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lamthuy
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SelfiesGen

Safetensors
gpt2
Model card Files
xet
 Community
lamthuy commited on
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  1. .idea/.gitignore +3 -0
  2. .idea/SelfiesGen.iml +8 -0
  3. .idea/inspectionProfiles/Project_Default.xml +51 -0
  4. .idea/inspectionProfiles/profiles_settings.xml +6 -0
  5. .idea/misc.xml +4 -0
  6. .idea/modules.xml +8 -0
  7. .idea/workspace.xml +36 -0
  8. .ipynb_checkpoints/Examples-checkpoint.ipynb +366 -0
  9. model.safetensors +1 -1
  10. trainer_state.json +0 -0
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+ {
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+ {
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+ "execution_count": 2,
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+ "id": "a1af2321-8860-4a3e-8406-a9ae587b97bf",
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+ "metadata": {},
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+ "outputs": [],
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+ "source": [
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+ "from transformers import AutoModelForCausalLM, AutoTokenizer\n",
11
+ "import selfies as sf\n",
12
+ "from rdkit import Chem\n",
13
+ "from typing import Optional\n",
14
+ "import numpy as np\n",
15
+ "import py3Dmol\n",
16
+ "from rdkit import Chem, DataStructs\n",
17
+ "from rdkit.Chem import AllChem\n",
18
+ "import torch\n",
19
+ "\n",
20
+ "def smiles_to_3d(smiles_list, width=400, height=300):\n",
21
+ " # Visualize the 3D structure using py3Dmol\n",
22
+ " view = py3Dmol.view(width=width, height=height)\n",
23
+ " for smiles in smiles_list:\n",
24
+ " # Generate the RDKit molecule object\n",
25
+ " mol = Chem.MolFromSmiles(smiles)\n",
26
+ " if mol is None:\n",
27
+ " raise ValueError(\"Invalid SMILES string\")\n",
28
+ "\n",
29
+ " # Add hydrogens to the molecule\n",
30
+ " mol = Chem.AddHs(mol)\n",
31
+ "\n",
32
+ " # Generate 3D coordinates\n",
33
+ " AllChem.EmbedMolecule(mol, randomSeed=42)\n",
34
+ " AllChem.UFFOptimizeMolecule(mol)\n",
35
+ "\n",
36
+ " # Generate the 3D structure in the form of a pdb string\n",
37
+ " pdb = Chem.MolToPDBBlock(mol)\n",
38
+ " view.addModel(pdb, 'pdb')\n",
39
+ " view.setStyle({'stick': {}})\n",
40
+ " view.zoomTo()\n",
41
+ " return view\n",
42
+ "\n",
43
+ " \n",
44
+ "# Load the checkpoint and the tokenizer\n",
45
+ "checkpoint_path = \"lamthuy/SelfiesGen\"\n",
46
+ "model = AutoModelForCausalLM.from_pretrained(checkpoint_path)\n",
47
+ "tokenizer = AutoTokenizer.from_pretrained(checkpoint_path)"
48
+ ]
49
+ },
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+ "id": "9b7066a4-6637-4d45-a0d9-3cc5e2ca0409",
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+ ]
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+ "output_type": "display_data"
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+ },
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+ {
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+ "data": {
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+ "text/plain": [
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+ "<py3Dmol.view at 0x2afd09c40>"
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+ ]
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+ },
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+ "execution_count": 9,
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+ "metadata": {},
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+ "output_type": "execute_result"
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+ }
121
+ ],
122
+ "source": [
123
+ "# Given a SMILES, get its fingerpint\n",
124
+ "smiles = \"CC(=O)OC1=CC=CC=C1C(=O)O\"\n",
125
+ "smiles_to_3d([smiles])"
126
+ ]
127
+ },
128
+ {
129
+ "cell_type": "code",
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+ "execution_count": 12,
131
+ "id": "05f9bf21-c998-4d63-870e-c1033ff91b31",
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+ "metadata": {},
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+ "outputs": [
134
+ {
135
+ "name": "stderr",
136
+ "output_type": "stream",
137
+ "text": [
138
+ "The attention mask and the pad token id were not set. As a consequence, you may observe unexpected behavior. Please pass your input's `attention_mask` to obtain reliable results.\n",
139
+ "Setting `pad_token_id` to `eos_token_id`:50256 for open-end generation.\n"
140
+ ]
141
+ },
142
+ {
143
+ "name": "stdout",
144
+ "output_type": "stream",
145
+ "text": [
146
+ "[C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=S][O][SEP]\n",
147
+ "[C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=NH2+1][O]\n",
148
+ "CC(=O)OC1=CC=CC=C1C(=[NH2+1])O\n"
149
+ ]
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+ },
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+ {
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+ "data": {
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+ " </div>\n",
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+ "<script>\n",
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+ "\n",
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+ "var loadScriptAsync = function(uri){\n",
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+ " return new Promise((resolve, reject) => {\n",
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+ " tag.async = true;\n",
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+ " };\n",
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+ " var firstScriptTag = document.getElementsByTagName('script')[0];\n",
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+ " firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n",
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+ "});\n",
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+ "};\n",
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+ "\n",
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+ "if(typeof $3Dmolpromise === 'undefined') {\n",
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+ "$3Dmolpromise = null;\n",
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+ " $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.2/3Dmol-min.js');\n",
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+ "}\n",
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+ "\n",
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+ "var viewer_1753264053659028 = null;\n",
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+ "var warn = document.getElementById(\"3dmolwarning_1753264053659028\");\n",
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+ "if(warn) {\n",
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+ " warn.parentNode.removeChild(warn);\n",
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+ "}\n",
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+ "$3Dmolpromise.then(function() {\n",
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+ "viewer_1753264053659028 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_1753264053659028\"),{backgroundColor:\"white\"});\n",
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+ "viewer_1753264053659028.zoomTo();\n",
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+ "\tviewer_1753264053659028.addModel(\"HETATM 1 C1 UNL 1 2.411 -2.582 -1.327 1.00 0.00 C \\nHETATM 2 C2 UNL 1 1.777 -1.233 -1.311 1.00 0.00 C \\nHETATM 3 O1 UNL 1 1.971 -0.444 -2.275 1.00 0.00 O \\nHETATM 4 O2 UNL 1 0.887 -0.908 -0.278 1.00 0.00 O \\nHETATM 5 C3 UNL 1 0.406 0.380 0.005 1.00 0.00 C \\nHETATM 6 C4 UNL 1 1.187 1.525 -0.250 1.00 0.00 C \\nHETATM 7 C5 UNL 1 0.691 2.798 0.033 1.00 0.00 C \\nHETATM 8 C6 UNL 1 -0.580 2.947 0.586 1.00 0.00 C \\nHETATM 9 C7 UNL 1 -1.357 1.822 0.866 1.00 0.00 C \\nHETATM 10 C8 UNL 1 -0.876 0.529 0.582 1.00 0.00 C \\nHETATM 11 C9 UNL 1 -1.702 -0.662 0.905 1.00 0.00 C \\nHETATM 12 N1 UNL 1 -2.996 -0.640 0.776 1.00 0.00 N1+\\nHETATM 13 O3 UNL 1 -1.073 -1.826 1.349 1.00 0.00 O \\nHETATM 14 H1 UNL 1 1.780 -3.281 -1.914 1.00 0.00 H \\nHETATM 15 H2 UNL 1 2.512 -2.964 -0.290 1.00 0.00 H \\nHETATM 16 H3 UNL 1 3.421 -2.524 -1.787 1.00 0.00 H \\nHETATM 17 H4 UNL 1 2.190 1.435 -0.643 1.00 0.00 H \\nHETATM 18 H5 UNL 1 1.299 3.672 -0.166 1.00 0.00 H \\nHETATM 19 H6 UNL 1 -0.957 3.936 0.813 1.00 0.00 H \\nHETATM 20 H7 UNL 1 -2.325 1.965 1.329 1.00 0.00 H \\nHETATM 21 H8 UNL 1 -3.567 -1.482 1.010 1.00 0.00 H \\nHETATM 22 H9 UNL 1 -3.499 0.198 0.408 1.00 0.00 H \\nHETATM 23 H10 UNL 1 -1.599 -2.662 1.576 1.00 0.00 H \\nCONECT 1 2 14 15 16\\nCONECT 2 3 3 4\\nCONECT 4 5\\nCONECT 5 6 6 10\\nCONECT 6 7 17\\nCONECT 7 8 8 18\\nCONECT 8 9 19\\nCONECT 9 10 10 20\\nCONECT 10 11\\nCONECT 11 12 12 13\\nCONECT 12 21 22\\nCONECT 13 23\\nEND\\n\",\"pdb\");\n",
196
+ "\tviewer_1753264053659028.setStyle({\"stick\": {}});\n",
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+ "\tviewer_1753264053659028.zoomTo();\n",
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+ "viewer_1753264053659028.render();\n",
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+ "});\n",
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+ "</script>"
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+ ]
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+ },
203
+ "metadata": {},
204
+ "output_type": "display_data"
205
+ },
206
+ {
207
+ "data": {
208
+ "text/plain": [
209
+ "<py3Dmol.view at 0x2afbaf020>"
210
+ ]
211
+ },
212
+ "execution_count": 12,
213
+ "metadata": {},
214
+ "output_type": "execute_result"
215
+ }
216
+ ],
217
+ "source": [
218
+ "s = sf.encoder(smiles)\n",
219
+ "s = s + \"[SEP]\"\n",
220
+ "print(s)\n",
221
+ "input_ids = tokenizer.encode(s, return_tensors=\"pt\")\n",
222
+ "n = input_ids.size(1)\n",
223
+ "# Generate output sequence\n",
224
+ "output_ids = model.generate(input_ids, max_length=128, num_beams=5, num_return_sequences=5,\n",
225
+ " early_stopping=True)\n",
226
+ "output = tokenizer.decode(output_ids[1][n:], skip_special_tokens=True)\n",
227
+ "print(output)\n",
228
+ "smiles = sf.decoder(output)\n",
229
+ "print(smiles)\n",
230
+ "smiles_to_3d([smiles])"
231
+ ]
232
+ },
233
+ {
234
+ "cell_type": "code",
235
+ "execution_count": 13,
236
+ "id": "dbe6cebd-c7d5-4da9-aac0-114f232cf147",
237
+ "metadata": {},
238
+ "outputs": [
239
+ {
240
+ "name": "stderr",
241
+ "output_type": "stream",
242
+ "text": [
243
+ "The attention mask and the pad token id were not set. As a consequence, you may observe unexpected behavior. Please pass your input's `attention_mask` to obtain reliable results.\n",
244
+ "Setting `pad_token_id` to `eos_token_id`:50256 for open-end generation.\n"
245
+ ]
246
+ },
247
+ {
248
+ "name": "stdout",
249
+ "output_type": "stream",
250
+ "text": [
251
+ "[C][C][=Branch1][C][=O][N][C][=C][C][=N][C][=C][Ring1][=Branch1][C][=Branch1][C][=S][O-1]\n",
252
+ "CC(=O)NC1=CC=NC=C1C(=S)[O-1]\n"
253
+ ]
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+ },
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+ {
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+ "data": {
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+ "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_17532640697518232\" style=\"position: relative; width: 400px; height: 300px;\">\n <p id=\"3dmolwarning_17532640697518232\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n return new Promise((resolve, reject) => {\n //this is to ignore the existence of requirejs amd\n var savedexports, savedmodule;\n if (typeof exports !== 'undefined') savedexports = exports;\n else exports = {}\n if (typeof module !== 'undefined') savedmodule = module;\n else module = {}\n\n var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\n exports = savedexports;\n module = savedmodule;\n resolve();\n };\n var firstScriptTag = document.getElementsByTagName('script')[0];\n firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.2/3Dmol-min.js');\n}\n\nvar viewer_17532640697518232 = null;\nvar warn = document.getElementById(\"3dmolwarning_17532640697518232\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_17532640697518232 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17532640697518232\"),{backgroundColor:\"white\"});\nviewer_17532640697518232.zoomTo();\n\tviewer_17532640697518232.addModel(\"HETATM 1 C1 UNL 1 3.341 0.506 -0.349 1.00 0.00 C \\nHETATM 2 C2 UNL 1 1.994 -0.109 -0.554 1.00 0.00 C \\nHETATM 3 O1 UNL 1 1.839 -0.974 -1.458 1.00 0.00 O \\nHETATM 4 N1 UNL 1 0.876 0.346 0.221 1.00 0.00 N \\nHETATM 5 C3 UNL 1 -0.424 -0.266 0.167 1.00 0.00 C \\nHETATM 6 C4 UNL 1 -0.537 -1.665 0.219 1.00 0.00 C \\nHETATM 7 C5 UNL 1 -1.798 -2.258 0.278 1.00 0.00 C \\nHETATM 8 N2 UNL 1 -2.913 -1.485 0.302 1.00 0.00 N \\nHETATM 9 C6 UNL 1 -2.844 -0.130 0.260 1.00 0.00 C \\nHETATM 10 C7 UNL 1 -1.602 0.521 0.177 1.00 0.00 C \\nHETATM 11 C8 UNL 1 -1.585 1.998 0.085 1.00 0.00 C \\nHETATM 12 S1 UNL 1 -0.600 2.783 -0.963 1.00 0.00 S \\nHETATM 13 O2 UNL 1 -2.485 2.742 0.838 1.00 0.00 O1-\\nHETATM 14 H1 UNL 1 3.531 0.642 0.736 1.00 0.00 H \\nHETATM 15 H2 UNL 1 4.133 -0.148 -0.770 1.00 0.00 H \\nHETATM 16 H3 UNL 1 3.376 1.493 -0.854 1.00 0.00 H \\nHETATM 17 H4 UNL 1 1.005 1.188 0.826 1.00 0.00 H \\nHETATM 18 H5 UNL 1 0.344 -2.292 0.249 1.00 0.00 H \\nHETATM 19 H6 UNL 1 -1.889 -3.335 0.323 1.00 0.00 H \\nHETATM 20 H7 UNL 1 -3.764 0.442 0.270 1.00 0.00 H \\nCONECT 1 2 14 15 16\\nCONECT 2 3 3 4\\nCONECT 4 5 17\\nCONECT 5 6 6 10\\nCONECT 6 7 18\\nCONECT 7 8 8 19\\nCONECT 8 9\\nCONECT 9 10 10 20\\nCONECT 10 11\\nCONECT 11 12 12 13\\nEND\\n\",\"pdb\");\n\tviewer_17532640697518232.setStyle({\"stick\": {}});\n\tviewer_17532640697518232.zoomTo();\nviewer_17532640697518232.render();\n});\n</script>",
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+ " <p id=\"3dmolwarning_17532640697518232\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n",
261
+ " </div>\n",
262
+ "<script>\n",
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+ "\n",
264
+ "var loadScriptAsync = function(uri){\n",
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+ " return new Promise((resolve, reject) => {\n",
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+ " //this is to ignore the existence of requirejs amd\n",
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+ " var savedexports, savedmodule;\n",
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+ " if (typeof exports !== 'undefined') savedexports = exports;\n",
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+ " else exports = {}\n",
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+ " else module = {}\n",
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+ "\n",
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+ " var tag = document.createElement('script');\n",
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+ " tag.src = uri;\n",
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+ " tag.async = true;\n",
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+ "if(typeof $3Dmolpromise === 'undefined') {\n",
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+ "$3Dmolpromise = null;\n",
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+ " $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.2/3Dmol-min.js');\n",
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+ "}\n",
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+ "\n",
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+ "var viewer_17532640697518232 = null;\n",
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+ "var warn = document.getElementById(\"3dmolwarning_17532640697518232\");\n",
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+ "if(warn) {\n",
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+ " warn.parentNode.removeChild(warn);\n",
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+ "}\n",
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+ "$3Dmolpromise.then(function() {\n",
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+ "viewer_17532640697518232 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17532640697518232\"),{backgroundColor:\"white\"});\n",
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+ "viewer_17532640697518232.zoomTo();\n",
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+ "\tviewer_17532640697518232.addModel(\"HETATM 1 C1 UNL 1 3.341 0.506 -0.349 1.00 0.00 C \\nHETATM 2 C2 UNL 1 1.994 -0.109 -0.554 1.00 0.00 C \\nHETATM 3 O1 UNL 1 1.839 -0.974 -1.458 1.00 0.00 O \\nHETATM 4 N1 UNL 1 0.876 0.346 0.221 1.00 0.00 N \\nHETATM 5 C3 UNL 1 -0.424 -0.266 0.167 1.00 0.00 C \\nHETATM 6 C4 UNL 1 -0.537 -1.665 0.219 1.00 0.00 C \\nHETATM 7 C5 UNL 1 -1.798 -2.258 0.278 1.00 0.00 C \\nHETATM 8 N2 UNL 1 -2.913 -1.485 0.302 1.00 0.00 N \\nHETATM 9 C6 UNL 1 -2.844 -0.130 0.260 1.00 0.00 C \\nHETATM 10 C7 UNL 1 -1.602 0.521 0.177 1.00 0.00 C \\nHETATM 11 C8 UNL 1 -1.585 1.998 0.085 1.00 0.00 C \\nHETATM 12 S1 UNL 1 -0.600 2.783 -0.963 1.00 0.00 S \\nHETATM 13 O2 UNL 1 -2.485 2.742 0.838 1.00 0.00 O1-\\nHETATM 14 H1 UNL 1 3.531 0.642 0.736 1.00 0.00 H \\nHETATM 15 H2 UNL 1 4.133 -0.148 -0.770 1.00 0.00 H \\nHETATM 16 H3 UNL 1 3.376 1.493 -0.854 1.00 0.00 H \\nHETATM 17 H4 UNL 1 1.005 1.188 0.826 1.00 0.00 H \\nHETATM 18 H5 UNL 1 0.344 -2.292 0.249 1.00 0.00 H \\nHETATM 19 H6 UNL 1 -1.889 -3.335 0.323 1.00 0.00 H \\nHETATM 20 H7 UNL 1 -3.764 0.442 0.270 1.00 0.00 H \\nCONECT 1 2 14 15 16\\nCONECT 2 3 3 4\\nCONECT 4 5 17\\nCONECT 5 6 6 10\\nCONECT 6 7 18\\nCONECT 7 8 8 19\\nCONECT 8 9\\nCONECT 9 10 10 20\\nCONECT 10 11\\nCONECT 11 12 12 13\\nEND\\n\",\"pdb\");\n",
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+ "\tviewer_17532640697518232.setStyle({\"stick\": {}});\n",
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+ "\tviewer_17532640697518232.zoomTo();\n",
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+ "viewer_17532640697518232.render();\n",
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+ "});\n",
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+ "</script>"
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+ ]
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+ },
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+ "metadata": {},
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+ "output_type": "display_data"
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+ },
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+ {
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+ "data": {
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+ "text/plain": [
313
+ "<py3Dmol.view at 0x11fd5a780>"
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+ ]
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+ },
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+ "execution_count": 13,
317
+ "metadata": {},
318
+ "output_type": "execute_result"
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+ }
320
+ ],
321
+ "source": [
322
+ "input_ids[0][5] = tokenizer.mask_token_id\n",
323
+ "input_ids[0][9] = tokenizer.mask_token_id\n",
324
+ "input_ids[0][18] = tokenizer.mask_token_id\n",
325
+ "input_ids[0][11] = tokenizer.mask_token_id\n",
326
+ "# Generate output sequence\n",
327
+ "output_ids = model.generate(input_ids, max_length=128, num_beams=5, num_return_sequences=5,\n",
328
+ " early_stopping=True)\n",
329
+ "output = tokenizer.decode(output_ids[1][n:], skip_special_tokens=True)\n",
330
+ "print(output)\n",
331
+ "smiles = sf.decoder(output)\n",
332
+ "print(smiles)\n",
333
+ "smiles_to_3d([smiles])"
334
+ ]
335
+ },
336
+ {
337
+ "cell_type": "code",
338
+ "execution_count": null,
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+ "kernelspec": {
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+ "display_name": "Python 3 (ipykernel)",
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+ "pygments_lexer": "ipython3",
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+ "version": "3.12.10"
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+ }
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+ },
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+ "nbformat": 4,
365
+ "nbformat_minor": 5
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+ }
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