DrugGEN / gradio_app.py
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import gradio as gr
from inference import Inference
import PIL
from PIL import Image
import pandas as pd
import random
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
import shutil
import os
class DrugGENConfig:
submodel='DrugGEN'
inference_model="experiments/models/DrugGEN/"
sample_num=1000
inf_dataset_file="chembl45_test.pt"
inf_raw_file='data/chembl_test.smi'
inf_batch_size=1
mol_data_dir='data'
features=False
act='relu'
max_atom=45
dim=128
depth=1
heads=8
mlp_ratio=3
dropout=0.
log_sample_step=100
set_seed=True
seed=10
class NoTargetConfig(DrugGENConfig):
submodel="NoTarget"
dim=128
inference_model="experiments/models/NoTarget/"
model_configs = {
"DrugGEN": DrugGENConfig(),
"NoTarget": NoTargetConfig(),
}
def function(model_name: str, num_molecules: int, seed_num: int) -> tuple[PIL.Image, pd.DataFrame, str]:
'''
Returns:
image, score_df, file path
'''
if model_name == "DrugGEN-NoTarget":
model_name = "NoTarget"
config = model_configs[model_name]
config.sample_num = num_molecules
if seed_num is None or seed_num.strip() == "":
config.seed = random.randint(0, 10000)
else:
try:
config.seed = int(seed_num)
except ValueError:
raise gr.Error("The seed must be an integer value!")
inferer = Inference(config)
scores = inferer.inference() # create scores_df out of this
score_df = pd.DataFrame(scores, index=[0])
output_file_path = f'experiments/inference/{model_name}/inference_drugs.txt'
new_path = f'{model_name}_denovo_mols.smi'
os.rename(output_file_path, new_path)
with open(new_path) as f:
inference_drugs = f.read()
generated_molecule_list = inference_drugs.split("\n")[:-1]
rng = random.Random(config.seed)
if num_molecules > 12:
selected_molecules = rng.choices(generated_molecule_list, k=12)
else:
selected_molecules = generated_molecule_list
selected_molecules = [Chem.MolFromSmiles(mol) for mol in selected_molecules if Chem.MolFromSmiles(mol) is not None]
drawOptions = Draw.rdMolDraw2D.MolDrawOptions()
drawOptions.prepareMolsBeforeDrawing = False
drawOptions.bondLineWidth = 0.5
molecule_image = Draw.MolsToGridImage(
selected_molecules,
molsPerRow=3,
subImgSize=(400, 400),
maxMols=len(selected_molecules),
# legends=None,
returnPNG=False,
drawOptions=drawOptions,
highlightAtomLists=None,
highlightBondLists=None,
)
return molecule_image, score_df, new_path
with gr.Blocks() as demo:
with gr.Row():
with gr.Column(scale=1):
gr.Markdown("# DrugGEN: Target Centric De Novo Design of Drug Candidate Molecules with Graph Generative Deep Adversarial Networks")
with gr.Row():
gr.Markdown("[![arXiv](https://img.shields.io/badge/arXiv-2302.07868-b31b1b.svg)](https://arxiv.org/abs/2302.07868)")
gr.Markdown("[![github-repository](https://img.shields.io/badge/GitHub-black?logo=github)](https://github.com/HUBioDataLab/DrugGEN)")
with gr.Accordion("Expand to display information about models", open=False):
gr.Markdown("""
### Model Variations
- **DrugGEN** is the default model. The input of the generator is the real molecules (ChEMBL) dataset (to ease the learning process) and the discriminator compares the generated molecules with the real inhibitors of the given target protein.
- **DrugGEN-NoTarget** is the non-target-specific version of DrugGEN. This model only focuses on learning the chemical properties from the ChEMBL training dataset.
""")
model_name = gr.Radio(
choices=("DrugGEN", "DrugGEN-NoTarget"),
value="DrugGEN",
label="Select a model to make inference",
info=str("DrugGEN model designs small molecules to target the human AKT1 protein (UniProt id: P31749)." + '\n'
+ "DrugGEN-NoTarget model designs random drug-like small molecules.")
)
num_molecules = gr.Number(
label="Number of molecules to generate",
precision=0, # integer input
minimum=1,
value=1000,
maximum=10_000,
info="It will take ~20-60 seconds to generate 1000 mols."
)
seed_num = gr.Textbox(
label="RNG seed value",
value=None,
info="This is optional, it can be used for reproducibility."
)
submit_button = gr.Button(
value="Start Generating"
)
with gr.Column(scale=2):
scores_df = gr.Dataframe(
label="Scores",
headers=["Runtime (seconds)", "Validity", "Uniqueness", "Novelty (Train)", "Novelty (Inference)"]
)
file_download = gr.File(
label="Click to download generated molecules",
)
image_output = gr.Image(
label="Structures of randomly selected de novo molecules from the inference set:"
)
submit_button.click(function, inputs=[model_name, num_molecules, seed_num], outputs=[image_output, scores_df, file_download], api_name="inference")
#demo.queue(concurrency_count=1)
demo.queue()
demo.launch()