app.py

import streamlit as st
from streamlit_ketcher import st_ketcher
from stmol import showmol
import py3Dmol
import io
import ase.io as ase_io
import numpy as np
try:
    from StringIO import StringIO
except ImportError:
    from io import StringIO

import streamlit.components.v1 as components


import streamlit as st
from streamlit_ketcher import st_ketcher
WIDTH = 500
st.title("DCM-Net")
smiles = "OC(=O)[C@@H]1CCCN1"
# Create a molecule editor
smiles = st_ketcher(smiles)

# Output the SMILES string of the drawn molecule
st.write(f"SMILES input: {smiles}")


# color charges by magnitude
def color_charges(mono, nDCM, atoms):
    from matplotlib import cm
    from matplotlib.colors import Normalize

    norm = Normalize(vmin=-1, vmax=1)
    cmap = cm.get_cmap("bwr")
    mappable = cm.ScalarMappable(norm=norm, cmap=cmap)
    elem = atoms.numbers
    pccolors = mappable.to_rgba(mono.flatten()[: len(atoms.numbers)])
    from ase.data.colors import jmol_colors

    atomcolors = [jmol_colors[_] for _ in elem]
    atomcolors_ = []
    for _ in atomcolors:
        atomcolors_.append(np.append(_, 0.015))
    dcmcolors = mappable.to_rgba(mono.flatten()[: len(elem) * nDCM])
    return dcmcolors


from dcm_app import run_dcm
# Create a 3D view
def render_3d(atoms, dcm_charges=None, dcmcolors=None):
    view = py3Dmol.view()

    view.startjs += '''\n
    let customColorize = function(atom){
        // attribute elem is from https://3dmol.csb.pitt.edu/doc/AtomSpec.html#elem
        if (atom.elem === 'X'){
            return "#FF0000" // red
        }
        else if (atom.elem === 'He'){
            return "#0000FF" // blue
        }
        else{
            return $3Dmol.getColorFromStyle(atom, {colorscheme: "whiteCarbon"});
        }
    }    
    \n'''

    if atoms is not None:
        # Write structure to xyz file.
        xyz = io.StringIO()
        ase_io.write(xyz, atoms, format='xyz')
        
        view.addModel(xyz.getvalue(), 'xyz')
        view.setStyle({'stick': {'radius': 0.1}, 'sphere': {'scale': 0.25}})

    if dcm_charges is not None:
        xyz_dcm = io.StringIO()
        ase_io.write(xyz_dcm, dcm_charges, format='xyz')
        view.addModel(xyz_dcm.getvalue(), 'xyz')
        view.setStyle({'model': -1}, {'stick': {'radius': 0.01}, 'sphere': {'scale': 0.05}})
    view.startjs = view.startjs.replace('"customColorize"', 'customColorize')
    view.zoomTo()
    return view

# create a slider for n_dcm
n_dcm = st.slider("Number of Distributed Charges per Atom", min_value=1, max_value=4, value=4)

# create a button to run the DCM-Net
if st.button("Run DCM-Net"):
    # bail if smiles is not valid
    if smiles is None or smiles == "":
        st.error("Please enter a valid SMILES string")
        st.stop()

    # start a spinner
    with st.spinner("Running DCM-Net..."):
        results = run_dcm(smiles, n_dcm)
        print(results)
        ase_atoms = results["atoms"]
        col1, col2 = st.columns(2)
        with col1:
            showmol(render_3d(ase_atoms), height=300, width=WIDTH)
        with col2:
            st.image(results["smiles_image"])
    st.subheader("Model Output")
    if n_dcm >= 1:
        st.markdown("### DCM-1")
        dcmcolors1 = color_charges(results["mono_dc1"], 1, ase_atoms)
        # two columns showing combined and just the dcmol
        col1, col2 = st.columns(2)
        with col1:
            showmol(render_3d(ase_atoms, results["dcmol"]), height=300, width=WIDTH)
        with col2:
            showmol(render_3d(None, results["dcmol"], dcmcolors1), height=300, width=WIDTH)

        if n_dcm >= 2:
            st.markdown("### DCM-2")
            dcmcolors2 = color_charges(results["mono_dc2"], 2, ase_atoms)
            col1, col2 = st.columns(2)
            with col1:
                showmol(render_3d(ase_atoms, results["dcmol2"]), height=300, width=WIDTH)
            with col2:
                showmol(render_3d(None, results["dcmol2"], dcmcolors2), height=300, width=WIDTH)

        if n_dcm >= 3:
            st.markdown("### DCM-3")
            dcmcolors3 = color_charges(results["mono_dc3"], 3, ase_atoms)
            col1, col2 = st.columns(2)
            with col1:
                showmol(render_3d(ase_atoms, results["dcmol3"]), height=300, width=WIDTH)
            with col2:
                showmol(render_3d(None, results["dcmol3"], dcmcolors3), height=300, width=WIDTH)

        if n_dcm >= 4:
            st.markdown("### DCM-4")
            dcmcolors4 = color_charges(results["mono_dc4"], 4, ase_atoms)
            col1, col2 = st.columns(2)
            with col1:
                showmol(render_3d(ase_atoms, results["dcmol4"]), height=300, width=WIDTH)
            with col2:
                showmol(render_3d(None, results["dcmol4"], dcmcolors4), height=300, width=WIDTH)