generateconf.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "import numpy as np\n",
    "import random\n",
    "import os\n",
    "import pickle\n",
    "import yaml\n",
    "from easydict import EasyDict\n",
    "\n",
    "import torch.nn as nn\n",
    "import torch.nn.functional as F\n",
    "import torch.optim as optim\n",
    "from torch.autograd import Variable\n",
    "from torch_geometric.data import Data, Dataset\n",
    "from torch_geometric.transforms import Compose\n",
    "from rdkit import Chem\n",
    "from confgf import models,dataset, runner, utils"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "# your account is:\n",
    "# user: yitaocai\n",
    "# pwd: UJCQqv77\n",
    "# ssh -p 5792 yitaocai@student07.ai-lab.jku.at"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'EasyDict' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_111709/1984119347.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig_path\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'r'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m     \u001b[0mconfig\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0myaml\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msafe_load\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mconfig\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mEasyDict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m: name 'EasyDict' is not defined"
     ]
    }
   ],
   "source": [
    "config_path = \"/system/user/yitaocai/PracticalAI/config/qm9_default.yml\"\n",
    "with open(config_path, 'r') as f:\n",
    "    config = yaml.safe_load(f)\n",
    "config = EasyDict(config)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "True\n"
     ]
    }
   ],
   "source": [
    "\n",
    "import torch\n",
    "print(torch.cuda.is_available()) \n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "if config.test.output_path is not None:\n",
    "    config.test.output_path = os.path.join(config.test.output_path, config.model.name)\n",
    "    if not os.path.exists(config.test.output_path):\n",
    "        os.makedirs(config.test.output_path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "!export CUDA_VISIBLE_DEVICES=0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Using device cpu as main device\n"
     ]
    }
   ],
   "source": [
    "\n",
    "# export CUDA_VISIBLE_DEVICES=1 before work\n",
    "# gpus = list(filter(lambda x: x is not None, config.train.gpus))\n",
    "# assert torch.cuda.device_count() >= len(gpus), 'do you set the gpus in config correctly?'\n",
    "\n",
    "\n",
    "# print(\"Let's use\", len(gpus), \"GPUs!\")\n",
    "  \n",
    "# config.train.device = device\n",
    "# config.train.gpus = gpus"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "set seed for random, numpy and torch\n"
     ]
    }
   ],
   "source": [
    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
    "print(\"Using device %s as main device\" % device)  \n",
    "np.random.seed(config.train.seed)\n",
    "random.seed(config.train.seed)\n",
    "torch.manual_seed(config.train.seed)\n",
    "if torch.cuda.is_available():\n",
    "    torch.cuda.manual_seed(config.train.seed)        \n",
    "    torch.cuda.manual_seed_all(config.train.seed)\n",
    "torch.backends.cudnn.benchmark = True\n",
    "print('set seed for random, numpy and torch')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading data from /Users/mindy/百度云同步盘/StudyResearch/SeminarPraticalAI/qm9_processed\n"
     ]
    }
   ],
   "source": [
    "load_path = os.path.join(config.data.base_path, '%s_processed' % config.data.dataset)\n",
    "print('loading data from %s' % load_path)\n",
    "\n",
    "train_data = []\n",
    "val_data = []\n",
    "test_data = []\n",
    "\n",
    "if config.data.test_set is not None:\n",
    "    with open(os.path.join(load_path, config.data.test_set), \"rb\") as fin:\n",
    "        test_data = pickle.load(fin)             \n",
    "else:\n",
    "    raise ValueError(\"do you set the test data ?\")              "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "train size : 0  ||  val size: 0  ||  test size: 24068 \n",
      "loading data done!\n",
      "got 200 molecules with 24068 confs\n",
      "len of test data: 200\n"
     ]
    }
   ],
   "source": [
    "print('train size : %d  ||  val size: %d  ||  test size: %d ' % (len(train_data), len(val_data), len(test_data)))\n",
    "print('loading data done!')\n",
    "\n",
    "transform = Compose([\n",
    "    utils.AddHigherOrderEdges(order=config.model.order),\n",
    "    utils.AddEdgeLength(),\n",
    "    utils.AddPlaceHolder(),\n",
    "    utils.AddEdgeName()\n",
    "])\n",
    "train_data = dataset.GEOMDataset(data=train_data, transform=transform)\n",
    "val_data = dataset.GEOMDataset(data=val_data, transform=transform)\n",
    "test_data = dataset.GEOMDataset_PackedConf(data=test_data, transform=transform)\n",
    "print('len of test data: %d' % len(test_data))\n",
    "\n",
    "model = models.DistanceScoreMatch(config)\n",
    "\n",
    "#optimizer = utils.get_optimizer(config.train.optimizer, model)    \n",
    "optimizer = None\n",
    "#scheduler = utils.get_scheduler(config.train.scheduler, optimizer)\n",
    "scheduler = None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Load checkpoint from /Users/mindy/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/config/confgf_checkpoint/checkpoint284\n"
     ]
    }
   ],
   "source": [
    "solver = runner.DefaultRunner(train_data, val_data, test_data, model, optimizer, scheduler, config)\n",
    "\n",
    "assert config.test.init_checkpoint is not None\n",
    "solver.load(config.test.init_checkpoint, epoch=config.test.epoch)\n",
    "\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Sampling positions: 100%|██████████| 50/50 [01:20<00:00,  1.61s/it]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pos generation of Nc1cc2nc3cc(N)ccc3cc2cc1.[Cl-].c12c([n+](C)c3c(c1)ccc(N)c3)cc(N)cc2 done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Sampling positions: 100%|██████████| 50/50 [00:48<00:00,  1.03it/s]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pos generation of c12cc(Br)c([O-])c(Br)c1oc1c(Br)c(=O)c(Br)cc-1c2-c1ccccc1C([O-])=O.[Na+].[Na+] done\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Sampling positions:   6%|▌         | 3/50 [00:12<03:21,  4.29s/it]\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m/var/folders/fm/rkc2wk_96490f5p5xyb8r5yr0000gn/T/ipykernel_8077/3799749858.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      8\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0msmiles\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mkey\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msmileslist\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      9\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 10\u001b[0;31m         threedconf =solver.generate_samples_from_smiles(smiles, generator, \\\n\u001b[0m\u001b[1;32m     11\u001b[0m                                             \u001b[0mnum_repeat\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkeep_traj\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m                                             out_path=None)\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/runner/default_runner.py\u001b[0m in \u001b[0;36mgenerate_samples_from_smiles\u001b[0;34m(self, smiles, generator, num_repeat, keep_traj, out_path)\u001b[0m\n\u001b[1;32m    321\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    322\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mgenerator\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'ConfGF'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 323\u001b[0;31m             \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpos_traj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mConfGF_generator\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtest\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgen\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# (sigams, 100, num_node, 3)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    324\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0mgenerator\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'ConfGFDist'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    325\u001b[0m             embedder = utils.Embed3D(step_size=self.config.test.gen.dg_step_size, \\\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/runner/default_runner.py\u001b[0m in \u001b[0;36mConfGF_generator\u001b[0;34m(self, data, config, pos_init)\u001b[0m\n\u001b[1;32m    271\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mpos_init\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    272\u001b[0m             \u001b[0mpos_init\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrandn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnum_nodes\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m3\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpos\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 273\u001b[0;31m         data, pos_traj = self.position_Langevin_Dynamics(data, pos_init, self._model, self._model.sigmas.data.clone(), \\\n\u001b[0m\u001b[1;32m    274\u001b[0m                                             \u001b[0mn_steps_each\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msteps_pos\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstep_lr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstep_lr_pos\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    275\u001b[0m                                             clip=config.clip, min_sigma=config.min_sigma)\n",
      "\u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/confgf/lib/python3.8/site-packages/torch/autograd/grad_mode.py\u001b[0m in \u001b[0;36mdecorate_context\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     26\u001b[0m         \u001b[0;32mdef\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     27\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 28\u001b[0;31m                 \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     29\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mcast\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mF\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     30\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/runner/default_runner.py\u001b[0m in \u001b[0;36mposition_Langevin_Dynamics\u001b[0;34m(self, data, pos_init, scorenet, sigmas, n_steps_each, step_lr, clip, min_sigma)\u001b[0m\n\u001b[1;32m    249\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    250\u001b[0m                 \u001b[0mnoise\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrandn_like\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpos\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msqrt\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstep_size\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0;36m2\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 251\u001b[0;31m                 \u001b[0mscore_d\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscorenet\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_score\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0md\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msigma\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# (num_edge, 1)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    252\u001b[0m                 \u001b[0mscore_pos\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconvert_score_d\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscore_d\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpos\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0medge_index\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0md\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    253\u001b[0m                 \u001b[0mscore_pos\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mutils\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclip_norm\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mscore_pos\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlimit\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mclip\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/confgf/lib/python3.8/site-packages/torch/autograd/grad_mode.py\u001b[0m in \u001b[0;36mdecorate_context\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     26\u001b[0m         \u001b[0;32mdef\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     27\u001b[0m             \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 28\u001b[0;31m                 \u001b[0;32mreturn\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     29\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mcast\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mF\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdecorate_context\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     30\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/models/scorenet.py\u001b[0m in \u001b[0;36mget_score\u001b[0;34m(self, data, d, sigma)\u001b[0m\n\u001b[1;32m    116\u001b[0m         \u001b[0medge_attr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0md_emb\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0medge_attr\u001b[0m \u001b[0;31m# (num_edge, hidden)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    117\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 118\u001b[0;31m         \u001b[0moutput\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnode_attr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    119\u001b[0m         \u001b[0mh_row\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mh_col\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"node_feature\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0medge_index\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"node_feature\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0medge_index\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;31m# (num_edge, hidden)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    120\u001b[0m         \u001b[0mdistance_feature\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mh_row\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mh_col\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdim\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# (num_edge, 2 * hidden)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/confgf/lib/python3.8/site-packages/torch/nn/modules/module.py\u001b[0m in \u001b[0;36m_call_impl\u001b[0;34m(self, *input, **kwargs)\u001b[0m\n\u001b[1;32m   1049\u001b[0m         if not (self._backward_hooks or self._forward_hooks or self._forward_pre_hooks or _global_backward_hooks\n\u001b[1;32m   1050\u001b[0m                 or _global_forward_hooks or _global_forward_pre_hooks):\n\u001b[0;32m-> 1051\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mforward_call\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1052\u001b[0m         \u001b[0;31m# Do not call functions when jit is used\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1053\u001b[0m         \u001b[0mfull_backward_hooks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnon_full_backward_hooks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/layers/gin.py\u001b[0m in \u001b[0;36mforward\u001b[0;34m(self, data, node_attr, edge_attr)\u001b[0m\n\u001b[1;32m    109\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    110\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mconv_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mconv\u001b[0m \u001b[0;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconvs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 111\u001b[0;31m             \u001b[0mhidden\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconv_input\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0medge_index\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    112\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mconv_idx\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconvs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0;36m1\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mactivation\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    113\u001b[0m                 \u001b[0mhidden\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mactivation\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhidden\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/confgf/lib/python3.8/site-packages/torch/nn/modules/module.py\u001b[0m in \u001b[0;36m_call_impl\u001b[0;34m(self, *input, **kwargs)\u001b[0m\n\u001b[1;32m   1049\u001b[0m         if not (self._backward_hooks or self._forward_hooks or self._forward_pre_hooks or _global_backward_hooks\n\u001b[1;32m   1050\u001b[0m                 or _global_forward_hooks or _global_forward_pre_hooks):\n\u001b[0;32m-> 1051\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mforward_call\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1052\u001b[0m         \u001b[0;31m# Do not call functions when jit is used\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1053\u001b[0m         \u001b[0mfull_backward_hooks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnon_full_backward_hooks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/layers/gin.py\u001b[0m in \u001b[0;36mforward\u001b[0;34m(self, x, edge_index, edge_attr, size)\u001b[0m\n\u001b[1;32m     45\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     46\u001b[0m         \u001b[0;31m# propagate_type: (x: OptPairTensor, edge_attr: OptTensor)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 47\u001b[0;31m         \u001b[0mout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpropagate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0medge_index\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0medge_attr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msize\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     48\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     49\u001b[0m         \u001b[0mx_r\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/confgf/lib/python3.8/site-packages/torch_geometric/nn/conv/message_passing.py\u001b[0m in \u001b[0;36mpropagate\u001b[0;34m(self, edge_index, size, **kwargs)\u001b[0m\n\u001b[1;32m    235\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    236\u001b[0m             \u001b[0mmsg_kwargs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minspector\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdistribute\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'message'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcoll_dict\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 237\u001b[0;31m             \u001b[0mout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmessage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mmsg_kwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    238\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    239\u001b[0m             \u001b[0;31m# For `GNNExplainer`, we require a separate message and aggregate\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/百度云同步盘/StudyResearch/SeminarPraticalAI/ConfGF-main/confgf/layers/gin.py\u001b[0m in \u001b[0;36mmessage\u001b[0;34m(self, x_j, edge_attr)\u001b[0m\n\u001b[1;32m     55\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mmessage\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mx_j\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mTensor\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mTensor\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0mTensor\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     56\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mactivation\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 57\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mactivation\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx_j\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     58\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     59\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mx_j\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0medge_attr\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/usr/local/Caskroom/miniconda/base/envs/confgf/lib/python3.8/site-packages/torch/nn/functional.py\u001b[0m in \u001b[0;36mrelu\u001b[0;34m(input, inplace)\u001b[0m\n\u001b[1;32m   1296\u001b[0m         \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrelu_\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1297\u001b[0m     \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1298\u001b[0;31m         \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrelu\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1299\u001b[0m     \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1300\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "smilesfile =\"/system/user/yitaocai/PracticalAI/tox21_random.txt\"\n",
    "generator = \"ConfGF\"\n",
    "if smilesfile is not None:\n",
    "    with open(smilesfile, \"r\") as f:\n",
    "        lines = f.readlines()\n",
    "    smileslist = [line.strip().split(\"\\t\") for line in lines]\n",
    "    confdata = {}\n",
    "    for smiles,key in smileslist[0:1000]:\n",
    "\n",
    "        threedconf =solver.generate_samples_from_smiles(smiles, generator, \\\n",
    "                                            num_repeat=1, keep_traj=True,\n",
    "                                            out_path=None)\n",
    "        confdata[key] = threedconf\n",
    "    out_path = config.test.output_path\n",
    "    if out_path is not None:\n",
    "        with open(os.path.join(out_path, 'CONFDATA1.pkl'), \"wb\") as fout:\n",
    "            pickle.dump(confdata, fout)\n",
    "            print('save generated %s samples to %s done!' % (generator, out_path))\n",
    "\n",
    "    # print('pos generation of %s done' % return_data.smiles) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'confdata' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_114395/3872728994.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m: name 'confdata' is not defined"
     ]
    }
   ],
   "source": [
    "len(confdata)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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