add covalent inhibitors split

binding_affinity.py

@@ -49,8 +49,8 @@ _LICENSE = "BSD two-clause"
 _URL = "https://huggingface.co/datasets/jglaser/binding_affinity/resolve/main/"
 _data_dir = "data/"
 _file_names = {'default': _data_dir+'all.parquet',
-               'default_512': _data_dir+'all_512.parquet',
-               'no_kras': _data_dir+'all_nokras.parquet'}
+               'no_kras': _data_dir+'all_nokras.parquet',
+               'cov': _data_dir+'cov.parquet'}
 
 _URLs = {name: _URL+_file_names[name] for name in _file_names}
 
@@ -124,22 +124,22 @@ class BindingAffinity(datasets.ArrowBasedBuilder):
                     'filepath': files["default"],
                 },
             ),
-            datasets.SplitGenerator(
-                name='train_512',
+
+           datasets.SplitGenerator(
+                name='no_kras',
                 # These kwargs will be passed to _generate_examples
                 gen_kwargs={
-                    "filepath": files["default_512"],
+                    "filepath": files["no_kras"],
                 },
-            ),
 
            datasets.SplitGenerator(
-                name='no_kras',
+                name='covalent',
                 # These kwargs will be passed to _generate_examples
                 gen_kwargs={
-                    "filepath": files["no_kras"],
+                    "filepath": files["cov"],
                 },
-            ),
 
+            ),
         ]
 
     def _generate_tables(

combine_dbs.ipynb

@@ -617,7 +617,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 7,
    "id": "4ccf2ee5-d369-4c0e-bb91-792765d661bf",
    "metadata": {},
    "outputs": [],
@@ -627,7 +627,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 2,
    "id": "8a4bbb18-e62f-4774-ac6b-8a1be68204c1",
    "metadata": {},
    "outputs": [],
@@ -638,7 +638,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 3,
    "id": "d210fe56-a7eb-4adc-a77a-14c0c6d0034e",
    "metadata": {},
    "outputs": [
@@ -648,7 +648,7 @@
        "2568079"
       ]
      },
-     "execution_count": 21,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -659,7 +659,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 4,
    "id": "d12b365d-98bd-4b61-b836-1a08d2e55418",
    "metadata": {},
    "outputs": [],
@@ -670,7 +670,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 8,
    "id": "80c15210-1af3-436e-970b-f81fc596fb41",
    "metadata": {},
    "outputs": [],
@@ -680,7 +680,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 9,
    "id": "30c314b8-8fe7-48ae-a2b8-149de1471b0c",
    "metadata": {},
    "outputs": [
@@ -696,7 +696,7 @@
        "dtype: object"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -707,7 +707,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 10,
    "id": "70a0a820-4d0c-4472-af96-9c301c0ab204",
    "metadata": {},
    "outputs": [],
@@ -717,7 +717,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 11,
    "id": "13d092fa-5625-40d0-b7ec-e3405ea20279",
    "metadata": {},
    "outputs": [
@@ -934,7 +934,7 @@
        "[2568079 rows x 9 columns]"
       ]
      },
-     "execution_count": 26,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -945,7 +945,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 12,
    "id": "30f7fff7-3cfe-41c8-97c9-666f3e256222",
    "metadata": {},
    "outputs": [
@@ -955,7 +955,7 @@
        "Index(['seq', 'smiles', 'affinity_uM', 0, 1, 2, 3, 4, 5], dtype='object')"
       ]
      },
-     "execution_count": 27,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -966,7 +966,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 13,
    "id": "16d2b26e-984f-4c71-af19-a3e711ed9ca2",
    "metadata": {},
    "outputs": [],
@@ -976,7 +976,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 14,
    "id": "27fa2150-8152-444b-ba5b-24bea39fc098",
    "metadata": {},
    "outputs": [
@@ -986,7 +986,7 @@
        "Index(['smiles', 'affinity_uM'], dtype='object')"
       ]
      },
-     "execution_count": 29,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -997,7 +997,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 15,
    "id": "89edacbc-52f3-4a76-90b0-95273f5e53b3",
    "metadata": {},
    "outputs": [],
@@ -1250,7 +1250,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 23,
    "id": "8f949038-d07d-4d3a-a47e-b825cc9018ca",
    "metadata": {},
    "outputs": [],
@@ -1260,7 +1260,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 24,
    "id": "0c027988-0b44-4010-ad61-7d70eead1654",
    "metadata": {},
    "outputs": [],
@@ -1270,7 +1270,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 25,
    "id": "6aeba020-b6ff-4633-902e-4df74463eb2f",
    "metadata": {},
    "outputs": [],
@@ -1280,7 +1280,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 26,
    "id": "91196eee-5fd0-4aa4-927a-5c1a3f436ac8",
    "metadata": {},
    "outputs": [
@@ -1290,7 +1290,7 @@
        "(array([6.51286529]), array([2.4379995]))"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 26,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1301,7 +1301,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 28,
    "id": "56269dcb-e691-4759-949d-7bfdd02f5fd4",
    "metadata": {},
    "outputs": [],
@@ -1311,7 +1311,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 50,
    "id": "c6c64066-4032-4247-a8b9-00388176cc7b",
    "metadata": {},
    "outputs": [],
@@ -1322,7 +1322,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 30,
    "id": "469cf0dd-7b87-4245-973c-2a445e1fcca9",
    "metadata": {},
    "outputs": [
@@ -1334,7 +1334,7 @@
        "      dtype='object')"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1345,7 +1345,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 31,
    "id": "d91c0d91-474c-4ab2-9a5e-3b7861f7a832",
    "metadata": {},
    "outputs": [
@@ -1371,7 +1371,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 32,
    "id": "0e895ef5-1812-46c7-a4c2-dd6619b49157",
    "metadata": {},
    "outputs": [
@@ -1381,7 +1381,7 @@
        "1927202"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 32,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1392,36 +1392,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
-   "id": "b85f8b72-8dfc-4a24-b5b8-51fcbe6dcf63",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'with_mean': True,\n",
-       " 'with_std': True,\n",
-       " 'copy': True,\n",
-       " 'n_features_in_': 1,\n",
-       " 'n_samples_seen_': 1927202,\n",
-       " 'mean_': array([6.51286529]),\n",
-       " 'var_': array([2.4379995]),\n",
-       " 'scale_': array([1.56140946])}"
-      ]
-     },
-     "execution_count": 25,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "scaler.__dict__"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 26,
-   "id": "ec0ef8e2-c0e9-4c9b-bf3a-c98cc3889475",
+   "execution_count": 34,
+   "id": "3af855d3-a943-4574-985c-540d3f6b6f80",
    "metadata": {},
    "outputs": [
     {
@@ -1437,7 +1409,7 @@
        " 'scale_': array([1.56140946])}"
       ]
      },
-     "execution_count": 26,
+     "execution_count": 34,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1478,7 +1450,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 35,
    "id": "8dec95dc-a014-4d39-ae51-8de981173573",
    "metadata": {},
    "outputs": [],
@@ -1489,7 +1461,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 45,
+   "execution_count": 36,
    "id": "3f90eadd-d7e4-4104-961f-adaf5437e24b",
    "metadata": {},
    "outputs": [],
@@ -1499,7 +1471,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 46,
+   "execution_count": 37,
    "id": "f5f5335a-8f28-4058-8647-fcc8f7d2f841",
    "metadata": {},
    "outputs": [
@@ -1509,7 +1481,7 @@
        "1926799"
       ]
      },
-     "execution_count": 46,
+     "execution_count": 37,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1528,10 +1500,75 @@
     "df_nokras.to_parquet('data/all_nokras.parquet')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "4838f164-aed7-4f2d-a047-df647dfb8ea6",
+   "metadata": {},
+   "source": [
+    "**with covalently binding ligands only**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "id": "c0d250a3-5680-446c-9c98-7d6623643304",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from rdkit.Chem import SDMolSupplier\n",
+    "suppl = SDMolSupplier('data/CovPDB_ligands.sdf')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 44,
+   "id": "0c7c0b26-1f2a-4b80-8117-f1e02719aac9",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n",
+      "RDKit WARNING: [19:54:53] Warning: molecule is tagged as 3D, but all Z coords are zero\n"
+     ]
+    }
+   ],
+   "source": [
+    "from rdkit import Chem\n",
+    "cov_smiles = [Chem.MolToSmiles(m) for m in suppl]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 63,
+   "id": "258f593c-1cba-45cb-936e-8c1360075926",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_cov = df[df['smiles'].isin(cov_smiles)]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 66,
+   "id": "ee3fa0bc-9ad3-4ea7-9393-cbc7504f634c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_cov.reset_index(drop=True).to_parquet('data/cov.parquet')"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bfbf0bcd-8cd5-4efa-a9ca-f8d7ee5870e0",
+   "id": "b068dbaa-6d77-402d-ab9b-fb4f266dc854",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -1539,7 +1576,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -1553,7 +1590,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.9.4"
   }
  },
  "nbformat": 4,

data/cov.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:17b5e84f7057d6716b9e1d01bbeb207d14e0f067368d964f8fd2d232b11f1e7e
+size 98027