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pdbbind-2020-general-all-equal-only.parquet

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pdbbind-2020-general-ic50-equal-only.parquet

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pdbbind-2020-general-ic50.parquet

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pdbbind-2020-general-kd.parquet

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pdbbind-2020-general-ki.parquet

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pdbbind-2020-general.parquet

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pdbbind-2020-refined-kd.parquet

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pdbbind-2020-refined-ki.parquet

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pdbbind-2020-refined.parquet

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 version https://git-lfs.github.com/spec/v1
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-size 1496256
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+size 1496252

standardize_data.ipynb

@@ -148,249 +148,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Processing PDBbind data:   4%|▍         | 217/5316 [00:07<02:49, 30.11it/s][20:24:42] sanitize [20:24:42] 5ohj_ligand: [21:40:54] 3mof_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   6%|▋         | 337/5316 [00:11<02:50, 29.27it/s][21:40:58] Explicit valence for atom # 6 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:   8%|▊         | 448/5316 [00:14<01:47, 45.24it/s][21:40:58] sanitize [21:40:58] 4lhm_ligand: [21:41:01] 2rk8_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  12%|█▏        | 617/5316 [00:19<02:12, 35.44it/s][21:41:06] Explicit valence for atom # 8 P, 6, is greater than permitted\n",
-      "Processing PDBbind data:  17%|█▋        | 915/5316 [00:28<02:26, 30.05it/s][21:41:06] sanitize [21:41:06] 1wc1_ligand: [21:41:15] Can't kekulize mol.  Unkekulized atoms: 3 4 19 20 22\n",
-      "Processing PDBbind data:  18%|█▊        | 944/5316 [00:28<01:39, 43.98it/s][21:41:15] sanitize [21:41:15] 4kcx_ligand: [21:41:15] 3t01_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  29%|██▉       | 1560/5316 [00:44<01:21, 45.81it/s][21:41:31] 1bq4_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  37%|███▋      | 1946/5316 [00:53<01:22, 40.88it/s][21:41:40] 6gon_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  48%|████▊     | 2530/5316 [01:07<01:00, 46.02it/s][21:41:54] Explicit valence for atom # 35 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  55%|█████▌    | 2944/5316 [01:17<00:53, 44.65it/s][21:41:54] sanitize [21:41:54] 5dhu_ligand: [21:42:04] 4ew2_ligand: warning - charged amidine and isFixed atom.\n",
-      "Processing PDBbind data:  56%|█████▌    | 2962/5316 [01:17<00:56, 41.64it/s][21:42:04] 1nki_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  57%|█████▋    | 3026/5316 [01:19<00:47, 47.84it/s][21:42:06] 4ew3_ligand: warning - charged amidine and isFixed atom.\n",
-      "Processing PDBbind data:  70%|███████   | 3730/5316 [01:35<00:33, 47.52it/s][21:42:22] Explicit valence for atom # 17 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  80%|████████  | 4269/5316 [01:47<00:20, 51.52it/s][21:42:22] sanitize [21:42:22] 5tmp_ligand: [21:42:34] Explicit valence for atom # 17 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  87%|████████▋ | 4632/5316 [01:54<00:13, 49.42it/s][21:42:34] sanitize [21:42:34] 5n6s_ligand: [21:42:41] Can't kekulize mol.  Unkekulized atoms: 0 2 3 4 5\n",
-      "Processing PDBbind data:  91%|█████████ | 4836/5316 [01:58<00:09, 51.38it/s][21:42:41] sanitize [21:42:41] 1mue_ligand: [21:42:46] Explicit valence for atom # 38 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  94%|█████████▎| 4980/5316 [02:01<00:04, 68.25it/s][21:42:46] sanitize [21:42:46] 4xtw_ligand: [21:42:48] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 5\n",
-      "Processing PDBbind data:  98%|█████████▊| 5205/5316 [02:06<00:02, 45.74it/s][21:42:48] sanitize [21:42:48] 1ksn_ligand: [21:42:53] Explicit valence for atom # 38 N, 5, is greater than permitted\n",
-      "Processing PDBbind data: 100%|█████████▉| 5310/5316 [02:08<00:00, 50.89it/s][21:42:53] sanitize [21:42:53] 4xtx_ligand: [21:42:55] Can't kekulize mol.  Unkekulized atoms: 0 1 3 4 5\n",
-      "Processing PDBbind data: 100%|██████████| 5316/5316 [02:08<00:00, 41.40it/s]\n",
-      "Processing PDBbind data:   0%|          | 37/19443 [00:01<12:22, 26.13it/s][21:42:55] sanitize [21:42:55] 1sl3_ligand: [21:42:56] 1o4n_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   0%|          | 56/19443 [00:01<11:00, 29.35it/s][21:42:57] 2it4_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   6%|▌         | 1193/19443 [00:25<05:04, 59.99it/s][21:43:20] Can't kekulize mol.  Unkekulized atoms: 2 3 4 5 6\n",
-      "[21:43:20] sanitize [21:43:20] 1hyz_ligand: [21:43:20] Explicit valence for atom # 1 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:   6%|▋         | 1216/19443 [00:25<10:11, 29.81it/s][21:43:20] sanitize [21:43:20] 4c71_ligand: [21:43:21] Can't kekulize mol.  Unkekulized atoms: 2 4 6 7 8 9 10 11 12\n",
-      "Processing PDBbind data:   7%|▋         | 1318/19443 [00:27<03:55, 76.83it/s][21:43:21] sanitize [21:43:21] 4kw6_ligand: [21:43:23] 3c14_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   7%|▋         | 1367/19443 [00:28<05:47, 51.95it/s][21:43:24] 2hwg_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   7%|▋         | 1406/19443 [00:29<04:17, 70.06it/s][21:43:24] Explicit valence for atom # 22 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:   8%|▊         | 1609/19443 [00:33<06:15, 47.45it/s][21:43:24] sanitize [21:43:24] 4y63_ligand: [21:43:28] 1w70_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   9%|▊         | 1657/19443 [00:34<05:31, 53.65it/s][21:43:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:43:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:43:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:43:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "Processing PDBbind data:   9%|▉         | 1719/19443 [00:35<06:23, 46.21it/s][21:43:31] 5jid_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:   9%|▉         | 1829/19443 [00:37<04:03, 72.46it/s][21:43:32] Explicit valence for atom # 5 P, 6, is greater than permitted\n",
-      "Processing PDBbind data:  11%|█         | 2077/19443 [00:42<05:05, 56.82it/s][21:43:32] sanitize [21:43:32] 1yhm_ligand: [21:43:37] 5jim_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  11%|█         | 2123/19443 [00:43<05:19, 54.23it/s][21:43:38] 3tvl_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  12%|█▏        | 2247/19443 [00:45<05:03, 56.71it/s][21:43:41] 2rk7_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  13%|█▎        | 2533/19443 [00:50<05:15, 53.52it/s][21:43:46] Explicit valence for atom # 0 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  15%|█▌        | 2928/19443 [00:57<04:15, 64.51it/s][21:43:46] sanitize [21:43:46] 3nok_ligand: [21:43:52] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4\n",
-      "Processing PDBbind data:  16%|█▌        | 3023/19443 [00:59<05:31, 49.58it/s][21:43:52] sanitize [21:43:52] 5ujo_ligand: [21:43:54] 6rsa_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  16%|█▌        | 3052/19443 [00:59<05:58, 45.69it/s][21:43:55] Can't kekulize mol.  Unkekulized atoms: 0 2 3 6 7 8 9 10 11\n",
-      "Processing PDBbind data:  16%|█▌        | 3111/19443 [01:00<04:18, 63.11it/s][21:43:55] sanitize [21:43:55] 2vr0_ligand: [21:43:56] Explicit valence for atom # 26 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  17%|█▋        | 3320/19443 [01:05<05:56, 45.20it/s][21:43:56] sanitize [21:43:56] 2aoh_ligand: [21:44:00] Explicit valence for atom # 14 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  19%|█▊        | 3613/19443 [01:11<04:38, 56.90it/s][21:44:00] sanitize [21:44:00] 3ksl_ligand: [21:44:06] 1t5a_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  19%|█▉        | 3674/19443 [01:12<05:03, 51.94it/s][21:44:07] Explicit valence for atom # 6 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  20%|██        | 3927/19443 [01:15<03:41, 70.06it/s][21:44:07] sanitize [21:44:07] 5dhr_ligand: [21:44:11] 2o1c_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  21%|██        | 4061/19443 [01:18<05:27, 46.98it/s][21:44:13] 2dua_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  23%|██▎       | 4434/19443 [01:24<02:59, 83.56it/s][21:44:20] 4lil_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  24%|██▎       | 4587/19443 [01:27<04:49, 51.32it/s][21:44:23] Explicit valence for atom # 9 B, 5, is greater than permitted\n",
-      "Processing PDBbind data:  26%|██▌       | 4965/19443 [01:34<05:07, 47.11it/s][21:44:23] sanitize [21:44:23] 3mmr_ligand: [21:44:29] Explicit valence for atom # 1 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  27%|██▋       | 5161/19443 [01:38<04:15, 55.79it/s][21:44:29] sanitize [21:44:29] 6i76_ligand: [21:44:33] Explicit valence for atom # 20 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  28%|██▊       | 5424/19443 [01:42<04:27, 52.35it/s][21:44:33] sanitize [21:44:33] 3o8g_ligand: [21:44:38] 6pvu_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  28%|██▊       | 5470/19443 [01:43<03:29, 66.57it/s][21:44:38] Explicit valence for atom # 34 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  28%|██▊       | 5508/19443 [01:43<03:01, 76.91it/s][21:44:38] sanitize [21:44:38] 5dhs_ligand: [21:44:39] Explicit valence for atom # 37 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  30%|██▉       | 5807/19443 [01:50<04:02, 56.18it/s][21:44:39] sanitize [21:44:39] 6hvs_ligand: [21:44:45] Explicit valence for atom # 18 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  31%|███       | 6025/19443 [01:55<04:09, 53.69it/s][21:44:45] sanitize [21:44:45] 4xjr_ligand: [21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:44:50] Explicit valence for atom # 0 B, 5, is greater than permitted\n",
-      "Processing PDBbind data:  33%|███▎      | 6441/19443 [02:02<03:40, 58.93it/s][21:44:50] sanitize [21:44:50] 3vjt_ligand: [21:44:57] Explicit valence for atom # 10 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  34%|███▍      | 6638/19443 [02:05<03:30, 60.95it/s][21:44:57] sanitize [21:44:57] 1h07_ligand: [21:45:01] Explicit valence for atom # 4 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  34%|███▍      | 6701/19443 [02:07<04:05, 51.96it/s][21:45:01] sanitize [21:45:01] 4inr_ligand: [21:45:02] Explicit valence for atom # 0 P, 6, is greater than permitted\n",
-      "Processing PDBbind data:  35%|███▌      | 6898/19443 [02:10<02:46, 75.39it/s][21:45:02] sanitize [21:45:02] 3bho_ligand_experimental: [21:45:05] 6goo_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  37%|███▋      | 7120/19443 [02:14<03:19, 61.74it/s][21:45:10] Explicit valence for atom # 15 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  37%|███▋      | 7215/19443 [02:16<03:30, 58.21it/s][21:45:10] sanitize [21:45:10] 4i60_ligand: [21:45:11] Can't kekulize mol.  Unkekulized atoms: 3 4 19 20 22\n",
-      "Processing PDBbind data:  40%|███▉      | 7723/19443 [02:25<03:27, 56.50it/s][21:45:11] sanitize [21:45:11] 6gu6_ligand: [21:45:20] Can't kekulize mol.  Unkekulized atoms: 2 3 4 5 6\n",
-      "Processing PDBbind data:  41%|████      | 7906/19443 [02:27<02:37, 73.06it/s][21:45:20] sanitize [21:45:20] 5HLM_LIGAND: [21:45:22] Explicit valence for atom # 1 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  41%|████▏     | 8066/19443 [02:30<03:24, 55.66it/s][21:45:22] sanitize [21:45:22] 3fy0_ligand: [21:45:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:45:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "Processing PDBbind data:  42%|████▏     | 8119/19443 [02:31<03:17, 57.39it/s][21:45:26] Explicit valence for atom # 33 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  45%|████▌     | 8798/19443 [02:43<02:57, 59.91it/s][21:45:26] sanitize [21:45:26] 5dht_ligand: [21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm.\n",
-      "[21:45:38] Explicit valence for atom # 0 B, 5, is greater than permitted\n",
-      "Processing PDBbind data:  46%|████▋     | 8995/19443 [02:47<03:28, 50.21it/s][21:45:38] sanitize [21:45:38] 3vjs_ligand: [21:45:42] Explicit valence for atom # 17 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  47%|████▋     | 9094/19443 [02:48<03:01, 57.18it/s][21:45:42] sanitize [21:45:42] 3wd2_ligand: [21:45:44] Explicit valence for atom # 35 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  47%|████▋     | 9145/19443 [02:49<02:39, 64.47it/s][21:45:44] sanitize [21:45:44] 4wvs_ligand: [21:45:45] Explicit valence for atom # 35 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  48%|████▊     | 9410/19443 [02:54<02:14, 74.55it/s][21:45:45] sanitize [21:45:45] 6hva_ligand: [21:45:49] 6da4_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  51%|█████     | 9936/19443 [03:02<02:34, 61.64it/s][21:45:58] Can't kekulize mol.  Unkekulized atoms: 0 26\n",
-      "Processing PDBbind data:  51%|█████▏    | 9970/19443 [03:03<03:17, 47.90it/s][21:45:58] sanitize [21:45:58] 2q2n_ligand: [21:45:59] Explicit valence for atom # 36 N, 6, is greater than permitted\n",
-      "Processing PDBbind data:  52%|█████▏    | 10014/19443 [03:04<02:47, 56.24it/s][21:45:59] sanitize [21:45:59] 6hvr_ligand: [21:45:59] Explicit valence for atom # 34 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  53%|█████▎    | 10391/19443 [03:10<02:31, 59.85it/s][21:45:59] sanitize [21:45:59] 6hv5_ligand: [21:46:06] 6dud_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  54%|█████▍    | 10544/19443 [03:12<02:11, 67.83it/s][21:46:08] Can't kekulize mol.  Unkekulized atoms: 9 10 27 30 32\n",
-      "Processing PDBbind data:  55%|█████▍    | 10634/19443 [03:14<02:33, 57.43it/s][21:46:08] sanitize [21:46:08] 5wjj_ligand: [21:46:09] 2j7w_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  55%|█████▍    | 10650/19443 [03:14<02:37, 55.84it/s][21:46:10] Can't kekulize mol.  Unkekulized atoms: 0 1 3 4 5 6 8 9 10\n",
-      "Processing PDBbind data:  56%|█████▌    | 10860/19443 [03:18<03:27, 41.43it/s][21:46:10] sanitize [21:46:10] 3lp2_ligand: [21:46:14] 4u5t_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "[21:46:14] Explicit valence for atom # 14 Sb, 7, is greater than permitted\n",
-      "Processing PDBbind data:  59%|█████▊    | 11401/19443 [03:27<01:50, 72.52it/s][21:46:14] sanitize [21:46:14] 4u5t_ligand: [21:46:23] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:23] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:23] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:23] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:23] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "Processing PDBbind data:  59%|█████▉    | 11546/19443 [03:29<02:38, 49.73it/s] [21:46:25] Explicit valence for atom # 12 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  60%|█████▉    | 11642/19443 [03:32<02:21, 55.04it/s][21:46:25] sanitize [21:46:25] 3fxz_ligand: [21:46:27] Warning - O.co2 with degree >1.\n",
-      "Processing PDBbind data:  60%|█████▉    | 11659/19443 [03:32<03:05, 41.94it/s][21:46:28] Can't kekulize mol.  Unkekulized atoms: 0 3 4 6 7 8 9 10 11\n",
-      "Processing PDBbind data:  60%|██████    | 11727/19443 [03:33<02:04, 62.03it/s][21:46:28] sanitize [21:46:28] 3lp1_ligand: [21:46:29] Can't kekulize mol.  Unkekulized atoms: 0 2 3 6 7 8 9 10 11\n",
-      "Processing PDBbind data:  63%|██████▎   | 12260/19443 [03:43<02:16, 52.65it/s][21:46:29] sanitize [21:46:29] 5yjy_ligand: [21:46:38] Warning - O.co2 with degree >1.\n",
-      "Processing PDBbind data:  64%|██████▍   | 12443/19443 [03:46<01:27, 79.72it/s][21:46:42] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:42] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:42] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:46:42] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "Processing PDBbind data:  65%|██████▌   | 12643/19443 [03:49<01:45, 64.31it/s][21:46:45] Can't kekulize mol.  Unkekulized atoms: 9 10 11 13 14 15 16 17 18\n",
-      "Processing PDBbind data:  66%|██████▌   | 12763/19443 [03:51<01:36, 69.38it/s][21:46:45] sanitize [21:46:45] 1nu1_ligand: [21:46:47] Explicit valence for atom # 12 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  67%|██████▋   | 13036/19443 [03:56<01:22, 78.09it/s][21:46:47] sanitize [21:46:47] 2ci9_ligand: [21:46:51] Explicit valence for atom # 17 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  68%|██████▊   | 13149/19443 [03:58<02:39, 39.58it/s][21:46:51] sanitize [21:46:51] 5i23_ligand: [21:46:53] 6db4_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  69%|██████▊   | 13321/19443 [04:00<01:18, 78.07it/s][21:46:56] Can't kekulize mol.  Unkekulized atoms: 31 32 33 34 35\n",
-      "Processing PDBbind data:  70%|██████▉   | 13543/19443 [04:04<01:22, 71.65it/s][21:46:56] sanitize [21:46:56] 2fm5_ligand: [21:47:00] Explicit valence for atom # 25 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  72%|███████▏  | 14052/19443 [04:13<01:25, 63.33it/s][21:47:00] sanitize [21:47:00] 3cst_ligand: [21:47:09] Warning - O.co2 with degree >1.\n",
-      "Processing PDBbind data:  73%|███████▎  | 14105/19443 [04:14<01:24, 63.01it/s][21:47:10] Explicit valence for atom # 6 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  73%|███████▎  | 14192/19443 [04:16<01:39, 52.58it/s][21:47:10] sanitize [21:47:10] 1qpf_ligand: [21:47:11] Explicit valence for atom # 37 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  74%|███████▎  | 14302/19443 [04:18<01:08, 74.65it/s][21:47:11] sanitize [21:47:11] 6huc_ligand: [21:47:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:47:13] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "Processing PDBbind data:  74%|███████▎  | 14331/19443 [04:19<01:40, 50.67it/s][21:47:14] Explicit valence for atom # 10 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  74%|███████▍  | 14397/19443 [04:20<01:15, 66.41it/s][21:47:14] sanitize [21:47:14] 6g02_ligand: [21:47:15] Can't kekulize mol.  Unkekulized atoms: 3 4 5 15 17\n",
-      "Processing PDBbind data:  76%|███████▋  | 14843/19443 [04:28<01:21, 56.19it/s][21:47:15] sanitize [21:47:15] 5tyk_ligand: [21:47:23] Explicit valence for atom # 10 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  78%|███████▊  | 15088/19443 [04:32<01:18, 55.34it/s][21:47:23] sanitize [21:47:23] 6n54_ligand: [21:47:28] Explicit valence for atom # 36 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  78%|███████▊  | 15246/19443 [04:35<01:06, 63.44it/s][21:47:28] sanitize [21:47:28] 3zp9_ligand: [21:47:30] Explicit valence for atom # 15 N, 5, is greater than permitted\n",
-      "[21:47:30] sanitize [21:47:30] 6n53_ligand: [21:47:30] Explicit valence for atom # 14 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  80%|████████  | 15594/19443 [04:42<01:02, 61.52it/s][21:47:30] sanitize [21:47:30] 6n55_ligand: [21:47:37] Explicit valence for atom # 35 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  81%|████████  | 15760/19443 [04:44<01:00, 60.86it/s][21:47:37] sanitize [21:47:37] 6htr_ligand: [21:47:40] Explicit valence for atom # 34 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  83%|████████▎ | 16087/19443 [04:51<00:56, 59.52it/s][21:47:40] sanitize [21:47:40] 6htd_ligand: [21:47:46] Explicit valence for atom # 36 N, 6, is greater than permitted\n",
-      "Processing PDBbind data:  83%|████████▎ | 16156/19443 [04:52<00:57, 57.59it/s][21:47:46] sanitize [21:47:46] 6hub_ligand: [21:47:47] Explicit valence for atom # 2 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  84%|████████▍ | 16313/19443 [04:55<01:14, 41.75it/s][21:47:47] sanitize [21:47:47] 4rlp_ligand: [21:47:51] 1epq_ligand: warning - O.co2 with non C.2 or S.o2 neighbor.\n",
-      "Processing PDBbind data:  84%|████████▍ | 16399/19443 [04:57<01:13, 41.32it/s][21:47:53] 1ao8_ligand: warning - charged amidine and isFixed atom.\n",
-      "Processing PDBbind data:  85%|████████▍ | 16437/19443 [04:58<01:22, 36.44it/s][21:47:54] Explicit valence for atom # 18 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  86%|████████▌ | 16625/19443 [05:01<00:55, 51.20it/s][21:47:54] sanitize [21:47:54] 3whw_ligand: [21:47:56] Explicit valence for atom # 8 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  88%|████████▊ | 17033/19443 [05:09<00:44, 54.27it/s][21:47:56] sanitize [21:47:56] 2pll_ligand: [21:48:04] Warning - O.co2 with degree >1.\n",
-      "Processing PDBbind data:  89%|████████▊ | 17241/19443 [05:13<00:54, 40.47it/s][21:48:08] Explicit valence for atom # 17 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  91%|█████████ | 17617/19443 [05:19<00:25, 72.99it/s][21:48:08] sanitize [21:48:08] 4bcb_ligand: [21:48:14] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:48:14] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:48:14] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:48:14] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "[21:48:14] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry\n",
-      "Processing PDBbind data:  92%|█████████▏| 17882/19443 [05:23<00:21, 74.17it/s][21:48:18] 6mny_ligand: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation.\n",
-      "Processing PDBbind data:  94%|█████████▍| 18312/19443 [05:30<00:18, 61.23it/s][21:48:26] Can't kekulize mol.  Unkekulized atoms: 4 5 6 7 8 9 14 15 16 17 18 19 20 21 22 23 24\n",
-      "Processing PDBbind data:  95%|█████████▍| 18444/19443 [05:32<00:13, 72.32it/s][21:48:26] sanitize [21:48:26] 3kck_ligand: [21:48:27] Explicit valence for atom # 7 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  95%|█████████▌| 18490/19443 [05:33<00:11, 82.96it/s][21:48:27] sanitize [21:48:27] 6pgx_ligand: [21:48:28] Explicit valence for atom # 4 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  95%|█████████▌| 18541/19443 [05:34<00:17, 50.46it/s][21:48:28] sanitize [21:48:28] 4inu_ligand: [21:48:29] Can't kekulize mol.  Unkekulized atoms: 33 34 35 37 38\n",
-      "Processing PDBbind data:  97%|█████████▋| 18850/19443 [05:39<00:09, 65.85it/s][21:48:29] sanitize [21:48:29] 3v9b_ligand: [21:48:34] Explicit valence for atom # 9 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  97%|█████████▋| 18863/19443 [05:39<00:07, 77.95it/s][21:48:34] sanitize [21:48:34] 1a7x_ligand: [21:48:34] Explicit valence for atom # 11 C, 5, is greater than permitted\n",
-      "Processing PDBbind data:  98%|█████████▊| 19005/19443 [05:41<00:05, 73.43it/s][21:48:34] sanitize [21:48:34] 3bwf_ligand: [21:48:36] Can't kekulize mol.  Unkekulized atoms: 20 21 22 23 24\n",
-      "Processing PDBbind data:  98%|█████████▊| 19061/19443 [05:42<00:05, 66.40it/s][21:48:36] sanitize [21:48:36] 5lwe_ligand: [21:48:37] Explicit valence for atom # 22 N, 5, is greater than permitted\n",
-      "Processing PDBbind data:  99%|█████████▊| 19186/19443 [05:43<00:03, 71.68it/s][21:48:37] sanitize [21:48:37] 5g0q_ligand: [21:48:39] Can't kekulize mol.  Unkekulized atoms: 38 39 40 41 42\n",
-      "Processing PDBbind data: 100%|██████████| 19443/19443 [05:47<00:00, 55.97it/s] \n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "from pathlib import Path\n",
@@ -463,7 +223,7 @@
     "                        entry = {\n",
     "                            'smiles_can': smiles,\n",
     "                            'seq': sequence,\n",
-    "                            'neg_log_10_affinity_M': neg_log_10_affinity,\n",
+    "                            'neg_log10_affinity_M': neg_log_10_affinity,\n",
     "                            'affinity_uM': 10**(6-neg_log_10_affinity)\n",
     "                        }\n",
     "                        \n",