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.logo("data/banner.png") Titlelogo = Image.open('data/banner.png') st.image(Titlelogo) st.write("### **:gray[Your] :rainbow[Molecule] :gray[playground]**") st.markdown((":gray[Visualize and Convert your] :rainbow[Molecule]")) 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', 'cube','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": "#CA86FF", "width": 0.05}) 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='Line', 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', '#323232', 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()