remove hetero atoms

data/pdbbind_with_contacts.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:904aa3f182745b92c36d97fdc8a4b14a7a19bfe2f88cf05be38ea35f2287d6c3
-size 366634766
+oid sha256:90b17f9e0253534a0ffd558c231de5d715c5620ab5985fcec59cb7c759f145ee
+size 267149495

pdbbind.ipynb

@@ -111,7 +111,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 7,
    "id": "aa358835-55f3-4551-9217-e76a15de4fe8",
    "metadata": {},
    "outputs": [],
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 8,
    "id": "802cb9bc-2563-4d7f-9a76-3be2d9263a36",
    "metadata": {},
    "outputs": [],
@@ -132,7 +132,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 9,
    "id": "d8e71a8c-11a3-41f0-ab61-3ddc57e10961",
    "metadata": {},
    "outputs": [],
@@ -142,7 +142,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 10,
    "id": "ed3fe035-6035-4d39-b072-d12dc0a95857",
    "metadata": {},
    "outputs": [],
@@ -157,7 +157,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 11,
    "id": "cd26125b-e68b-4fa3-846e-2b6e7f635fe0",
    "metadata": {},
    "outputs": [
@@ -177,7 +177,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 12,
    "id": "9c7c9849-2345-4baf-89e7-d412f52353b6",
    "metadata": {},
    "outputs": [
@@ -248,7 +248,7 @@
        "dask.array<blocks, shape=(700, 2046, 510), dtype=float32, chunksize=(700, 2046, 510), chunktype=numpy.ndarray>"
       ]
      },
-     "execution_count": 27,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -259,17 +259,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 13,
    "id": "0bd8e9b9-9713-4572-bd7f-dc47da9fce91",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "[16221, 16201, 16193, 16189]"
+       "[16232, 16228, 16226, 16223]"
       ]
      },
-     "execution_count": 28,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -280,17 +280,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 14,
    "id": "87493934-3839-476a-a975-7da057c320da",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "16221"
+       "16232"
       ]
      },
-     "execution_count": 29,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -301,7 +301,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 15,
    "id": "42e95d84-ef27-4417-9479-8b356462b8c3",
    "metadata": {},
    "outputs": [],
@@ -323,7 +323,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 16,
    "id": "5520a925-693f-43f0-9e76-df2e128f272e",
    "metadata": {},
    "outputs": [
@@ -356,7 +356,7 @@
        "    <tr>\n",
        "      <th>0</th>\n",
        "      <td>10gs</td>\n",
-       "      <td>[1025, 1026, 1074, 1077, 1079, 3083, 3084, 308...</td>\n",
+       "      <td>[3083, 3084, 3086, 3087, 3088, 3089, 3094, 309...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
@@ -384,14 +384,14 @@
       ],
       "text/plain": [
        "   name                                        contacts_5A\n",
-       "0  10gs  [1025, 1026, 1074, 1077, 1079, 3083, 3084, 308...\n",
+       "0  10gs  [3083, 3084, 3086, 3087, 3088, 3089, 3094, 309...\n",
        "1  184l  [39945, 39946, 39947, 39948, 43010, 43012, 430...\n",
        "2  186l  [39943, 39944, 39945, 43010, 43011, 43012, 430...\n",
        "3  187l  [39937, 39938, 39947, 43009, 43010, 43012, 430...\n",
        "4  188l  [39937, 39938, 39940, 39941, 43009, 43010, 430..."
       ]
      },
-     "execution_count": 31,
+     "execution_count": 16,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -402,7 +402,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 17,
    "id": "4982c3b1-5ce9-4f17-9834-a02c4e136bc2",
    "metadata": {},
    "outputs": [],
@@ -412,7 +412,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 18,
    "id": "f6cdee43-33c6-445c-8619-ace20f90638c",
    "metadata": {},
    "outputs": [],
@@ -429,19 +429,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": null,
    "id": "8f49f871-76f6-4fb2-b2db-c0794d4c07bf",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "CPU times: user 8min 48s, sys: 12min 3s, total: 20min 52s\n",
-      "Wall time: 3min 20s\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%%time\n",
     "df_all_contacts = ddf_all.compute()"
@@ -449,7 +440,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": null,
    "id": "45e4b4fa-6338-4abe-bd6e-8aea46e2a09c",
    "metadata": {},
    "outputs": [],
@@ -459,21 +450,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": null,
    "id": "7c3db301-6565-4053-bbd4-139bb41dd1c4",
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "(array([6.34974652]), array([3.56691843]))"
-      ]
-     },
-     "execution_count": 36,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from sklearn.preprocessing import StandardScaler\n",
     "scaler = StandardScaler()\n",
@@ -483,7 +463,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": null,
    "id": "c9d674bb-d6a2-4810-aa2b-e3bc3b4bbc98",
    "metadata": {},
    "outputs": [],
@@ -495,7 +475,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8e5f99f3-4aa6-44c9-afd8-9c62bdef9d5f",
+   "id": "0e532f31-9157-47e9-be82-86c13565f3da",
    "metadata": {},
    "outputs": [],
    "source": []

pdbbind.py

@@ -72,7 +72,8 @@ def parse_complex(fn):
 
         close_residues = [neighbor_search.search(center=t, level='R', radius=cutoff) for t in token_pos]
         first_residue = next(structure.get_residues()).get_id()[1]
-        residue_id = [[c.get_id()[1]-first_residue for c in query] for query in close_residues] # zero-based
+        residue_id = [[c.get_id()[1]-first_residue for c in query if not c.get_id()[0].startswith(('H','W'))]
+            for query in close_residues] # zero-based, exclude hetero atoms
 
         # contact map
         contact_map = np.zeros((max_seq, max_smiles),dtype=np.float32)