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philopon/wedge_dash_svg.ipynb

Created December 10, 2018 04:27
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wedge_dash_svg.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from rdkit.Chem import AllChem as Chem, Draw\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"from IPython.core.display import SVG"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = Chem.MolFromSmiles(\"CN1CCN(CC1)C(=O)O[C@H]2C3=NC=CN=C3C(=O)N2C4=NC=C(C=C4)Cl\")\n",
"Chem.Compute2DCoords(mol)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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"text/plain": [
"<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x117FDD3C8>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Draw.MolsToGridImageは中でChem.WedgeMolBondsが呼ばれ、Dashed bondが表示される\n",
"# https://github.com/rdkit/rdkit/blob/8bed437c5f00e974e60fe6d6a67b8a1096854e5d/rdkit/Chem/Draw/MolDrawing.py#L357\n",
"Draw.MolsToGridImage([mol])"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[]"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# 勝手にBondDirがassignされる事はない\n",
"[b.GetBondDir() for b in mol.GetBonds() if b.GetBondDir() != Chem.BondDir.NONE]"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
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"<path d=\"M 62.3033,251.683 60.0985,265.353\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"192.62\" y=\"142.199\"><tspan>N</tspan></text>\n",
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"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"75.6106\" y=\"144.888\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"39.1669\" y=\"189.633\"><tspan>N</tspan></text>\n",
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# ので、そのまま描画しても表示されない\n",
"drawer = Draw.MolDraw2DSVG(300, 300)\n",
"drawer.DrawMolecule(mol, 0)\n",
"drawer.FinishDrawing()\n",
"SVG(drawer.GetDrawingText())"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[rdkit.Chem.rdchem.BondDir.BEGINDASH]"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# こんな感じで予め Chem.WedgeMolBonds を読んでおくと、\n",
"Chem.EmbedMolecule(mol) # 3D構造からBondDirをassignしてるっぽいので一応 (https://github.com/rdkit/rdkit/blob/8bed437c5f00e974e60fe6d6a67b8a1096854e5d/Code/GraphMol/FileParsers/MolFileStereochem.cpp#L526)\n",
"Chem.WedgeMolBonds(mol, mol.GetConformer()) # BondDirをassign\n",
"Chem.Compute2DCoords(mol) # 再度2D構造を計算\n",
"[b.GetBondDir() for b in mol.GetBonds() if b.GetBondDir() != Chem.BondDir.NONE]"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"scrolled": true
},
"outputs": [
{
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"<path d=\"M 40.8795,203.303 38.6748,216.972\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path d=\"M 49.0014,194.795 47.4581,204.364\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\"/>\n",
"<path d=\"M 47.4581,204.364 45.9147,213.933\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\"/>\n",
"<path d=\"M 38.6748,216.972 64.5081,238.013\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path d=\"M 46.7579,214.962 64.8412,229.69\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\"/>\n",
"<path d=\"M 64.5081,238.013 95.6466,226.161\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path d=\"M 66.8085,230.008 88.6054,221.711\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\"/>\n",
"<path d=\"M 64.5081,238.013 62.3033,251.683\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path d=\"M 62.3033,251.683 60.0985,265.353\" style=\"fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path d=\"M 95.6466,226.161 100.952,193.269\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path d=\"M 89.8638,220.166 93.5774,197.141\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-dasharray:6,6\"/>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"251.907\" y=\"172.619\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"192.62\" y=\"142.199\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"160.954\" y=\"93.7123\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"134.61\" y=\"145.056\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"121.262\" y=\"71.0908\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"55.4762\" y=\"60.4804\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000\" x=\"18.8227\" y=\"126.381\"><tspan>O</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"75.6106\" y=\"144.888\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF\" x=\"39.1669\" y=\"189.633\"><tspan>N</tspan></text>\n",
"<text style=\"font-size:11px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00\" x=\"52.91\" y=\"276.459\"><tspan>Cl</tspan></text>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# SVGでもちゃんと表示される\n",
"drawer = Draw.MolDraw2DSVG(300, 300)\n",
"drawer.DrawMolecule(mol, 0)\n",
"drawer.FinishDrawing()\n",
"SVG(drawer.GetDrawingText())"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"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": "3.6.7"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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