Skip to content

Commit

Permalink
g
Browse files Browse the repository at this point in the history
  • Loading branch information
@RiesBen
RiesBen committed Mar 31, 2024
1 parent 5ccd367 commit 2bfc215
Showing 1 changed file with 144 additions and 85 deletions.
229 changes: 144 additions & 85 deletions examples/konnektor_bench.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,46 +11,25 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 4,
"metadata": {
"collapsed": false,
"ExecuteTime": {
"end_time": "2024-02-27T10:47:42.556235500Z",
"start_time": "2024-02-27T10:47:40.807827200Z"
"end_time": "2024-03-31T17:41:53.972958Z",
"start_time": "2024-03-31T17:41:53.909892Z"
}
},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from gufe import SmallMoleculeComponent\n",
"\n",
"from gufe import LigandAtomMapping\n",
"import numpy as np\n",
"\n",
"\n",
"def build_random_dataset(n=20):\n",
"\n",
" class genMapper:\n",
" def suggest_mappings(molA, molB):\n",
" yield LigandAtomMapping(molA, molB, {})\n",
"\n",
" \n",
" class genScorer:\n",
" vals = np.random.random(int(n**2))\n",
" i=0\n",
" \n",
" def __call__(self, x):\n",
" v=self.vals[self.i]\n",
" self.i= (self.i+1)%n\n",
" return v\n",
"\n",
" mols = [Chem.AddHs(Chem.MolFromSmiles(\"C\"*i)) for i in range(1, int(n))]\n",
" [Chem.rdDistGeom.EmbedMolecule(m) for m in mols]\n",
" compounds = [ SmallMoleculeComponent(name=str(i), rdkit=m) for i,m in enumerate(mols)]\n",
"\n",
" return compounds, genMapper, genScorer\n",
"\n",
"compounds, genMapper, genScorer= build_random_dataset()"
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" !pip install -U https://github.com/conda-incubator/condacolab/archive/cuda-version-12.tar.gz\n",
" import condacolab\n",
" condacolab.install_mambaforge()\n",
" !wget -q https://raw.githubusercontent.com/OpenFreeEnergy/konnektor/main/examples/environment.yaml\n",
" !mamba env update -q --name=base --file=environment.yaml\n"
]
},
{
Expand All @@ -62,21 +41,18 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {
"ExecuteTime": {
"end_time": "2024-02-27T10:48:00.339633100Z",
"start_time": "2024-02-27T10:48:00.306561400Z"
"end_time": "2024-03-31T17:41:57.220978Z",
"start_time": "2024-03-31T17:41:57.207310Z"
}
},
"outputs": [],
"source": [
"import random\n",
"import numpy as np\n",
"from konnektor import network_analysis as ana\n",
"from konnektor import network_tools as tools\n",
"\n",
"\n",
"def get_edge_failure_robustness(network, failure_rate=0.05, nrepeats=20):\n",
" edges = list(network.edges)\n",
" connected=[]\n",
Expand All @@ -99,7 +75,7 @@
"metadata": {
"is_executing": true,
"ExecuteTime": {
"start_time": "2024-02-27T10:48:09.542681400Z"
"start_time": "2024-03-31T17:43:36.135439Z"
}
},
"outputs": [
Expand All @@ -109,36 +85,138 @@
"application/vnd.jupyter.widget-view+json": {
"version_major": 2,
"version_minor": 0,
"model_id": "f9a29c456a7e454e9c85948f2dd294b2"
"model_id": "73374f4fdb76474992c2bbfefbdd804f"
}
},
"metadata": {},
"output_type": "display_data"
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 197.31it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 143.94it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 142.83it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 110.24it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 51.02it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 132.57it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 68.04it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"Build Cluster Networks: 100%|██████████| 3/3 [00:00<00:00, 94.46it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 1 5\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 0 12\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 2 12\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 1 16\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 2 16\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 0 20\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 1 20\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 0 24\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 2 24\n",
"('list index out of range',)\n",
"<class 'konnektor.network_planners.generators.diversity_network_planner.DiversityNetworkPlanner'> 0 28\n",
"('list index out of range',)\n"
"ERR a cycle can not be larger, than the number of nodes.\n",
"ERR a cycle can not be larger, than the number of nodes.\n"
]
}
],
Expand All @@ -148,6 +226,7 @@
"import numpy as np\n",
"import pandas as pd\n",
"from konnektor import network_analysis as ana\n",
"from konnektor.utils.toy_data import build_random_dataset\n",
"from konnektor.network_planners import (MaximalNetworkPlanner, \n",
" RadialLigandNetworkPlanner, \n",
" StarrySkyLigandNetworkPlanner,\n",
Expand All @@ -171,8 +250,8 @@
" for net in networker:\n",
" try:\n",
" start = datetime.now()\n",
" planner = net(mapper=genMapper, scorer=genScorer())\n",
" \n",
" planner = net(mapper=genMapper(), scorer=genScorer())\n",
" \n",
" #Build\n",
" network = planner(compounds)\n",
" network.name= planner.__class__.__name__.replace(\"Planner\", \"\").replace(\"MinimalSpanningTree\", \"MST\").replace(\"Ligand\", \"\")\n",
Expand Down Expand Up @@ -200,17 +279,6 @@
"df = pd.DataFrame(ncomp)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"start_time": "2024-02-27T10:47:44.655567500Z"
}
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 27,
Expand Down Expand Up @@ -408,22 +476,13 @@
"source": [
"fig.savefig(\"../.img/Network_Overview.png\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"t.microseconds"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "konnnektor",
"name": "python3",
"language": "python",
"name": "konnektor"
"display_name": "Python 3 (ipykernel)"
},
"language_info": {
"codemirror_mode": {
Expand Down

0 comments on commit 2bfc215

Please sign in to comment.