add more cutoff distances

Untitled.ipynb

@@ -0,0 +1,76 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "7e0c5ceb-24ca-426a-a99b-5e5f63561246",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from datasets import load_dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "03a41685-5d16-4555-a24b-c87d72a233fe",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Using custom data configuration default\n",
+      "Reusing dataset protein_ligand_contacts (/ccs/home/glaser/.cache/huggingface/datasets/jglaser___protein_ligand_contacts/default/1.4.1/2aba91a819153bdd9a95ce28edf727166722133978758c388eb80b7d587ecce7)\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "66fc86548a21486fa95dd318a6dba0bd",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "  0%|          | 0/1 [00:00<?, ?it/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "ds = load_dataset('jglaser/protein_ligand_contacts')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bae10159-fc53-4dd8-9c7d-07837103dee3",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

data/pdbbind_with_contacts.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:46dfc8d5f369cfe05c12955b45e15b3d8991014d01e0d5f28530b0bb0c6a6eb3
-size 16075354
+oid sha256:3d715ac89988ff2b436c53390e408145d3e6d2a9dd6771d29b52d5a48f0cb29d
+size 157147287

pdbbind.ipynb

@@ -123,43 +123,27 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "d6dda488-f709-4fe7-b372-080042cf7c66",
+   "id": "802cb9bc-2563-4d7f-9a76-3be2d9263a36",
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_complex = pd.read_parquet('data/pdbbind_complex.parquet')"
+    "cutoffs = [5,8,11]"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "ed3fe035-6035-4d39-b072-d12dc0a95857",
+   "id": "d6dda488-f709-4fe7-b372-080042cf7c66",
    "metadata": {},
    "outputs": [],
    "source": [
-    "import dask.array as da\n",
-    "import dask.dataframe as dd\n",
-    "from dask.bag import from_delayed\n",
-    "from dask import delayed\n",
-    "import pyarrow as pa\n",
-    "import pyarrow.parquet as pq"
+    "dfs_complex = {c: pd.read_parquet('data/pdbbind_complex_{}.parquet'.format(c)) for c in cutoffs}"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 10,
-   "id": "cd26125b-e68b-4fa3-846e-2b6e7f635fe0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "contacts_dask = da.from_npy_stack('data/pdbbind_contacts')\n",
-    "contacts_dask = contacts_dask.reshape(-1,contacts_dask.shape[-2]*contacts_dask.shape[-1])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "id": "0e773f9d-6555-49c0-b0af-202c5e19b2cc",
+   "id": "aebc6791-5bb0-4828-9697-79bc243f8992",
    "metadata": {},
    "outputs": [
     {
@@ -191,33 +175,33 @@
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>2lbv</td>\n",
-       "      <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
-       "      <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
+       "      <td>10gs</td>\n",
+       "      <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
+       "      <td>[NH3+]C(CCC(=O)NC(CSCc1ccccc1)C(=O)NC(C(=O)O)c...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>1lt6</td>\n",
-       "      <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
-       "      <td>O=[N+]([O-])c1cccc(OC2OC(CO)C(O)C(O)C2O)c1</td>\n",
+       "      <td>184l</td>\n",
+       "      <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
+       "      <td>CC(C)Cc1ccccc1</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>4lwi</td>\n",
-       "      <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
-       "      <td>COc1ccc(-c2c(-c3cc(C(C)C)c(O)cc3O)noc2NC(=O)C2...</td>\n",
+       "      <td>186l</td>\n",
+       "      <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
+       "      <td>CCCCc1ccccc1</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>6oyz</td>\n",
-       "      <td>VQLQESGGGLVQTGGSLTLSCATSGRSFSLYAMAWFRQAPGKEREF...</td>\n",
-       "      <td>COC1C(O)C(n2ccc(=O)[nH]c2=O)OC1C(OC1OC(C(=O)NC...</td>\n",
+       "      <td>187l</td>\n",
+       "      <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
+       "      <td>Cc1ccc(C)cc1</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>4i11</td>\n",
-       "      <td>GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...</td>\n",
-       "      <td>CC1(C)Cc2ccccc2C(NC(Cc2ccccc2)C(=O)O)=N1</td>\n",
+       "      <td>188l</td>\n",
+       "      <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
+       "      <td>Cc1ccccc1C</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
@@ -225,32 +209,58 @@
       ],
       "text/plain": [
        "   name                                                seq  \\\n",
-       "0  2lbv  MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...   \n",
-       "1  1lt6  APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...   \n",
-       "2  4lwi  VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...   \n",
-       "3  6oyz  VQLQESGGGLVQTGGSLTLSCATSGRSFSLYAMAWFRQAPGKEREF...   \n",
-       "4  4i11  GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...   \n",
+       "0  10gs  PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...   \n",
+       "1  184l  MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...   \n",
+       "2  186l  MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...   \n",
+       "3  187l  MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...   \n",
+       "4  188l  MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...   \n",
        "\n",
        "                                              smiles  \n",
-       "0                          CCCCCCCCCCCCCCCCCCCC(=O)O  \n",
-       "1         O=[N+]([O-])c1cccc(OC2OC(CO)C(O)C(O)C2O)c1  \n",
-       "2  COc1ccc(-c2c(-c3cc(C(C)C)c(O)cc3O)noc2NC(=O)C2...  \n",
-       "3  COC1C(O)C(n2ccc(=O)[nH]c2=O)OC1C(OC1OC(C(=O)NC...  \n",
-       "4           CC1(C)Cc2ccccc2C(NC(Cc2ccccc2)C(=O)O)=N1  "
+       "0  [NH3+]C(CCC(=O)NC(CSCc1ccccc1)C(=O)NC(C(=O)O)c...  \n",
+       "1                                     CC(C)Cc1ccccc1  \n",
+       "2                                       CCCCc1ccccc1  \n",
+       "3                                       Cc1ccc(C)cc1  \n",
+       "4                                         Cc1ccccc1C  "
       ]
      },
-     "execution_count": 11,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "df_complex.head()"
+    "list(dfs_complex.values())[0].head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "ed3fe035-6035-4d39-b072-d12dc0a95857",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import dask.array as da\n",
+    "import dask.dataframe as dd\n",
+    "from dask.bag import from_delayed\n",
+    "from dask import delayed\n",
+    "import pyarrow as pa\n",
+    "import pyarrow.parquet as pq"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 12,
+   "id": "cd26125b-e68b-4fa3-846e-2b6e7f635fe0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "contacts_dask = [da.from_npy_stack('data/pdbbind_contacts_{}'.format(c)) for c in cutoffs]\n",
+    "contacts_dask = [c.reshape(-1,c.shape[-2]*c.shape[-1]) for c in contacts_dask]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
    "id": "9c7c9849-2345-4baf-89e7-d412f52353b6",
    "metadata": {},
    "outputs": [
@@ -298,37 +308,106 @@
        "dask.array<blocks, shape=(438, 1043460), dtype=float32, chunksize=(438, 1043460), chunktype=numpy.ndarray>"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "contacts_dask.blocks[1]"
+    "contacts_dask[0].blocks[1]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 14,
+   "id": "0bd8e9b9-9713-4572-bd7f-dc47da9fce91",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[16206, 16181, 16172]"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "[len(c) for c in contacts_dask]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "87493934-3839-476a-a975-7da057c320da",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "16206"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "contacts_dask[0].shape[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "1f7815ec-cddf-4bae-b72c-89cdf56cc1f9",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "name                                                   9lpr\n",
+       "seq       ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARI...\n",
+       "smiles    CC(C)CC(NC(=O)C1CCCN1C(=O)C(C)NC(=O)C(C)[NH3+]...\n",
+       "Name: 16205, dtype: object"
+      ]
+     },
+     "execution_count": 16,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "dfs_complex[5].iloc[16205]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
    "id": "42e95d84-ef27-4417-9479-8b356462b8c3",
    "metadata": {},
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "def chunk_to_sparse(chunk, idx_chunk):\n",
-    "    res = df_complex.iloc[idx_chunk].copy()\n",
-    "    # pad to account for [CLS] and [SEP]\n",
-    "    res['contacts'] = [np.where(np.pad(a,pad_width=(1,1)))[0] for a in chunk]\n",
-    "    return res\n",
+    "all_partitions = []\n",
+    "for c, cutoff in zip(contacts_dask,cutoffs):\n",
+    "    def chunk_to_sparse(rcut, chunk, idx_chunk):\n",
+    "        res = dfs_complex[rcut].iloc[idx_chunk][['name']].copy()\n",
+    "        # pad to account for [CLS] and [SEP]\n",
+    "        res['contacts_{}A'.format(rcut)] = [np.where(np.pad(a,pad_width=(1,1)))[0] for a in chunk]\n",
+    "        return res\n",
     "\n",
-    "partitions = [delayed(chunk_to_sparse)(b,k)\n",
-    "              for b,k in zip(contacts_dask.blocks, da.arange(contacts_dask.shape[0],chunks=contacts_dask.chunks[0:1]).blocks)\n",
-    "             ]"
+    "    partitions = [delayed(chunk_to_sparse)(cutoff,b,k)\n",
+    "                  for b,k in zip(c.blocks, da.arange(c.shape[0],chunks=c.chunks[0:1]).blocks)\n",
+    "                 ]\n",
+    "    all_partitions.append(partitions)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 18,
    "id": "5520a925-693f-43f0-9e76-df2e128f272e",
    "metadata": {},
    "outputs": [
@@ -354,106 +433,87 @@
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
        "      <th>name</th>\n",
-       "      <th>seq</th>\n",
-       "      <th>smiles</th>\n",
-       "      <th>contacts</th>\n",
+       "      <th>contacts_5A</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>2lbv</td>\n",
-       "      <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
-       "      <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
-       "      <td>[1043, 2569, 2570, 2573, 2575, 6121, 6122, 612...</td>\n",
+       "      <td>10gs</td>\n",
+       "      <td>[1021, 1022, 1070, 1073, 1075, 3071, 3072, 307...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>1lt6</td>\n",
-       "      <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
-       "      <td>O=[N+]([O-])c1cccc(OC2OC(CO)C(O)C(O)C2O)c1</td>\n",
-       "      <td>[513, 517, 519, 520, 521, 522, 524, 525, 545, ...</td>\n",
+       "      <td>184l</td>\n",
+       "      <td>[39279, 39280, 39281, 39282, 42332, 42334, 423...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>4lwi</td>\n",
-       "      <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
-       "      <td>COc1ccc(-c2c(-c3cc(C(C)C)c(O)cc3O)noc2NC(=O)C2...</td>\n",
-       "      <td>[520, 522, 525, 541, 543, 545, 546, 547, 1038,...</td>\n",
+       "      <td>186l</td>\n",
+       "      <td>[39277, 39278, 39279, 42332, 42333, 42334, 423...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>6oyz</td>\n",
-       "      <td>VQLQESGGGLVQTGGSLTLSCATSGRSFSLYAMAWFRQAPGKEREF...</td>\n",
-       "      <td>COC1C(O)C(n2ccc(=O)[nH]c2=O)OC1C(OC1OC(C(=O)NC...</td>\n",
-       "      <td>[35195, 35197, 35199, 35201, 35205, 35210, 352...</td>\n",
+       "      <td>187l</td>\n",
+       "      <td>[39271, 39272, 39281, 42331, 42332, 42334, 423...</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>4i11</td>\n",
-       "      <td>GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...</td>\n",
-       "      <td>CC1(C)Cc2ccccc2C(NC(Cc2ccccc2)C(=O)O)=N1</td>\n",
-       "      <td>[36231, 36232, 36234, 36235, 36236, 36237, 362...</td>\n",
+       "      <td>188l</td>\n",
+       "      <td>[39271, 39272, 39274, 39275, 42331, 42332, 423...</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "   name                                                seq  \\\n",
-       "0  2lbv  MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...   \n",
-       "1  1lt6  APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...   \n",
-       "2  4lwi  VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...   \n",
-       "3  6oyz  VQLQESGGGLVQTGGSLTLSCATSGRSFSLYAMAWFRQAPGKEREF...   \n",
-       "4  4i11  GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...   \n",
-       "\n",
-       "                                              smiles  \\\n",
-       "0                          CCCCCCCCCCCCCCCCCCCC(=O)O   \n",
-       "1         O=[N+]([O-])c1cccc(OC2OC(CO)C(O)C(O)C2O)c1   \n",
-       "2  COc1ccc(-c2c(-c3cc(C(C)C)c(O)cc3O)noc2NC(=O)C2...   \n",
-       "3  COC1C(O)C(n2ccc(=O)[nH]c2=O)OC1C(OC1OC(C(=O)NC...   \n",
-       "4           CC1(C)Cc2ccccc2C(NC(Cc2ccccc2)C(=O)O)=N1   \n",
-       "\n",
-       "                                            contacts  \n",
-       "0  [1043, 2569, 2570, 2573, 2575, 6121, 6122, 612...  \n",
-       "1  [513, 517, 519, 520, 521, 522, 524, 525, 545, ...  \n",
-       "2  [520, 522, 525, 541, 543, 545, 546, 547, 1038,...  \n",
-       "3  [35195, 35197, 35199, 35201, 35205, 35210, 352...  \n",
-       "4  [36231, 36232, 36234, 36235, 36236, 36237, 362...  "
+       "   name                                        contacts_5A\n",
+       "0  10gs  [1021, 1022, 1070, 1073, 1075, 3071, 3072, 307...\n",
+       "1  184l  [39279, 39280, 39281, 39282, 42332, 42334, 423...\n",
+       "2  186l  [39277, 39278, 39279, 42332, 42333, 42334, 423...\n",
+       "3  187l  [39271, 39272, 39281, 42331, 42332, 42334, 423...\n",
+       "4  188l  [39271, 39272, 39274, 39275, 42331, 42332, 423..."
       ]
      },
-     "execution_count": 20,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "partitions[0].compute().head()"
+    "all_partitions[0][0].compute().head()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 19,
    "id": "4982c3b1-5ce9-4f17-9834-a02c4e136bc2",
    "metadata": {},
    "outputs": [],
    "source": [
-    "ddf = dd.from_delayed(partitions)"
+    "ddfs = [dd.from_delayed(p) for p in all_partitions]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 20,
    "id": "f6cdee43-33c6-445c-8619-ace20f90638c",
    "metadata": {},
    "outputs": [],
    "source": [
-    "ddf_all = ddf.merge(df_filter, on='name').drop(columns=['affinity'])"
+    "ddf_all = None\n",
+    "for d in ddfs:\n",
+    "    if ddf_all is not None:\n",
+    "        ddf_all = ddf_all.merge(d, on='name')\n",
+    "    else:\n",
+    "        ddf_all = d\n",
+    "ddf_all = ddf_all.merge(df_filter,on='name')\n",
+    "ddf_all = ddf_all.merge(list(dfs_complex.values())[0],on='name')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 21,
    "id": "8f49f871-76f6-4fb2-b2db-c0794d4c07bf",
    "metadata": {},
    "outputs": [
@@ -461,8 +521,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPU times: user 2min 8s, sys: 3min 26s, total: 5min 35s\n",
-      "Wall time: 2min 12s\n"
+      "CPU times: user 6min 9s, sys: 12min 7s, total: 18min 17s\n",
+      "Wall time: 7min 36s\n"
      ]
     }
    ],
@@ -473,7 +533,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 22,
    "id": "45e4b4fa-6338-4abe-bd6e-8aea46e2a09c",
    "metadata": {},
    "outputs": [],
@@ -483,17 +543,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 23,
    "id": "7c3db301-6565-4053-bbd4-139bb41dd1c4",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "(array([6.3455065]), array([3.57430038]))"
+       "(array([6.35008182]), array([3.56554195]))"
       ]
      },
-     "execution_count": 25,
+     "execution_count": 23,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -507,7 +567,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 24,
    "id": "c9d674bb-d6a2-4810-aa2b-e3bc3b4bbc98",
    "metadata": {},
    "outputs": [],
@@ -516,206 +576,6 @@
     "df_all_contacts.drop(columns=['name','affinity_quantity']).astype({'affinity': 'float32','neg_log10_affinity_M': 'float32'}).to_parquet('data/pdbbind_with_contacts.parquet',index=False)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 127,
-   "id": "ec1afbc1-8072-4818-a925-0a9a6ad04759",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_all = df_complex.merge(df_filter,on='name').drop('affinity',axis=1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 128,
-   "id": "744f1e6e-a097-4b8f-8d4b-1a54f564dab8",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>name</th>\n",
-       "      <th>seq</th>\n",
-       "      <th>smiles</th>\n",
-       "      <th>affinity_uM</th>\n",
-       "      <th>affinity_quantity</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>2lbv</td>\n",
-       "      <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",
-       "      <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",
-       "      <td>0.026</td>\n",
-       "      <td>Kd</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>1</th>\n",
-       "      <td>1lt6</td>\n",
-       "      <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",
-       "      <td>O=[N+]([O-])c1cccc(OC2OC(CO)C(O)C(O)C2O)c1</td>\n",
-       "      <td>500.000</td>\n",
-       "      <td>IC50</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>2</th>\n",
-       "      <td>4lwi</td>\n",
-       "      <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",
-       "      <td>COc1ccc(-c2c(-c3cc(C(C)C)c(O)cc3O)noc2NC(=O)C2...</td>\n",
-       "      <td>0.023</td>\n",
-       "      <td>IC50</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>3</th>\n",
-       "      <td>6oyz</td>\n",
-       "      <td>VQLQESGGGLVQTGGSLTLSCATSGRSFSLYAMAWFRQAPGKEREF...</td>\n",
-       "      <td>COC1C(O)C(n2ccc(=O)[nH]c2=O)OC1C(OC1OC(C(=O)NC...</td>\n",
-       "      <td>0.185</td>\n",
-       "      <td>IC50</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>4</th>\n",
-       "      <td>4i11</td>\n",
-       "      <td>GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...</td>\n",
-       "      <td>CC1(C)Cc2ccccc2C(NC(Cc2ccccc2)C(=O)O)=N1</td>\n",
-       "      <td>27.200</td>\n",
-       "      <td>IC50</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>...</th>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "      <td>...</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20822</th>\n",
-       "      <td>2bok</td>\n",
-       "      <td>IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQ...</td>\n",
-       "      <td>C[N+](C)(C)CCCN1C(=O)C2C(C1=O)C(c1ccc(C(=N)N)c...</td>\n",
-       "      <td>0.280</td>\n",
-       "      <td>Ki</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20823</th>\n",
-       "      <td>4j46</td>\n",
-       "      <td>GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD...</td>\n",
-       "      <td>CCC(C)C(NC(=O)C1CCCN1C(=O)C(NC(=O)C(C)[NH3+])C...</td>\n",
-       "      <td>5.240</td>\n",
-       "      <td>Ki</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20824</th>\n",
-       "      <td>4j46</td>\n",
-       "      <td>GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD...</td>\n",
-       "      <td>CCC(C)C(NC(=O)C1CCCN1C(=O)C(NC(=O)C(C)[NH3+])C...</td>\n",
-       "      <td>5.240</td>\n",
-       "      <td>Ki</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20825</th>\n",
-       "      <td>2c80</td>\n",
-       "      <td>DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...</td>\n",
-       "      <td>CCCCCCSCC(NC(=O)CCC([NH3+])C(=O)O)C(=O)NCC(=O)O</td>\n",
-       "      <td>4.700</td>\n",
-       "      <td>Kd</td>\n",
-       "    </tr>\n",
-       "    <tr>\n",
-       "      <th>20826</th>\n",
-       "      <td>2c80</td>\n",
-       "      <td>DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...</td>\n",
-       "      <td>CCCCCCSCC(NC(=O)CCC([NH3+])C(=O)O)C(=O)NCC(=O)O</td>\n",
-       "      <td>4.700</td>\n",
-       "      <td>Kd</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "<p>20827 rows × 5 columns</p>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "       name                                                seq  \\\n",
-       "0      2lbv  MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...   \n",
-       "1      1lt6  APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...   \n",
-       "2      4lwi  VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...   \n",
-       "3      6oyz  VQLQESGGGLVQTGGSLTLSCATSGRSFSLYAMAWFRQAPGKEREF...   \n",
-       "4      4i11  GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGA...   \n",
-       "...     ...                                                ...   \n",
-       "20822  2bok  IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQ...   \n",
-       "20823  4j46  GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD...   \n",
-       "20824  4j46  GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD...   \n",
-       "20825  2c80  DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...   \n",
-       "20826  2c80  DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...   \n",
-       "\n",
-       "                                                  smiles  affinity_uM  \\\n",
-       "0                              CCCCCCCCCCCCCCCCCCCC(=O)O        0.026   \n",
-       "1             O=[N+]([O-])c1cccc(OC2OC(CO)C(O)C(O)C2O)c1      500.000   \n",
-       "2      COc1ccc(-c2c(-c3cc(C(C)C)c(O)cc3O)noc2NC(=O)C2...        0.023   \n",
-       "3      COC1C(O)C(n2ccc(=O)[nH]c2=O)OC1C(OC1OC(C(=O)NC...        0.185   \n",
-       "4               CC1(C)Cc2ccccc2C(NC(Cc2ccccc2)C(=O)O)=N1       27.200   \n",
-       "...                                                  ...          ...   \n",
-       "20822  C[N+](C)(C)CCCN1C(=O)C2C(C1=O)C(c1ccc(C(=N)N)c...        0.280   \n",
-       "20823  CCC(C)C(NC(=O)C1CCCN1C(=O)C(NC(=O)C(C)[NH3+])C...        5.240   \n",
-       "20824  CCC(C)C(NC(=O)C1CCCN1C(=O)C(NC(=O)C(C)[NH3+])C...        5.240   \n",
-       "20825    CCCCCCSCC(NC(=O)CCC([NH3+])C(=O)O)C(=O)NCC(=O)O        4.700   \n",
-       "20826    CCCCCCSCC(NC(=O)CCC([NH3+])C(=O)O)C(=O)NCC(=O)O        4.700   \n",
-       "\n",
-       "      affinity_quantity  \n",
-       "0                    Kd  \n",
-       "1                  IC50  \n",
-       "2                  IC50  \n",
-       "3                  IC50  \n",
-       "4                  IC50  \n",
-       "...                 ...  \n",
-       "20822                Ki  \n",
-       "20823                Ki  \n",
-       "20824                Ki  \n",
-       "20825                Kd  \n",
-       "20826                Kd  \n",
-       "\n",
-       "[20827 rows x 5 columns]"
-      ]
-     },
-     "execution_count": 128,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "df_all"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 14,
-   "id": "8f75499c-8895-4395-867e-7d9a9d394910",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_all.to_parquet('data/pdbbind.parquet')"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

pdbbind.py

@@ -90,6 +90,7 @@ if __name__ == '__main__':
 
     filenames = glob.glob('data/pdbbind/v2020-other-PL/*')
     filenames.extend(glob.glob('data/pdbbind/refined-set/*'))
+    filenames = sorted(filenames)
     comm = MPI.COMM_WORLD
     with MPICommExecutor(comm, root=0) as executor:
         if executor is not None:
@@ -103,5 +104,5 @@ if __name__ == '__main__':
             import pandas as pd
             df = pd.DataFrame({'name': names, 'seq': seqs, 'smiles': all_smiles})
             all_contacts = da.from_array(all_contacts, chunks=chunk_size)
-            da.to_npy_stack('data/pdbbind_contacts/', all_contacts)
-            df.to_parquet('data/pdbbind_complex.parquet')
+            da.to_npy_stack('data/pdbbind_contacts_{}/'.format(cutoff), all_contacts)
+            df.to_parquet('data/pdbbind_complex_{}.parquet'.format(cutoff))

protein_ligand_contacts.py

@@ -78,7 +78,9 @@ class ProteinLigandContacts(datasets.ArrowBasedBuilder):
                 "affinity_uM": datasets.Value("float"),
                 "neg_log10_affinity_M": datasets.Value("float"),
                 "affinity": datasets.Value("float"),
-                "contacts": datasets.Sequence(datasets.Value('int64')),
+                "contacts_5A": datasets.Sequence(datasets.Value('int64')),
+                "contacts_8A": datasets.Sequence(datasets.Value('int64')),
+                "contacts_11A": datasets.Sequence(datasets.Value('int64')),
                 # These are the features of your dataset like images, labels ...
             }
         )