app.py

import streamlit as st
from streamlit_ketcher import st_ketcher
from rdkit import Chem
from rdkit.Chem import Draw, AllChem, rdDetermineBonds, Descriptors

import py3Dmol
from stmol import showmol
from io import StringIO
import sys
import subprocess
import time
import streamlit_shadcn_ui as ui
import streamlit_shadcn_ui as ui

from PIL import Image


try:
    # from openbabel import OBMol, OBConversion
    import openbabel
except ModuleNotFoundError as e:
    subprocess.Popen([f'{sys.executable} -m pip install --global-option=build_ext --global-option="-I/usr/include/openbabel3" --global-option="-L/usr/lib/openbabel" openbabel==2.4.1'], shell=True)
    subprocess.Popen([f'{sys.executable} -m pip install --global-option=build_ext --global-option="-I/home/appuser/include/openbabel3" --global-option="-L/home/appuser/lib/openbabel" openbabel==2.4.1'], shell=True)
    subprocess.Popen([f'{sys.executable} -m pip install --global-option=build_ext --global-option="-I/home/appuser/usr/include/openbabel3" --global-option="-L/home/appuser/usr/lib/openbabel" openbabel==2.4.1'], shell=True)
    # wait for subprocess to install package before running your actual code below
    #print('openbabel python not importing')
    time.sleep(90)
    
from openbabel import pybel


st.set_page_config(page_title="CHEMVERTINA", page_icon="data/favicon.png", layout="centered")


st.write("### **:rainbow[CHEMVERTINA] :gray[| Your Molecule Playground]**")
Titlelogo = Image.open('data/logo.png')
st.image(Titlelogo)
st.markdown((":gray[Visualize and Convert your] :rainbow[Molecule]"))

st.divider()



supported_input_formats =  ['xyz', 'cif', 'pdb', 'mol', 'mol2', 'sdf', 'tmol', 'poscar', 'cub', 'cube', 'mcif', 'mmcif', 'pwscf', 'smi']
supported_output_formats = ['cif', 'tmol', 'xyz', 'sdf', 'pdb', 'smiles', 'mcif', 'mmcif', 'mdl', 'mol', 'mol2', 'smi',]
     
data = '''12

C      1.525098    0.401299   -0.169919
C      1.267282   -0.890923   -0.090842
S     -0.375869   -1.429467   -0.350672
C     -1.364069   -0.186583   -0.232712
C     -0.787332    1.146673    0.059053
O      0.519018    1.327928   -0.452149
H      2.534310    0.743140   -0.012656
H      2.085372   -1.592058    0.136539
H     -0.704143   -2.346960    0.640753
H     -2.462024   -0.305561   -0.365090
H     -0.753918    1.233523    1.179450
H     -1.483725    1.898990   -0.341753
'''
    
#   st.components.v1.iframe("https://pubchem.ncbi.nlm.nih.gov/periodic-table/#view=table&embed=true", width=800, height=800, scrolling=True)
col1, col2 = st.columns(2)
col1.write('## Input Molecule')
input_format = col1.selectbox('Firstly, select the input file format',
        supported_input_formats, )

input_text_area = col1.empty()
uploaded_file = col1.file_uploader("or Choose a file from your local data")
if uploaded_file is not None:
        # To read file as bytes:
    bytes_data = uploaded_file.getvalue()
        
    #uploaded_file_name = uploaded_file.name.split(".")
    #input_up_format = uploaded_file_name[-1]
        
    
        # To convert to a string based IO:
    stringio = StringIO(uploaded_file.getvalue().decode("utf-8"))
    
            # To read file as string:
    string_data = stringio.read()
    placeholder_xyz_str = string_data
    input_geom_str = input_text_area.text_area(label='Enter the contents of the source file here', value = placeholder_xyz_str, placeholder = 'Put your text here', height=400)

elif uploaded_file is None:
        
    input_geom_str = input_text_area.text_area(label='Secondly, paste the file contents here', value = data, placeholder = 'Paste the contents of your file here', height=400, key = 'input_text_area')
    # # Get rid of empty lines
    # input_geom_str = os.linesep.join([s for s in input_geom_str.splitlines() if s])
    
mol = pybel.readstring(input_format, input_geom_str)
        # mol.make3D()
    
        
    
    ## OUTPUT ##
col2.write('## Output')
output_format = col2.selectbox('Select the output file format',
        supported_output_formats)
output_geom_str = mol.write(output_format)
col2.text_area(label='Converted file structure', value=output_geom_str, height=400)
col2.download_button(
         label="Download the output",
         data=output_geom_str,
         file_name='your_new_output.'+output_format,
         mime='text/csv',)

st.divider()

st.subheader("Visualization Scene")
col3, col4 = st.columns(2)


def vis_your_molecule():
    newviewer = py3Dmol.view(width=400, height=400)
    structure_for_visualization = ''
    try:
        mol = pybel.readstring(input_format, input_geom_str)
                # mol.make3D()
    
        structure_for_visualization = mol.write('xyz')
    except Exception as e:
        print('There was a problem with the conversion', e)
    
    newviewer.addModel(structure_for_visualization, 'xyz')
    newviewer.setBackgroundColor(bcolor2)
        
    newviewer.setStyle(stylemd2)
    newviewer.setViewStyle({"style": "outline", "color": "#323232", "width": 0.03})
        
    if spin2:
        newviewer.spin(True)
    else:
        newviewer.spin(False)   
    
    if box2:
        newviewer.addBox({'center': {'x': 0,'y': 0,'z': 0},
                    # 'dimensions': {'w': 1, 'h': 1, 'd': 1}, # scalars
                    'dimensions': {'w': {'x': 8, 'y': 8, 'z': 0}, #[1, 1, 0], #np.array([1,1,0]),
                                   'h': {'x': 8, 'y': -8, 'z': 0}, # [1, -1, 0], #np.array([1,-1,0]),
                                   'd': {'x': 0, 'y': 0, 'z': 8}, # [0, 0, 1], #np.array([0,0,1]),
                                   },
                    'color': '#C791FB',
                    'alpha': 0.5,
                    })
    else:
        pass
    
    showmol(newviewer,height=400,width=400)

with col3:

    st.markdown("Select your Model!")
    styles3d2 = {"Line Model": {"line": {}},
                "Cross Model": {"cross":{}},
                "Stick Model": {"stick": {}, "sphere": {"scale": 0}},
                "Ball and Stick Model": {"stick": {}, "sphere": {"scale": 0.3}},
                "CPK Model": {"sphere": {}}
                }
    list_style2 = ['Line', 'Cross', 'Stick', 'Ball and Stick', 'CPK']
    value2 = ui.tabs(options=list_style2, default_value='Ball and Stick', key="flowers")
    
    spin2 = st.toggle('Animate', value=False, key=5)
    box2 = st.toggle('Show Box', value=False, key=6)
    bcolor2 = st.color_picker('Pick Background Color', '#ffffff', key=7)

def stylem2(value2):
    if value2 == list_style2[0]:
        value4 = styles3d2["Line Model"]
    elif value2 ==  list_style2[1]:
        value4 = styles3d2["Cross Model"]
    elif value2 == list_style2[2]:
        value4 = styles3d2["Stick Model"]
    elif value2 == list_style2[3]:
        value4 = styles3d2["Ball and Stick Model"]
    elif value2 == list_style2[4]:
        value4 = styles3d2["CPK Model"]
    return value4


stylemd2 = stylem2(value2)



with col4:
    vis_your_molecule()