{"cells":[{"metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true},"cell_type":"markdown","source":"# Visualize molecule structure\n\nThe plots are interactive, you can rotate, zoom in/out, etc."},{"metadata":{"_cell_guid":"79c7e3d0-c299-4dcb-8224-4455121ee9b0","_uuid":"d629ff2d2480ee46fbb7e2d37f6b5fab8052498a","trusted":true},"cell_type":"code","source":"import os\nimport numpy as np\nimport pandas as pd\nimport matplotlib.pyplot as plt\nimport seaborn as sns\n\nimport plotly.offline as py\nimport plotly.graph_objs as go\n\nfrom plotly import tools\n\ncolor = sns.color_palette()\n%matplotlib inline\npy.init_notebook_mode(connected=True)\n\npd.options.mode.chained_assignment = None\npd.options.display.max_columns = 999","execution_count":1,"outputs":[{"output_type":"display_data","data":{"text/html":" \n "},"metadata":{}}]},{"metadata":{"trusted":true},"cell_type":"code","source":"train_df = pd.read_csv('../input/train.csv')\nstructure_df = pd.read_csv('../input/structures.csv')","execution_count":2,"outputs":[]},{"metadata":{"_kg_hide-input":true,"_kg_hide-output":true,"trusted":true},"cell_type":"code","source":"def show_molecule(mdata, mstruct):\n mdata = mdata.merge(right=mstruct, how='left',\n left_on=['molecule_name', 'atom_index_0'],\n right_on=['molecule_name', 'atom_index'])\n mdata.rename(index=str, columns={\"x\": \"x0\", \"y\": \"y0\", \"z\": \"z0\", \"atom\": \"atom0\"}, inplace=True)\n mdata.drop(['atom_index'], axis=1, inplace=True)\n\n mdata = mdata.merge(right=mstruct, how='left',\n left_on=['molecule_name', 'atom_index_1'],\n right_on=['molecule_name', 'atom_index']\n )\n mdata.rename(index=str, columns={\"x\": \"x1\", \"y\": \"y1\", \"z\": \"z1\", \"atom\": \"atom1\"}, inplace=True)\n mdata.drop(['atom_index'], axis=1, inplace=True) \n \n data = []\n \n atoms = mstruct['atom'].unique()\n types = mdata['type'].unique()\n \n atom_cfg = {\n 'H': {\"name\": \"Hydrogen\", \"color\": \"#757575\", \"size\": 4},\n 'C': {\"name\": \"Carbon\", \"color\": \"#f44336\", \"size\": 12},\n 'O': {\"name\": \"Oxygen\", \"color\": \"#03a9f4\", \"size\": 12},\n 'N': {\"name\": \"Nitrogen\", \"color\": \"#ff9800\", \"size\": 12},\n 'F': {\"name\": \"Fluorine\", \"color\": \"#673ab7\", \"size\": 12},\n }\n \n type_cfg = {\n '2JHH': {\"color\": \"#757575\", \"width\": 2},\n '3JHH': {\"color\": \"#757575\", \"width\": 3},\n\n '1JHC': {\"color\": \"#f44336\", \"width\": 1},\n '2JHC': {\"color\": \"#f44336\", \"width\": 2},\n '3JHC': {\"color\": \"#f44336\", \"width\": 3},\n\n '1JHN': {\"color\": \"#ff9800\", \"width\": 2},\n '2JHN': {\"color\": \"#ff9800\", \"width\": 2},\n '3JHN': {\"color\": \"#ff9800\", \"width\": 3},\n }\n\n for atom, config in atom_cfg.items(): \n if atom in atoms:\n data.append(\n go.Scatter3d(\n x=mstruct[mstruct['atom'] == atom]['x'].values,\n y=mstruct[mstruct['atom'] == atom]['y'].values,\n z=mstruct[mstruct['atom'] == atom]['z'].values,\n mode='markers',\n marker=dict(\n color=config['color'],\n size=config['size'],\n opacity=0.8\n ),\n name=config['name']\n )\n )\n\n for ctype, config in type_cfg.items():\n if ctype in types:\n eX = []; eY = []; eZ = []\n for row in mdata[mdata['type'] == ctype].iterrows():\n rd = row[1]\n eX += [rd['x0'], rd['x1']]\n eY += [rd['y0'], rd['y1']]\n eZ += [rd['z0'], rd['z1']] \n \n data.append(\n go.Scatter3d(\n x=eX,\n y=eY,\n z=eZ,\n mode='lines',\n line=dict(color=config['color'], width=config['width']),\n name=ctype\n )\n ) \n\n axis=dict(showbackground=False, showline=False, zeroline=False, showgrid=False, showticklabels=False, title='')\n layout = go.Layout(\n margin=dict(l=50, r=50, b=50, t=50),\n width=720,\n height=640,\n showlegend=True,\n scene=dict(\n xaxis=dict(axis),\n yaxis=dict(axis),\n zaxis=dict(axis),\n )\n )\n fig = go.Figure(data=data, layout=layout)\n py.iplot(fig, filename='molecule')","execution_count":11,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"molecule = 'dsgdb9nsd_000001'\nshow_molecule(train_df[train_df['molecule_name'] == molecule], structure_df[structure_df['molecule_name'] == molecule])","execution_count":12,"outputs":[{"output_type":"display_data","data":{"text/html":"","application/vnd.plotly.v1+json":{"config":{"linkText":"Export to plot.ly","plotlyServerURL":"https://plot.ly","responsive":true,"showLink":false},"data":[{"marker":{"color":"#757575","opacity":0.8,"size":4},"mode":"markers","name":"Hydrogen","type":"scatter3d","uid":"66f892ba-6c6a-4b12-8b2f-b6503fba9fcf","x":[0.002150416,1.011730843,-0.540815069,-0.5238136345000001],"y":[-0.0060313176,1.4637511619999999,1.447526614,1.437932644],"z":[0.0019761204,0.0002765748,-0.8766437152,0.9063972942]},{"marker":{"color":"#f44336","opacity":0.8,"size":12},"mode":"markers","name":"Carbon","type":"scatter3d","uid":"e0e6b1f2-a5ae-4ea2-a92b-613c22f6223d","x":[-0.012698135900000001],"y":[1.085804158],"z":[0.008000995799999999]},{"line":{"color":"#757575","width":2},"mode":"lines","name":"2JHH","type":"scatter3d","uid":"c8c55810-25ef-4bce-904b-b3c209fb38d9","x":[0.002150416,1.011730843,0.002150416,-0.540815069,0.002150416,-0.5238136345000001,1.011730843,-0.540815069,1.011730843,-0.5238136345000001,-0.540815069,-0.5238136345000001],"y":[-0.0060313176,1.4637511619999999,-0.0060313176,1.447526614,-0.0060313176,1.437932644,1.4637511619999999,1.447526614,1.4637511619999999,1.437932644,1.447526614,1.437932644],"z":[0.0019761204,0.0002765748,0.0019761204,-0.8766437152,0.0019761204,0.9063972942,0.0002765748,-0.8766437152,0.0002765748,0.9063972942,-0.8766437152,0.9063972942]},{"line":{"color":"#f44336","width":1},"mode":"lines","name":"1JHC","type":"scatter3d","uid":"6e8f1448-9948-45ff-b5b8-63853bea771e","x":[0.002150416,-0.012698135900000001,1.011730843,-0.012698135900000001,-0.540815069,-0.012698135900000001,-0.5238136345000001,-0.012698135900000001],"y":[-0.0060313176,1.085804158,1.4637511619999999,1.085804158,1.447526614,1.085804158,1.437932644,1.085804158],"z":[0.0019761204,0.008000995799999999,0.0002765748,0.008000995799999999,-0.8766437152,0.008000995799999999,0.9063972942,0.008000995799999999]}],"layout":{"height":640,"margin":{"b":50,"l":50,"r":50,"t":50},"scene":{"xaxis":{"showbackground":false,"showgrid":false,"showline":false,"showticklabels":false,"title":{"text":""},"zeroline":false},"yaxis":{"showbackground":false,"showgrid":false,"showline":false,"showticklabels":false,"title":{"text":""},"zeroline":false},"zaxis":{"showbackground":false,"showgrid":false,"showline":false,"showticklabels":false,"title":{"text":""},"zeroline":false}},"showlegend":true,"width":720}}},"metadata":{}}]},{"metadata":{"trusted":true},"cell_type":"code","source":"molecule = 'dsgdb9nsd_128739'\nshow_molecule(train_df[train_df['molecule_name'] == molecule], structure_df[structure_df['molecule_name'] == molecule])","execution_count":78,"outputs":[{"output_type":"display_data","data":{"text/html":"","application/vnd.plotly.v1+json":{"config":{"linkText":"Export to plot.ly","plotlyServerURL":"https://plot.ly","responsive":true,"showLink":false},"data":[{"marker":{"color":"#757575","opacity":0.8,"size":4},"mode":"markers","name":"Hydrogen","type":"scatter3d","uid":"8531f93f-05f6-4936-a769-46df7489cd0f","x":[1.02821642,-0.5649449746999999,-0.4571379271,1.34932916],"y":[1.7812944569999998,1.78411015,1.5690703190000002,-3.577845383],"z":[0.0626465149,-0.7303207795000001,1.049230532,-2.600135327]},{"marker":{"color":"#f44336","opacity":0.8,"size":12},"mode":"markers","name":"Carbon","type":"scatter3d","uid":"19ce4217-376e-4a42-9605-bfb23b20fa58","x":[0.0190090754,0.6078128235,1.257143159,0.6388464281],"y":[1.3615416580000002,-0.5875199586,-2.512778415,-2.065687641],"z":[0.0918588269,-1.098044528,-2.410262672,-1.165281568]},{"marker":{"color":"#03a9f4","opacity":0.8,"size":12},"mode":"markers","name":"Oxygen","type":"scatter3d","uid":"1b37d47e-ab76-403d-a1c2-077806216753","x":[0.0649398857,1.6312772130000002,0.20786134],"y":[-0.0692419202,-0.3935487274,-2.804034073],"z":[-0.0055050188,-3.153500091,-0.3037577703]},{"marker":{"color":"#ff9800","opacity":0.8,"size":12},"mode":"markers","name":"Nitrogen","type":"scatter3d","uid":"144ac74d-4226-4020-a392-cf7942ea88d2","x":[1.071127137,1.71728615],"y":[0.1874954014,-1.737420908],"z":[-2.025960342,-3.331813136]},{"line":{"color":"#757575","width":2},"mode":"lines","name":"2JHH","type":"scatter3d","uid":"b8846fec-0594-4ce8-81ef-6647370a7f5a","x":[1.02821642,-0.5649449746999999,1.02821642,-0.4571379271,-0.5649449746999999,-0.4571379271],"y":[1.7812944569999998,1.78411015,1.7812944569999998,1.5690703190000002,1.78411015,1.5690703190000002],"z":[0.0626465149,-0.7303207795000001,0.0626465149,1.049230532,-0.7303207795000001,1.049230532]},{"line":{"color":"#f44336","width":1},"mode":"lines","name":"1JHC","type":"scatter3d","uid":"afa8fed2-714e-4421-9ee1-3ad6ef87b514","x":[1.02821642,0.0190090754,-0.5649449746999999,0.0190090754,-0.4571379271,0.0190090754,1.34932916,1.257143159],"y":[1.7812944569999998,1.3615416580000002,1.78411015,1.3615416580000002,1.5690703190000002,1.3615416580000002,-3.577845383,-2.512778415],"z":[0.0626465149,0.0918588269,-0.7303207795000001,0.0918588269,1.049230532,0.0918588269,-2.600135327,-2.410262672]},{"line":{"color":"#f44336","width":2},"mode":"lines","name":"2JHC","type":"scatter3d","uid":"474045e9-0a56-4485-b615-8a73920ab716","x":[1.34932916,0.6388464281],"y":[-3.577845383,-2.065687641],"z":[-2.600135327,-1.165281568]},{"line":{"color":"#f44336","width":3},"mode":"lines","name":"3JHC","type":"scatter3d","uid":"472bbb3e-5645-4451-9c77-960b4bb7a9a8","x":[1.02821642,0.6078128235,-0.5649449746999999,0.6078128235,-0.4571379271,0.6078128235,1.34932916,0.6078128235],"y":[1.7812944569999998,-0.5875199586,1.78411015,-0.5875199586,1.5690703190000002,-0.5875199586,-3.577845383,-0.5875199586],"z":[0.0626465149,-1.098044528,-0.7303207795000001,-1.098044528,1.049230532,-1.098044528,-2.600135327,-1.098044528]},{"line":{"color":"#ff9800","width":2},"mode":"lines","name":"2JHN","type":"scatter3d","uid":"1a2cef2f-ea66-4c73-9b79-30698d19b9a8","x":[1.34932916,1.71728615],"y":[-3.577845383,-1.737420908],"z":[-2.600135327,-3.331813136]}],"layout":{"height":640,"margin":{"b":50,"l":50,"r":50,"t":50},"scene":{"xaxis":{"showbackground":false,"showgrid":false,"showline":false,"showticklabels":false,"title":{"text":""},"zeroline":false},"yaxis":{"showbackground":false,"showgrid":false,"showline":false,"showticklabels":false,"title":{"text":""},"zeroline":false},"zaxis":{"showbackground":false,"showgrid":false,"showline":false,"showticklabels":false,"title":{"text":""},"zeroline":false}},"showlegend":true,"width":720}}},"metadata":{}}]},{"metadata":{"trusted":true},"cell_type":"code","source":"molecule = 'dsgdb9nsd_000037'","execution_count":13,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"mstructure = structure_df[structure_df['molecule_name'] == molecule]\nmstructure.head(20)","execution_count":14,"outputs":[{"output_type":"execute_result","execution_count":14,"data":{"text/plain":" molecule_name atom_index atom x y z\n256 dsgdb9nsd_000037 0 C 0.106538 1.435120 0.033361\n257 dsgdb9nsd_000037 1 O 0.426866 0.047169 0.093099\n258 dsgdb9nsd_000037 2 C 0.507149 -0.636527 -1.063183\n259 dsgdb9nsd_000037 3 O 0.769270 -1.799550 -1.110105\n260 dsgdb9nsd_000037 4 H 0.923493 2.003851 0.484657\n261 dsgdb9nsd_000037 5 H -0.037578 1.769272 -1.000574\n262 dsgdb9nsd_000037 6 H -0.812696 1.608019 0.598733\n263 dsgdb9nsd_000037 7 H 0.304585 -0.002319 -1.949656","text/html":"\n\n
\n \n \n | \n molecule_name | \n atom_index | \n atom | \n x | \n y | \n z | \n
\n \n \n \n | 256 | \n dsgdb9nsd_000037 | \n 0 | \n C | \n 0.106538 | \n 1.435120 | \n 0.033361 | \n
\n \n | 257 | \n dsgdb9nsd_000037 | \n 1 | \n O | \n 0.426866 | \n 0.047169 | \n 0.093099 | \n
\n \n | 258 | \n dsgdb9nsd_000037 | \n 2 | \n C | \n 0.507149 | \n -0.636527 | \n -1.063183 | \n
\n \n | 259 | \n dsgdb9nsd_000037 | \n 3 | \n O | \n 0.769270 | \n -1.799550 | \n -1.110105 | \n
\n \n | 260 | \n dsgdb9nsd_000037 | \n 4 | \n H | \n 0.923493 | \n 2.003851 | \n 0.484657 | \n
\n \n | 261 | \n dsgdb9nsd_000037 | \n 5 | \n H | \n -0.037578 | \n 1.769272 | \n -1.000574 | \n
\n \n | 262 | \n dsgdb9nsd_000037 | \n 6 | \n H | \n -0.812696 | \n 1.608019 | \n 0.598733 | \n
\n \n | 263 | \n dsgdb9nsd_000037 | \n 7 | \n H | \n 0.304585 | \n -0.002319 | \n -1.949656 | \n
\n \n
\n
\n\n
\n \n \n | \n id | \n molecule_name | \n atom_index_0 | \n atom_index_1 | \n type | \n scalar_coupling_constant | \n
\n \n \n \n | 434 | \n 434 | \n dsgdb9nsd_000037 | \n 4 | \n 0 | \n 1JHC | \n 89.61690 | \n
\n \n | 435 | \n 435 | \n dsgdb9nsd_000037 | \n 4 | \n 2 | \n 3JHC | \n 4.23671 | \n
\n \n | 436 | \n 436 | \n dsgdb9nsd_000037 | \n 4 | \n 5 | \n 2JHH | \n -9.99405 | \n
\n \n | 437 | \n 437 | \n dsgdb9nsd_000037 | \n 4 | \n 6 | \n 2JHH | \n -8.74586 | \n
\n \n | 438 | \n 438 | \n dsgdb9nsd_000037 | \n 5 | \n 0 | \n 1JHC | \n 94.96520 | \n
\n \n | 439 | \n 439 | \n dsgdb9nsd_000037 | \n 5 | \n 2 | \n 3JHC | \n 10.76020 | \n
\n \n | 440 | \n 440 | \n dsgdb9nsd_000037 | \n 5 | \n 6 | \n 2JHH | \n -9.99519 | \n
\n \n | 441 | \n 441 | \n dsgdb9nsd_000037 | \n 6 | \n 0 | \n 1JHC | \n 89.61640 | \n
\n \n | 442 | \n 442 | \n dsgdb9nsd_000037 | \n 6 | \n 2 | \n 3JHC | \n 4.24490 | \n
\n \n | 443 | \n 443 | \n dsgdb9nsd_000037 | \n 7 | \n 0 | \n 3JHC | \n 3.78426 | \n
\n \n | 444 | \n 444 | \n dsgdb9nsd_000037 | \n 7 | \n 2 | \n 1JHC | \n 126.36100 | \n
\n \n
\n