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app.py

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+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()

environment_backup.yml

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+name: streamlit-conda-minimal
+channels:
+  - conda-forge
+  - anaconda
+dependencies:
+  - streamlit
+  - openbabel
+  - py3Dmol
+  - ipython
+

requirements.txt

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+datamol==0.12.2
+
+matplotlib==3.7.1
+medchem==2.0.3
+
+numpy==1.24.3
+pandas==1.5.3
+Pillow==9.4.0
+py3Dmol==2.0.4
+pyperclip==1.8.2
+rdkit==2023.9.1
+st_speckmol==0.0.6
+stmol==0.0.9
+streamlit
+streamlit_ketcher==0.0.1
+streamlit_scrollable_textbox==0.0.3
+streamlit_shadcn_ui==0.1.18
+ipython_genutils==0.1.0
+openbabel-wheel
+ipython