name: chemex\nchannels:\n - rdkit\n - defaults\ndependencies:\n - python=3.7\n - openpyxl\n - rdkit<\/code><\/pre>\n\n\n\n\u3053\u3053\u3067\u306f”environment.yml”\u3068\u3044\u3046\u30d5\u30a1\u30a4\u30eb\u540d\u3067\u4fdd\u5b58\u3059\u308b\u3053\u3068\u3068\u3057\u307e\u3059\u3002\u4e0a\u8a18\u306e\u5185\u5bb9\u3092\u30b3\u30d4\u30fc\uff06\u30da\u30fc\u30b9\u30c8\u3057\u3066\u30d5\u30a1\u30a4\u30eb\u3092\u4f5c\u6210\u3057\u307e\u3057\u3087\u3046\u3002\u305d\u3057\u3066\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067\u4eee\u60f3\u74b0\u5883\u3092\u4f5c\u6210\u3057\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n
$ conda env create -f environment.yml<\/code><\/pre>\n\n\n\n\u9014\u4e2d\u3067\u4f55\u304b\u805e\u304b\u308c\u305f\u3089”yes”\u3068\u7b54\u3048\u307e\u3057\u3087\u3046\u3002\u4f5c\u6210\u304c\u7d42\u4e86\u3057\u305f\u3089\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3067Python\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u5b9f\u884c\u3059\u308b\u74b0\u5883\u3092\u7acb\u3061\u4e0a\u3052\u307e\u3059\u3002<\/p>\n\n\n\n
$ conda activate chemex<\/code><\/pre>\n\n\n\n\u3053\u308c\u3067\u30d7\u30ed\u30b0\u30e9\u30e0\u5b9f\u52b9\u3059\u308b\u6e96\u5099\u304c\u6574\u3044\u307e\u3057\u305f\u3002<\/p>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u5b9f\u884c<\/h2>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u3068\u5165\u529b\u30c7\u30fc\u30bf\u306f\u3053\u3061\u3089\u304b\u3089\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n
ChemEx.zip<\/a>\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/a><\/div>\n\n\n\n\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u305fzip\u30d5\u30a1\u30a4\u30eb\u3092\u89e3\u51cd\u3059\u308b\u3068Python\u30d7\u30ed\u30b0\u30e9\u30e0\u3068\u5316\u5408\u7269\u30c7\u30fc\u30bf\u30d5\u30a1\u30a4\u30eb\u304c\u73fe\u308c\u307e\u3059\u3002\u5316\u5408\u7269\u30c7\u30fc\u30bf\u306fSDF\u3068SMILES\u306e2\u7a2e\u985e\u304c\u3042\u308a\u307e\u3059\u3002\u4e0a\u3067\u8aac\u660e\u3057\u305f\u901a\u308a\u3001conda\u30b3\u30de\u30f3\u30c9\u3067\u4eee\u60f3\u74b0\u5883\u3092\u7acb\u3061\u4e0a\u3052\u3066\u304b\u3089\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3057\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n
$ python ChemEx.py sample1.sdf out.xlsx<\/code><\/pre>\n\n\n\n\u3053\u306e\u30b3\u30de\u30f3\u30c9\u306fSDF\u3092\u5165\u529b\u3059\u308b\u5834\u5408\u3067\u3059\u304c\u3001SMILES\u3067\u3082\u540c\u3058\u3067\u3059\u3002\u30b3\u30de\u30f3\u30c9\u304c\u6b63\u5e38\u52d5\u4f5c\u3057\u305f\u5834\u5408”out.xlsx”\u3068\u3044\u3046\u30a8\u30af\u30bb\u30eb\u30d5\u30a1\u30a4\u30eb\u304c\u4f5c\u6210\u3055\u308c\u307e\u3059\u3002\u3053\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u30a8\u30af\u30bb\u30eb\u3067\u958b\u304f\u3068\u4e0b\u56f3\u306e\u3088\u3046\u306a\u5316\u5408\u7269\u30ea\u30b9\u30c8\u304c\u898b\u3089\u308c\u308b\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
![\"\"](\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2022\/08\/excel1-1024x625.png\")
\u4f5c\u6210\u3055\u308c\u305f\u5316\u5408\u7269\u30ea\u30b9\u30c8\u306e\u30a8\u30af\u30bb\u30eb\u30b7\u30fc\u30c8<\/figcaption><\/figure><\/div>\n\n\n\n\u3053\u3093\u306a\u611f\u3058\u3067\u30a8\u30af\u30bb\u30eb\u3067\u5316\u5408\u7269\u306e\u69cb\u9020\u5f0f\u304c\u78ba\u8a8d\u3067\u304d\u307e\u3059\u3002SDF\u4e2d\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u8aad\u307f\u53d6\u3063\u3066\u30ea\u30b9\u30c8\u5316\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
\u30d7\u30ed\u30b0\u30e9\u30e0\u89e3\u8aac<\/h2>\n\n\n\n
\u4eca\u56de\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u306f\u4ee5\u4e0b\u306e\u3068\u304a\u308a\u3067\u3059\u3002<\/p>\n\n\n\n
1 #!\/usr\/bin\/env python3\n2 # coding: UTF-8\n3 import sys\n4 import os\n5 import argparse\n6 from rdkit import Chem\n7 from rdkit.Chem import AllChem\n8 from rdkit.Chem import Draw\n9 import openpyxl\n10 from openpyxl.styles.alignment import Alignment\n11 \n12 \n13 # \u30d5\u30a1\u30a4\u30eb\u304b\u3089\u5206\u5b50\u3092\u8aad\u307f\u8fbc\u307f\u305f\u3081\u306e\u51e6\u7406\u3092\u3057\u3066\u30a4\u30c6\u30ec\u30fc\u30bf\u3092\u8fd4\u3059\u3002\n14 def ChemSupplier(filename):\n15 # \u5165\u529b\u30d5\u30a1\u30a4\u30eb\u306e\u5b58\u5728\u30c1\u30a7\u30c3\u30af\n16 if os.path.exists(filename) == False:\n17 print(\"\u30d5\u30a1\u30a4\u30eb\u304c\u5b58\u5728\u3057\u307e\u305b\u3093\")\n18 quit()\n19 \n20 # \u62e1\u5f35\u5b50\u3092\u53d6\u5f97\u3059\u308b\n21 root, ext = os.path.splitext(filename)\n22 ext = ext.lower()\n23 \n24 # SDF or SMILES\u306e\u8aad\u307f\u8fbc\u307f\u8a2d\u5b9a\n25 if ext == \".smi\":\n26 suppl = Chem.SmilesMolSupplier(filename, delimiter=\"\\t\", titleLine=True)\n27 elif ext == \".sdf\":\n28 suppl = Chem.SDMolSupplier(filename)\n29 else:\n30 print(\"\u4e0d\u660e\u306a\u62e1\u5f35\u5b50\u3067\u3059\")\n31 sys.exit()\n32 \n33 return suppl\n34 \n35 \n36 # \u5206\u5b50\u306b\u4ed8\u5c5e\u3059\u308b\u30d7\u30ed\u30d1\u30c6\u30a3\u306e\u30ea\u30b9\u30c8\u3092\u53d6\u5f97\u3059\u308b\u3002\n37 def Propaties(suppl):\n38 mol = next(suppl)\n39 propnames = mol.GetPropNames()\n40 suppl.reset() # suppl\u3092\u5148\u982d\u306b\u623b\u3059\n41 \n42 return propnames\n43 \n44 \n45 if __name__ == \"__main__\":\n46 p = argparse.ArgumentParser(description=\"sdf\u307e\u305f\u306fsmi\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u30a8\u30af\u30bb\u30eb(xlsx)\u3092\u4f5c\u6210\u3057\u307e\u3059\")\n47 p.add_argument(\"input\", help=\"input (sdf or smi)\")\n48 p.add_argument(\"output\", help=\"output (xlsx)\")\n49 p.add_argument(\"-n\", action=\"store_false\", help=\"\u5206\u5b50\u540d\u306e\u307f\u51fa\u529b\u3057\u3001\u4ed6\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u306f\u51fa\u529b\u3057\u306a\u3044\")\n50 args = p.parse_args()\n51 \n52 suppl = ChemSupplier(args.input)\n53 propnames = Propaties(suppl)\n54 \n55 # excel\u30d5\u30a1\u30a4\u30eb\u4f5c\u6210\u306e\u305f\u3081\u306e\u30ef\u30fc\u30af\u30d6\u30c3\u30af\u751f\u6210\n56 wb = openpyxl.Workbook()\n57 ws = wb.worksheets[0]\n58 \n59 # \u30d8\u30c3\u30c0\u30fc\u3092\u8a18\u8ff0\u3057\u307e\u3059\u3002\n60 ws.cell(row=1, column=1).value = \"structure\" # \u7b2c1\u5217\u306f\u69cb\u9020\u5f0f\u3068\u3057\u307e\u3059\u3002\n61 ws.column_dimensions[\"A\"].width = 40 # \u30bb\u30eb\u306e\u5e45\u309240\u306b\u3057\u307e\u3059\u3002\n62 ws.cell(row=1, column=2).value = \"id\" # \u7b2c2\u5217\u306f\u5316\u5408\u7269ID\u3068\u3057\u307e\u3059\u3002\n63 # \u7b2c3\u5217\u4ee5\u964d\u306bSD\u30d5\u30a1\u30a4\u30eb\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u3092\u5165\u308c\u307e\u3059\u3002\n64 for i, p in enumerate(propnames):\n65 ws.cell(row=1, column=3 + i).value = p\n66 \n67 for i, mol in enumerate(suppl):\n68 # \u69cb\u9020\u5f0f\u3092\u753b\u50cf\u30d5\u30a1\u30a4\u30eb\u3092\u751f\u6210\u3057\u307e\u3059\u3002\n69 mol = Chem.RemoveHs(mol)\n70 AllChem.Compute2DCoords(mol)\n71 img = Draw.MolToImage(mol, size=(320, 130))\n72 # \u30bb\u30eb\u306b\u753b\u50cf\u3092\u633f\u5165\u3057\u307e\u3059\u3002\n73 img = openpyxl.drawing.image.Image(img)\n74 ws.row_dimensions[i + 2].height = 100\n75 ws.add_image(img, ws.cell(row=i + 2, column=1).coordinate)\n76 \n77 # \u5206\u5b50\u306eID\u3092\u633f\u5165\u3057\u307e\u3059\u3002\n78 molname = mol.GetProp(\"_Name\")\n79 ws.cell(row=i + 2, column=2).value = molname\n80 ws.cell(row=i + 2, column=2).alignment = Alignment(vertical=\"center\")\n81 \n82 # \u5206\u5b50\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u306e\u5024\u3092\u30bb\u30eb\u306b\u633f\u5165\u3057\u307e\u3059\u3002\n83 for j, p in enumerate(propnames):\n84 val = mol.GetProp(p)\n85 ws.cell(row=i + 2, column=3 + j).value = val\n86 ws.cell(row=i + 2, column=3 + j).alignment = Alignment(vertical=\"center\")\n87 \n88 wb.save(args.output) # \u30a8\u30af\u30bb\u30eb\u30d5\u30a1\u30a4\u30eb\u306b\u51fa\u529b<\/code><\/pre>\n\n\n\n\u305d\u308c\u3067\u306f\u7c21\u5358\u306b\u89e3\u8aac\u3057\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002\u6700\u521d\u306e10\u884c\u306f\u5229\u7528\u3059\u308b\u30e9\u30a4\u30d6\u30e9\u30ea\u3092\u30a4\u30f3\u30dd\u30fc\u30c8\u3057\u3066\u3044\u307e\u3059\u3002\u305d\u3057\u306614\u301c33\u884c\u76ee\u306fMDLSD\u5f62\u5f0f\u304bSMILES\u5f62\u5f0f\u306e\u5316\u5408\u7269\u30d5\u30a1\u30a4\u30eb\u3092\u5f15\u6570\u3068\u3057\u3066\u3001\u5316\u5408\u7269\u306e\u30a4\u30c6\u30ec\u30fc\u30bf\u3092\u8fd4\u3059\u95a2\u6570\u3092\u5b9a\u7fa9\u3057\u3066\u304a\u308a\u307e\u3059\u3002\u5316\u5408\u7269\u306e\u30d5\u30a1\u30a4\u30eb\u5f62\u5f0f\u306f\u30d5\u30a1\u30a4\u30eb\u540d\u306e\u62e1\u5f35\u5b50\u304b\u3089\u5224\u65ad\u3057\u3066\u3044\u307e\u3059\u300237\u301c42\u884c\u76ee\u306fSD\u30d5\u30a1\u30a4\u30eb\u4e2d\u306e\u5148\u982d\u5206\u5b50\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u30ea\u30b9\u30c8\u3092\u8aad\u307f\u53d6\u3063\u3066\u3044\u307e\u3059\u3002\u3053\u3053\u3067\u8aad\u307f\u53d6\u3063\u305f\u30ea\u30b9\u30c8\u304c\u30a8\u30af\u30bb\u30eb\u30d5\u30a1\u30a4\u30eb\u306e\u5217\u540d\u3068\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n
\u3053\u306e\u30d7\u30ed\u30b0\u30e9\u30e0\u3067\u306f\u30a8\u30af\u30bb\u30eb\u30d5\u30a1\u30a4\u30eb\u306e\u64cd\u4f5c\u306b”openpyxl”\u3092\u5229\u7528\u3057\u3066\u3044\u307e\u3059\u300256\u301c57\u884c\u76ee\u306fopenpyxl\u3067\u30ef\u30fc\u30af\u30d6\u30c3\u30af\u3068\u30ef\u30fc\u30af\u30b7\u30fc\u30c8\u3092\u65b0\u898f\u4f5c\u6210\u3057\u3066\u3044\u307e\u3059\u3002\u7d9a\u304f60\u301c65\u306f\u30a8\u30af\u30bb\u30eb\u30b7\u30fc\u30c8\u306e\u5148\u982d\u884c\u306b\u5217\u540d\u3092\u5165\u308c\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n
67\u884c\u76ee\u304b\u3089\u30a4\u30c6\u30ec\u30fc\u30bf\u304b\u3089\u5206\u5b50\u30921\u500b\u3065\u3064\u8aad\u307f\u53d6\u3063\u3066\u51e6\u7406\u3092\u958b\u59cb\u3057\u307e\u3059\u300269\u301c75\u884c\u76ee\u306f\u5206\u5b50\u306e2\u6b21\u5143\u69cb\u9020\u3092\u751f\u6210\u3057\u3066\u3001\u753b\u50cf\u30c7\u30fc\u30bf\uff08pillow\u306e\u5f62\u5f0f\uff09\u3092\u4f5c\u6210\u3057\u3066\u3001openpyxl\u306e\u753b\u50cf\u30c7\u30fc\u30bf\u5f62\u5f0f\u306b\u5909\u63db\u3057\u3066\u3001\u30a8\u30af\u30bb\u30eb\u30b7\u30fc\u30c8\u306e\u6240\u5b9a\u306e\u30bb\u30eb\u306b\u8cbc\u308a\u4ed8\u3051\u3066\u3044\u307e\u3059\u3002\u3053\u3053\u306e\u30dd\u30a4\u30f3\u30c8\u306f73\u884c\u76ee\u306eopenpyxl\u306e\u753b\u50cf\u30c7\u30fc\u30bf\u5f62\u5f0f\u306b\u5909\u63db\u3059\u308b\u90e8\u5206\u3067\u3059\u3002Python\u3067\u753b\u50cf\u30c7\u30fc\u30bf\u3084\u30d5\u30a1\u30a4\u30eb\u3092\u6271\u3046\u5834\u5408\u306f\u901a\u5e38pillow\u30e9\u30a4\u30d6\u30e9\u30ea\u3092\u5229\u7528\u3057\u307e\u3059\u304c\u3001openpyxl\u3067\u306f\u30c7\u30fc\u30bf\u5909\u63db\u3057\u306a\u3044\u3068\u30a8\u30e9\u30fc\u306b\u306a\u3063\u3066\u3057\u307e\u3044\u307e\u3059\u300278\u301c80\u884c\u76ee\u3067\u5206\u5b50\u306eID\uff08SD\u30d5\u30a1\u30a4\u30eb\u306e\u5206\u5b50\u30ec\u30b3\u30fc\u30c9\u6bce\u306e\u5148\u982d\u884c\u306e\u6587\u5b57\u5217\uff09\u3092\u30bb\u30eb\u306b\u5165\u308c\u3066\u3044\u307e\u3059\u300283\u301c86\u884c\u76ee\u306f\u5206\u5b50\u306e\u3059\u3079\u3066\u306e\u30d7\u30ed\u30d1\u30c6\u30a3\u306e\u5024\u3092\u30bb\u30eb\u306b\u5165\u308c\u3066\u3044\u307e\u3059\u3002\u6700\u5f8c\u306b88\u884c\u76ee\u3067\u30a8\u30af\u30bb\u30eb\u30d5\u30a1\u30a4\u30eb\u306b\u51fa\u529b\u3057\u307e\u3059\u3002<\/p>\n\n\n\n
\u307e\u3068\u3081<\/h2>\n\n\n\n
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