updated sutsom kinfraglib

volkamerlab · May 13, 2024 · 4ef05c8 · 4ef05c8
2 parents a588b6c + ccd65cd
commit 4ef05c8
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Showing 9 changed files with 19,862 additions and 9,877 deletions.
diff --git a/data/fragment_library_custom_filtered/AP.sdf b/data/fragment_library_custom_filtered/AP.sdf
diff --git a/data/fragment_library_custom_filtered/B1.sdf b/data/fragment_library_custom_filtered/B1.sdf
diff --git a/data/fragment_library_custom_filtered/FP.sdf b/data/fragment_library_custom_filtered/FP.sdf
diff --git a/data/fragment_library_custom_filtered/GA.sdf b/data/fragment_library_custom_filtered/GA.sdf
diff --git a/data/fragment_library_custom_filtered/SE.sdf b/data/fragment_library_custom_filtered/SE.sdf
diff --git a/kinfraglib/filters/pipeline.py b/kinfraglib/filters/pipeline.py
@@ -98,9 +98,13 @@ def start_pipeline(
         os.makedirs(dir)
 
     PATH_DATA_CUSTOM = pathlib.Path(dir)    # define Path to custom data
+
+    # to prevent showing personal paths in the notebooks
+    dir_print_version = str(dir).split("../../")[1] if len(str(dir).split("../../")) == 2 else dir
 
     print(
-        "Your custom kinfraglib, the chosen parameters log file and the filtering results will be stored in " + str(PATH_DATA_CUSTOM)    # noqa E501
+        "Your custom kinfraglib, the chosen parameters log file and the filtering results will be stored in " 
+        + dir_print_version   # noqa E501
     )
     # save chosen parameters in created timestamp dir to save log file and created library
     param_list = [

diff --git a/notebooks/custom_kinfraglib/1_4_custom_filters_pairwise_retrosynthesizability.ipynb b/notebooks/custom_kinfraglib/1_4_custom_filters_pairwise_retrosynthesizability.ipynb
@@ -1124,7 +1124,31 @@
     },
     "metadata": {}
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[0;31mSignature:\u001b[0m \u001b[0mfilters\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mretro\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_valid_fragment_pairs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfragment_library\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mDocstring:\u001b[0m\n",
+      "Gets all possible fragment pairs and validates if their bond type, BRICS environment type\n",
+      "and adjacent subpockets are matching. Then it creates the SMILES string from the combined\n",
+      "pairs.\n",
+      "\n",
+      "Parameters\n",
+      "----------\n",
+      "fragment_libray : dict\n",
+      "    fragments organized in subpockets including all information\n",
+      "\n",
+      "Returns\n",
+      "-------\n",
+      "DataFrame\n",
+      "    SMILES from valid paired fragments.\n",
+      "\u001b[0;31mFile:\u001b[0m      ~/KinFragLib/kinfraglib/filters/retro.py\n",
+      "\u001b[0;31mType:\u001b[0m      function"
+     ]
+    }
+   ],
    "source": [
     "?filters.retro.get_valid_fragment_pairs"
    ]
@@ -1155,13 +1179,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Number of fragments:  778\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "Number of fragments:  778\n",
       "Number of unique pairs: 46415\n"
      ]
     }
@@ -1221,32 +1239,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "ASKCOS query started for 0 fragments.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "ASKCOS query started for 0 fragments.\n",
       "ASKCOS query finished.\n",
-      "Comparing ASKCOS children with fragments..\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Checking if all fragment pairs were requested..\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "Comparing ASKCOS children with fragments..\n",
+      "Checking if all fragment pairs were requested..\n",
       "All fragment pairs were requested.\n",
       "Done.\n",
-      "CPU times: user 7min 57s, sys: 4.61 s, total: 8min 2s\n",
-      "Wall time: 9min 59s\n"
+      "CPU times: user 10min 3s, sys: 4.8 s, total: 10min 8s\n",
+      "Wall time: 12min 21s\n"
      ]
     }
    ],
@@ -3272,7 +3272,19 @@
     },
     "metadata": {}
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "",
+     "evalue": "",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n",
+      "\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n",
+      "\u001b[1;31mClick <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. \n",
+      "\u001b[1;31mView Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
+     ]
+    }
+   ],
    "source": [
     "filters.retro.save_fragment_library_to_sdfs(\n",
     "    PATH_DATA_CUSTOM,\n",