app.py

import streamlit as st
from trainer import Trainer
import random

class DrugGENConfig:
    submodel='CrossLoss'
    act='relu'
    z_dim=16
    max_atom=45
    lambda_gp=1
    dim=128
    depth=1
    heads=8
    dec_depth=1
    dec_heads=8
    dec_dim=128
    mlp_ratio=3
    warm_up_steps=0
    dis_select='mlp'
    init_type='normal'
    batch_size=128
    epoch=50
    g_lr=0.00001
    d_lr=0.00001
    g2_lr=0.00001
    d2_lr=0.00001
    dropout=0.
    dec_dropout=0.
    n_critic=1
    beta1=0.9
    beta2=0.999
    resume_iters=None
    clipping_value=2
    features=False
    test_iters=10_000
    num_test_epoch=30_000
    inference_sample_num=1000
    num_workers=1
    mode="inference"
    inference_iterations=100
    inf_batch_size=1
    protein_data_dir='data/akt'
    drug_index='data/drug_smiles.index'
    drug_data_dir='data/akt'
    mol_data_dir='data'
    log_dir='experiments/logs'
    model_save_dir='experiments/models'
    # inference_model=""
    sample_dir='experiments/samples'
    result_dir="experiments/tboard_output"
    dataset_file="chembl45_train.pt"
    drug_dataset_file="akt_train.pt"
    raw_file='data/chembl_train.smi'
    drug_raw_file="data/akt_train.smi"
    inf_dataset_file="chembl45_test.pt"
    inf_drug_dataset_file='akt_test.pt'
    inf_raw_file='data/chembl_test.smi'
    inf_drug_raw_file="data/akt_test.smi"
    log_sample_step=1000
    set_seed=True
    seed=1
    resume=False
    resume_epoch=None
    resume_iter=None
    resume_directory=None
    
class ProtConfig(DrugGENConfig):
    submodel="Prot"
    inference_model="experiments/models/Prot"

class CrossLossConfig(DrugGENConfig):
    submodel="CrossLoss"
    inference_model="experiments/models/CrossLoss"

class NoTargetConfig(DrugGENConfig):
    submodel="NoTarget"
    inference_model="experiments/models/NoTarget"


model_configs = {
    "Prot": ProtConfig(),
    "CrossLoss": CrossLossConfig(),
    "NoTarget": NoTargetConfig(),
}


with st.sidebar:
    st.title("DrugGEN: Target Centric De Novo Design of Drug Candidate Molecules with Graph Generative Deep Adversarial Networks")
    st.write("[![arXiv](https://img.shields.io/badge/arXiv-2302.07868-b31b1b.svg)](https://arxiv.org/abs/2302.07868) [![github-repository](https://img.shields.io/badge/GitHub-black?logo=github)](https://github.com/HUBioDataLab/DrugGEN)")


    with st.form("model_selection_from"):

        model_name = st.radio(
        "Select a model to make inference",
        ('Prot', 'CrossLoss', 'NoTarget'))

        molecule_num_input = st.number_input('Number of molecules to generate', min_value=1, max_value=100_000, value=1000, step=1)

        seed_input = st.number_input("Input a seed for reproducibiliy", min_value=0, value=random.randint(1, 1000), step=1)
        
        submitted = st.form_submit_button("Start Computing")


if submitted:

    config = model_configs[model_name]

    config.inference_sample_num = molecule_num_input
    config.seed = seed_input
    
    with st.spinner(f'Creating the trainer class instance for {model_name}...'):
        trainer = Trainer(config)
    with st.spinner(f'Running inference function of {model_name} (this may take a while) ...'):
        results = trainer.inference()
    st.success(f"Inference of {model_name} took {results['runtime']:.2f} seconds.")

    with st.expander("Expand to see scores"):

        st.write(f"Fraction valid: {results['fraction_valid']}")
        st.write(f"Uniqueness: {results['uniqueness']}")
        st.write(f"Novelty score: {results['novelty']}")

    with open(f'experiments/inference/{model_name}/inference_drugs.txt') as f:
        inference_drugs = f.read()
    st.download_button(label="Click to download generated molecules", data=inference_drugs, file_name=f'{model_name}_inference.smi', mime="text/plain")

else:
    st.warning("Please select a model to make inference")