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Hi,</div>
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I am trying to use the buried_area function below. What are the arguments that I need to pass in?</div>
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<span style="color: #9b2393"><b>def</b></span> buried_area(operation, atoms1, atoms2,</p>
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<span> </span>probeRadius = <span style="color: #1c00cf">1.4</span>, vertexDensity =
<span style="color: #1c00cf">2.0</span>):</p>
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My current code is as follows:</div>
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<i>#calculate buried area</i></p>
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<b>import</b><span style="color: #000000"> os</span></p>
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<span style="color: #9b2393"><b>import</b></span> chimera</p>
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<span style="color: #9b2393"><b>import</b></span> xlsxwriter</p>
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<span style="color: #9b2393"><b>from</b></span> Measure <span style="color: #9b2393">
<b>import</b></span> measure</p>
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<span style="color: #9b2393"><b>from</b></span> chimera <span style="color: #9b2393">
<b>import</b></span> *</p>
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workbook = xlsxwriter.Workbook(<span style="color: #1c00cf">'contactArea.xlsx'</span>)</p>
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worksheet = workbook.add_worksheet()</p>
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<span style="color: #000000">Path = </span>"/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split"</p>
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i = <span style="color: #1c00cf">0</span></p>
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filelist = os.listdir(Path)</p>
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<span style="color: #9b2393"><b>for</b></span> x <span style="color: #9b2393"><b>in</b></span> filelist:</p>
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<span> </span><span style="color: #9b2393"><b>if</b></span> x.startswith(<span style="color: #c41a16">"trp.pdb."</span>):</p>
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<span style="color: #000000"><span> </span></span><i>#if (x == "trp.pdb.00001"):</i></p>
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<span> </span>opened = chimera.openModels.open(x, type =<span style="color: #c41a16">"PDB"</span>)</p>
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<span> </span>chimera.update.checkForChanges()</p>
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<span> </span><span style="color: #9b2393"><b>try</b></span>:</p>
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<span> </span>runCommand(<span style="color: #1c00cf">'surface :286-596'</span>)</p>
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<span> </span>runCommand(<span style="color: #1c00cf">'surface :899-1230'</span>)</p>
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<span> </span></p>
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<span> </span>y = measure.buried_area()</p>
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<span> </span>worksheet.write(i,<span style="color: #1c00cf">0</span>,x)</p>
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<span> </span>worksheet.write(i,<span style="color: #1c00cf">1</span>,y)</p>
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<span> </span><span style="color: #9b2393"><b>except</b></span>:</p>
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<span> </span>worksheet.write(i,<span style="color: #1c00cf">0</span>,x)</p>
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<span> </span>worksheet.write(i,<span style="color: #1c00cf">1</span>,<span style="color: #c41a16">"ERROR"</span>)</p>
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<span> </span>i = i + <span style="color: #1c00cf">1</span></p>
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<span> </span><span style="color: #9b2393"><b>print</b></span>(<span style="color: #c41a16">"Processed: "</span> + x)</p>
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<span> </span><span style="color: #9b2393"><b>print</b></span>(<span style="color: #c41a16">"Total #: "</span> + str(i))</p>
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<span> </span>runCommand(<span style="color: #1c00cf">'close all'</span>)</p>
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<span> </span>chimera.update.checkForChanges()</p>
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workbook.close()</p>
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Best,</div>
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Kevin</div>
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