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {},
"id": "occupied-dance",
"cell_type": "markdown",
"source": "### Missing ligands:"
},
{
"metadata": {
"trusted": true
},
"id": "peripheral-tractor",
"cell_type": "code",
"source": "smis = ('O[Co@OH1](Cl)(C)(N)(F)P','O[Co@OH1](Cl)(C)(N)F','O[Co@OH1](Cl)(C)N','O[Co@OH1](Cl)C')\nms = [Chem.MolFromSmiles(x) for x in smis]\nfor m in ms:\n rdDepictor.Compute2DCoords(m,canonOrient=False)\nDraw.MolsToGridImage(ms,legends=smis,molsPerRow=4)\n",
"execution_count": 13,
"outputs": [
{
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"text/plain": "<IPython.core.display.SVG object>"
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
]
},
{
"metadata": {},
"id": "infectious-safety",
"cell_type": "markdown",
"source": "Those last two are messed up, *sigh*"
},
{
"metadata": {},
"id": "thermal-publicity",
"cell_type": "markdown",
"source": "# 3D"
},
{
"metadata": {
"trusted": true
},
"id": "brief-teach",
"cell_type": "code",
"source": "IPythonConsole.ipython_3d = True",
"execution_count": 14,
"outputs": []
},
{
"metadata": {},
"id": "established-trailer",
"cell_type": "markdown",
"source": "## SP"
},
{
"metadata": {
"trusted": true
},
"id": "cross-attraction",
"cell_type": "code",
"source": "mols_2d = [Chem.MolFromSmiles(x) for x in \n ('C[Pt@SP1](F)(Cl)[H]','C[Pt@SP2](F)(Cl)[H]','C[Pt@SP3](F)(Cl)[H]')]\nmols = [Chem.AddHs(m) for m in mols_2d]\nfor mol in mols:\n rdDistGeom.EmbedMolecule(mol)\ndisplay(mols_2d[0])\nmols[0]",
"execution_count": 15,
"outputs": [
{
"output_type": "stream",
"text": "[06:48:15] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:48:15] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:48:15] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:48:15] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:48:15] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n[06:48:15] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
"name": "stderr"
},
{
"output_type": "display_data",
"data": {
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"metadata": {},
"id": "inappropriate-bonus",
"cell_type": "markdown",
"source": "## TB"
},
{
"metadata": {
"trusted": true
},
"id": "loved-directory",
"cell_type": "code",
"source": "mols_2d = [Chem.MolFromSmiles(x) for x in \n ('S[As@TB1](F)(Cl)(Br)N','S[As@TB2](F)(Cl)(Br)N','S[As@TB15](F)(Cl)(Br)N')]\nmols = [Chem.AddHs(m) for m in mols_2d]\nfor mol in mols:\n rdDistGeom.EmbedMolecule(mol)\ndisplay(mols_2d[0])\nmols[0]",
"execution_count": 17,
"outputs": [
{
"output_type": "stream",
"text": "[06:48:37] UFFTYPER: Unrecognized charge state for atom: 1\n[06:48:37] UFFTYPER: Unrecognized atom type: As5+3 (1)\n[06:48:37] UFFTYPER: Unrecognized charge state for atom: 1\n[06:48:37] UFFTYPER: Unrecognized atom type: As5+3 (1)\n[06:48:37] UFFTYPER: Unrecognized charge state for atom: 1\n[06:48:37] UFFTYPER: Unrecognized atom type: As5+3 (1)\n",
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},
"metadata": {}
}
]
},
{
"metadata": {},
"id": "athletic-terminal",
"cell_type": "markdown",
"source": "## OH"
},
{
"metadata": {
"trusted": true
},
"id": "painful-december",
"cell_type": "code",
"source": "mols_2d = [Chem.MolFromSmiles(x) for x in \n ('O[Co@OH1](Cl)(C)(N)(F)P','O[Co@OH3](Cl)(C)(N)(F)P','O[Co@OH27](Cl)(C)(N)(F)P')]\nmols = [Chem.AddHs(m) for m in mols_2d]\nfor mol in mols:\n rdDistGeom.EmbedMolecule(mol)\ndisplay(mols_2d[0])\nmols[0]",
"execution_count": 19,
"outputs": [
{
"output_type": "display_data",
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{
"metadata": {
"trusted": true
},
"id": "sweet-needle",
"cell_type": "code",
"source": "display(mols_2d[1])\nmols[1]",
"execution_count": 20,
"outputs": [
{
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},
{
"metadata": {
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},
"id": "nutritional-treasury",
"cell_type": "code",
"source": "",
"execution_count": null,
"outputs": []
},
{
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