app.py

import gradio as gr
import numpy as np
import pandas as pd
from tempfile import NamedTemporaryFile
from PIL import Image
from rdkit import RDLogger
from sklearn.model_selection import train_test_split

from molecule_generation_helpers import *
from property_prediction_helpers import *

DEBUG_VISIBLE = False
RDLogger.logger().setLevel(RDLogger.ERROR)

# Predefined dataset paths (these should be adjusted to your file paths)
predefined_datasets = {
    " ": " ",
    "BACE": "./data/bace/train.csv, ./data/bace/test.csv, smiles, Class",
    "ESOL": "./data/esol/train.csv, ./data/esol/test.csv, smiles, prop",
}

# Models
models_enabled = [
    "MorganFingerprint",
    "SMI-TED",
    "SELFIES-TED",
    "MHG-GED",
    "POS-EGNN",
]

blank_df = pd.DataFrame({"id": [], "Model": [], "Score": []})


# Function to load a predefined dataset from the local path
def load_predefined_dataset(dataset_name):
    val = predefined_datasets.get(dataset_name)
    if val:
        try:
            df = pd.read_csv(val.split(",")[0])
            return (
                df.head(),
                gr.update(choices=list(df.columns), value=None),
                gr.update(choices=list(df.columns), value=None),
                dataset_name.lower(),
            )
        except:
            pass
    else:
        dataset_name = "Custom"
    return (
        pd.DataFrame(),
        gr.update(choices=[], value=None),
        gr.update(choices=[], value=None),
        dataset_name.lower(),
    )


# Function to handle dataset selection (predefined or custom)
def handle_dataset_selection(selected_dataset, state):
    state["dataset_name"] = (
        selected_dataset if selected_dataset in predefined_datasets else "CUSTOM"
    )
    # Show file upload fields for train and test datasets if "Custom Dataset" is selected
    task_type = (
        "Classification"
        if selected_dataset == "BACE"
        else "Regression" if selected_dataset == "ESOL" else None
    )
    return (
        gr.update(visible=selected_dataset not in predefined_datasets or DEBUG_VISIBLE),
        task_type,
    )


# Function to select input and output columns and display a message
def select_columns(input_column, output_column, train_data, test_data, state):
    if train_data and test_data and input_column and output_column:
        return f"{train_data.name},{test_data.name},{input_column},{output_column},{state['dataset_name']}"
    return gr.update()


# Function to display the head of the uploaded CSV file
def display_csv_head(file):
    if file is not None:
        # Load the CSV file into a DataFrame
        df = pd.read_csv(file.name)
        return (
            df.head(),
            gr.update(choices=list(df.columns)),
            gr.update(choices=list(df.columns)),
        )
    return pd.DataFrame(), gr.update(choices=[]), gr.update(choices=[])


def process_custom_file(file, selected_dataset):
    if file and os.path.getsize(file.name) < 50 * 1024:
        df = pd.read_csv(file.name)
        if "input" in df.columns and "output" in df.columns:
            train, test = train_test_split(df, test_size=0.2)
            with NamedTemporaryFile(
                prefix="fm4m-train-", suffix=".csv", delete=False
            ) as train_file:
                train.to_csv(train_file.name, index=False)
            with NamedTemporaryFile(
                prefix="fm4m-test-", suffix=".csv", delete=False
            ) as test_file:
                test.to_csv(test_file.name, index=False)
            task_type = (
                "Classification" if df["output"].dtype == np.int64 else "Regression"
            )
            return train_file.name, test_file.name, "input", "output", task_type

    return (
        None,
        None,
        None,
        None,
        gr.update() if selected_dataset in predefined_datasets else None,
    )


def update_plot_choices(current, state):
    choices = []
    if state.get("roc_auc") is not None:
        choices.append("ROC-AUC")
    if state.get("RMSE") is not None:
        choices.append("Parity Plot")
    if state.get("x_batch") is not None:
        choices.append("Latent Space")
    if current in choices:
        return gr.update(choices=choices)
    return gr.update(choices=choices, value=None if len(choices) == 0 else choices[0])


def log_selected(df: pd.DataFrame, evt: gr.SelectData, state):
    state.update(state["results"].get(df.at[evt.index[0], 'id'], {}))


# Dictionary for SMILES strings and corresponding images (you can replace with your actual image paths)
smiles_image_mapping = {
    # Example SMILES for ethanol
    "Mol 1": {
        "smiles": "C=C(C)CC(=O)NC[C@H](CO)NC(=O)C=Cc1ccc(C)c(Cl)c1",
        "image": "img/img1.png",
    },
    # Example SMILES for butane
    "Mol 2": {
        "smiles": "C=CC1(CC(=O)NC[C@@H](CCCC)NC(=O)c2cc(Cl)cc(Br)c2)CC1",
        "image": "img/img2.png",
    },
    # Example SMILES for ethylamine
    "Mol 3": {
        "smiles": "C=C(C)C[C@H](NC(C)=O)C(=O)N1CC[C@H](NC(=O)[C@H]2C[C@@]2(C)Br)C(C)(C)C1",
        "image": "img/img3.png",
    },
    # Example SMILES for diethyl ether
    "Mol 4": {
        "smiles": "C=C1CC(CC(=O)N[C@H]2CCN(C(=O)c3ncccc3SC)C23CC3)C1",
        "image": "img/img4.png",
    },
    # Example SMILES for chloroethane
    "Mol 5": {
        "smiles": "C=CCS[C@@H](C)CC(=O)OCC",
        "image": "img/img5.png",
    },
}


# Load images for selection
def load_image(path):
    try:
        return Image.open(smiles_image_mapping[path]["image"])
    except:
        pass


# Function to handle image selection
def handle_image_selection(image_key):
    if not image_key:
        return None, None
    smiles = smiles_image_mapping[image_key]["smiles"]
    mol_image = smiles_to_image(smiles)
    return smiles, mol_image


# Introduction
with gr.Blocks() as introduction:
    with open("INTRODUCTION.md") as f:
        gr.Markdown(f.read(), sanitize_html=False)

# Property Prediction
with gr.Blocks() as property_prediction:
    state = gr.State({"model_name": "Default - Auto", "results": {}})
    gr.HTML(
        '''
    <p style="text-align: center">
        Task : Property Prediction
        <br>
        Models are finetuned with different combination of modalities on the uploaded or selected built data set.
    </p>
    '''
    )
    with gr.Row():
        with gr.Column():
            # Dropdown menu for predefined datasets including "Custom Dataset" option
            dataset_selector = gr.Dropdown(
                label="Select Dataset",
                choices=list(predefined_datasets.keys()) + ["Custom Dataset"],
            )
            # Display the message for selected columns
            selected_columns_message = gr.Textbox(
                label="Selected Columns Info", visible=DEBUG_VISIBLE
            )

            with gr.Accordion(
                "Custom Dataset Settings", open=True, visible=DEBUG_VISIBLE
            ) as settings:
                # File upload options for custom dataset (train and test)
                custom_file = gr.File(
                    label="Upload Custom Dataset",
                    file_types=[".csv"],
                )
                train_file = gr.File(
                    label="Upload Custom Train Dataset",
                    file_types=[".csv"],
                    visible=False,
                )
                train_display = gr.Dataframe(
                    label="Train Dataset Preview (First 5 Rows)",
                    interactive=False,
                    visible=DEBUG_VISIBLE,
                )

                test_file = gr.File(
                    label="Upload Custom Test Dataset",
                    file_types=[".csv"],
                    visible=False,
                )
                test_display = gr.Dataframe(
                    label="Test Dataset Preview (First 5 Rows)",
                    interactive=False,
                    visible=DEBUG_VISIBLE,
                )

                # Predefined dataset displays
                predefined_display = gr.Dataframe(
                    label="Predefined Dataset Preview (First 5 Rows)",
                    interactive=False,
                    visible=DEBUG_VISIBLE,
                )

                # Dropdowns for selecting input and output columns for the custom dataset
                input_column_selector = gr.Dropdown(
                    label="Select Input Column",
                    choices=[],
                    allow_custom_value=True,
                    visible=DEBUG_VISIBLE,
                )
                output_column_selector = gr.Dropdown(
                    label="Select Output Column",
                    choices=[],
                    allow_custom_value=True,
                    visible=DEBUG_VISIBLE,
                )

                # When a custom train file is uploaded, display its head and update column selectors
                train_file.change(
                    display_csv_head,
                    inputs=train_file,
                    outputs=[
                        train_display,
                        input_column_selector,
                        output_column_selector,
                    ],
                )

                # When a custom test file is uploaded, display its head
                test_file.change(
                    display_csv_head,
                    inputs=test_file,
                    outputs=[
                        test_display,
                        input_column_selector,
                        output_column_selector,
                    ],
                )

            model_checkbox = gr.CheckboxGroup(
                choices=models_enabled, label="Select Model", visible=DEBUG_VISIBLE
            )

            task_radiobutton = gr.Radio(
                choices=["Classification", "Regression"],
                label="Task Type",
                visible=DEBUG_VISIBLE,
            )

            # When a dataset is selected, show either file upload fields (for custom) or load predefined datasets
            # When a predefined dataset is selected, load its head and update column selectors
            dataset_selector.change(lambda: None, outputs=custom_file).then(
                handle_dataset_selection,
                inputs=[dataset_selector, state],
                outputs=[settings, task_radiobutton],
            ).then(
                load_predefined_dataset,
                inputs=dataset_selector,
                outputs=[
                    predefined_display,
                    input_column_selector,
                    output_column_selector,
                    selected_columns_message,
                ],
            )

            custom_file.change(
                process_custom_file,
                inputs=[custom_file, dataset_selector],
                outputs=[
                    train_file,
                    test_file,
                    input_column_selector,
                    output_column_selector,
                    task_radiobutton,
                ],
            )
            eval_clear_button = gr.Button("Clear")
            eval_button = gr.Button("Submit", variant="primary")
            step_slider = gr.Slider(
                minimum=0,
                maximum=31,
                value=0,
                label="Progress",
                show_label=True,
                interactive=False,
                visible=False,
            )

        # Right Column
        with gr.Column():
            log_table = gr.Dataframe(value=blank_df, interactive=False)

            plot_radio = gr.Radio(choices=[], label="Select Plot Type")

            plot_output = gr.Plot(label="Visualization")

            log_table.select(log_selected, [log_table, state]).success(
                update_plot_choices, inputs=[plot_radio, state], outputs=plot_radio
            ).then(display_plot, inputs=[plot_radio, state], outputs=plot_output)

            def clear_eval(state):
                state["results"] = {}
                return None, gr.update(choices=[], value=None), blank_df

            def eval_part(part, step, selector, show_progress=False):
                return (
                    part.then(
                        lambda: [models_enabled[x] for x in selector],
                        outputs=model_checkbox,
                    )
                    .then(
                        evaluate_and_log,
                        inputs=[
                            model_checkbox,
                            selected_columns_message,
                            task_radiobutton,
                            log_table,
                            state,
                        ],
                        outputs=log_table,
                        show_progress=show_progress,
                    )
                    .then(lambda: step, outputs=step_slider, show_progress=False)
                )

            part = (
                eval_button.click(
                    lambda: (
                        gr.update(interactive=False),
                        gr.update(interactive=False),
                    ),
                    outputs=[eval_clear_button, eval_button],
                )
                .then(
                    select_columns,
                    inputs=[
                        input_column_selector,
                        output_column_selector,
                        train_file,
                        test_file,
                        state,
                    ],
                    outputs=selected_columns_message,
                )
                .then(
                    clear_eval,
                    inputs=state,
                    outputs=[
                        plot_output,
                        plot_radio,
                        log_table,
                    ],
                )
            )
            part = part.then(
                lambda: gr.update(value=0, visible=True),
                outputs=step_slider,
                show_progress=False,
            )

            from itertools import combinations

            part_index = 1  # start index
            for r in range(1, 6):  # for group sizes 2 to 5
                for combo in combinations(range(5), r):  # 5 items: indices 0 to 4
                    if list(combo) == [0]:
                        part = eval_part(part, part_index, list(combo), True)
                    else: part = eval_part(part, part_index, list(combo))
                    part_index += 1


            """part = eval_part(part, 1, [0], True)
            part = eval_part(part, 2, [1])
            part = eval_part(part, 3, [2])
            part = eval_part(part, 4, [3])
            part = eval_part(part, 5, [4])
            part = eval_part(part, 6, [0, 1])
            part = eval_part(part, 7, [0, 2])
            part = eval_part(part, 8, [0, 3])
            part = eval_part(part, 9, [0, 4])
            part = eval_part(part, 10, [1, 2])
            part = eval_part(part, 11, [1, 3])
            part = eval_part(part, 12, [1, 4])
            part = eval_part(part, 13, [2, 3])
            part = eval_part(part, 14, [2, 4])
            part = eval_part(part, 15, [3, 4])

            part = eval_part(part, 16, [0, 1, 2])
            part = eval_part(part, 17, [0, 1, 3])
            part = eval_part(part, 18, [0, 1, 4])
            part = eval_part(part, 19, [0, 2, 3])
            part = eval_part(part, 20, [0, 2, 4])
            part = eval_part(part, 21, [0, 3, 4])
            part = eval_part(part, 22, [1, 2, 3])
            part = eval_part(part, 23, [1, 2, 4])
            part = eval_part(part, 24, [1, 3, 4])
            part = eval_part(part, 25, [2, 3, 4])

            part = eval_part(part, 26, [0, 1, 2, 3])
            part = eval_part(part, 27, [0, 1, 2, 4])
            part = eval_part(part, 28, [0, 1, 3, 4])
            part = eval_part(part, 29, [0, 2, 3, 4])
            part = eval_part(part, 30, [1, 2, 3, 4])

            part = eval_part(part, 31, [0,1, 2, 3, 4])"""


            part = part.then(
                lambda: gr.update(visible=False),
                outputs=step_slider,
                show_progress=False,
            )
            part.then(
                lambda: (
                    gr.update(interactive=True),
                    gr.update(interactive=True),
                ),
                outputs=[eval_clear_button, eval_button],
            )

            plot_radio.change(
                display_plot, inputs=[plot_radio, state], outputs=plot_output
            )

        eval_clear_button.click(
            clear_eval,
            inputs=state,
            outputs=[
                plot_output,
                plot_radio,
                log_table,
            ],
        ).then(lambda: " ", outputs=dataset_selector)


# Molecule Generation
with gr.Blocks() as molecule_generation:
    gr.HTML(
        '''
    <p style="text-align: center">
        Task : Molecule Generation
        <br>
        Generate a new molecule similar to the initial molecule with better drug-likeness and synthetic accessibility.
    </p>
    '''
    )
    with gr.Row():
        with gr.Column():
            smiles_input = gr.Textbox(label="Input SMILES String")
            image_display = gr.Image(label="Molecule Image", height=250, width=250)
            # Show images for selection
            with gr.Accordion("Select from sample molecules", open=False):
                image_selector = gr.Radio(
                    choices=list(smiles_image_mapping.keys()),
                    label="Select from sample molecules",
                    value=None,
                )
                image_selector.change(load_image, image_selector, image_display)
            clear_button = gr.Button("Clear")
            generate_button = gr.Button("Submit", variant="primary")

        # Right Column
        with gr.Column():
            gen_image_display = gr.Image(
                label="Generated Molecule Image", height=250, width=250
            )
            generated_output = gr.Textbox(label="Generated Output")
            property_table = gr.Dataframe(label="Molecular Properties Comparison")

            # Handle image selection
            image_selector.change(
                handle_image_selection,
                inputs=image_selector,
                outputs=[smiles_input, image_display],
            )
            smiles_input.change(
                smiles_to_image, inputs=smiles_input, outputs=image_display
            )

            # Generate button to display canonical SMILES and molecule image
            generate_button.click(
                lambda: (
                    gr.update(interactive=False),
                    gr.update(interactive=False),
                ),
                outputs=[clear_button, generate_button],
            ).then(
                generate_canonical,
                inputs=smiles_input,
                outputs=[property_table, generated_output, gen_image_display],
            ).then(
                lambda: (
                    gr.update(interactive=True),
                    gr.update(interactive=True),
                ),
                outputs=[clear_button, generate_button],
            )
        clear_button.click(
            lambda: (None, None, None, None, None, None),
            outputs=[
                smiles_input,
                image_display,
                image_selector,
                gen_image_display,
                generated_output,
                property_table,
            ],
        )


# Render with tabs
gr.TabbedInterface(
    [introduction, property_prediction, molecule_generation],
    ["Introduction", "Property Prediction", "Molecule Generation"],
).launch(server_name="0.0.0.0", allowed_paths=["./"])