Update app.py

app.py

@@ -93,21 +93,111 @@ smis = [ 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=
     "CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O"]
     
 confs = [smi2conf(s) for s in smis]
+import streamlit as st
+import streamlit.components.v1 as components
+import py3Dmol
+from rdkit import Chem
+from rdkit.Chem import Draw
+from rdkit.Chem import AllChem
 
-interact(conf_viewer, idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1))
-
-smis = [ 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=O)C(F)(Cl)Br',
-    'CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O',
-    'Cc1c(COc2cc(OCc3cccc(c3)C#N)c(CN3C[C@H](O)C[C@H]3C(O)=O)cc2Cl)cccc1-c1ccc2OCCOc2c1',
-    'CCCCC(=O)NCCCCC(=O)NCCCCCC(=O)[O-]',
-    "CC(NCCNCC1=CC=C(OCC2=C(C)C(C3=CC=CC=C3)=CC=C2)N=C1OC)=O"]
-
-confs = [smi2conf(s) for s in smis]
+st.title('SMILES  + RDKit + Py3DMOL :smiley:')
+def show(smi, style='stick'):
+    mol = Chem.MolFromSmiles(smi)
+    mol = Chem.AddHs(mol)
+    AllChem.EmbedMolecule(mol)
+    AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
+    mblock = Chem.MolToMolBlock(mol)
 
+    view = py3Dmol.view(width=400, height=400)
+    view.addModel(mblock, 'mol')
+    view.setStyle({style:{}})
+    view.zoomTo()
+    view.show()
+    view.render()
+    t =view.js()
+    f = open('viz.html', 'w')
+    f.write(t.startjs)
+    f.write(t.endjs)
+    f.close()
+
+compound_smiles=st.text_input('SMILES please','CC')
+m = Chem.MolFromSmiles(compound_smiles)
 
-interact(style_selector, 
-         idx=ipywidgets.IntSlider(min=0,max=len(class_0_list)-1, step=1),
-         s=ipywidgets.Dropdown(
-            options=['line', 'stick', 'sphere'],
-            value='line',
-            description='Style:'))
+Draw.MolToFile(m,'mol.png')
+
+
+show(compound_smiles)
+HtmlFile = open("viz.html", 'r', encoding='utf-8')
+source_code = HtmlFile.read() 
+c1,c2=st.beta_columns(2)
+with c1:
+  st.write('Molecule :coffee:')
+  st.image('mol.png')
+with c2:
+  components.html(source_code, height = 400,width=400)
+
+################ Sidebar ####################
+with st.sidebar.beta_expander('Rule One (Atoms and Bonds)'):
+  st.markdown('''
+## Atoms
+|If |then |
+|----|----|
+| Non-aromatic atoms |Uper case letters |
+| Aromatic atoms |lower case letters |
+|Atomic symbols has more than one letter | The second is lower case |
+## Bonds
+| Bond type| Bond symbol |
+|---|---|
+|Simple | - |
+|Double|=|
+|Triple|#|
+|Aromatic|*|
+| Disconnected structures|. |
+### Example:
+ CC   👉 There is a non-aromatic carbon attached to another non-aromatic carbon by a single bond.
+🛑 A bond between two lower case atom symbols is *aromatic*.
+''')
+
+with st.sidebar.beta_expander('Rule Two (Simple Chains)'):
+  st.markdown('''
+  ## Simple chains
+  * Structures are hydrogen suppresed (Molecules represented without hydrogens)
+  * If enough bonds are not identified by the user, the system will assume that connections
+  are satisfied by hidrogens.
+  * The user can explicitly identify hydrogen bonds, but if so the interpreter will assume that all of them are fully identified.
+  Note:
+  
+  *Because SMILES allows entry of all elements in the periodic table, 
+  and also utilizes hydrogen suppression, the user should be aware of chemicals with two letters 
+  that could be misinterpreted by the computer. For example, 'Sc' could be interpreted as a **sulfur**
+  atom connected to an aromatic **carbon** by a single bond, or it could be the symbol for **scandium**. 
+  The SMILES interpreter gives priority to the interpretation of a single bond connecting a sulfur atom and an aromatic carbon. 
+  To identify scandium the user should enter [Sc]*.
+  ''')
+
+with st.sidebar.beta_expander('Rule Three (Branches)'):
+  st.markdown('''
+  ## Branches
+  * A branch from a chain is specified by placing the SMILES symbol(s) for the branch between parenthesis. 
+  * The string in parentheses is placed directly after the symbol for the atom to which it is connected. 
+  * If it is connected by a double or triple bond, the bond symbol immediately follows the left parenthesis.
+  ''')
+
+with st.sidebar.beta_expander('Rule Four (Rings)'):
+  st.markdown('''
+  ## Rings
+  * SMILES allows a user to identify ring structures by using numbers to identify the opening and closing ring atom.
+  For example, in C1CCCCC1, the first carbon has a number '1' which connects by a single bond with the last carbon which also has a number '1'. 
+  The resulting structure is cyclohexane. Chemicals that have multiple rings may be identified by using different numbers for each ring.
+  * If a double, single, or aromatic bond is used for the ring closure, the bond symbol is placed before the ring closure number.
+  ''')
+
+with st.sidebar.beta_expander('Rule Five (Charged atoms)'):
+  st.markdown('''
+  ## Charged atoms
+  Charges on an atom can be used to override the knowledge regarding valence that is built into SMILES software. 
+  The format for identifying a charged atom consists of the atom followed by brackets which enclose the charge on the atom. 
+  The number of charges may be explicitly stated ({-1}) or not ({-}). 
+  ''')
+st.sidebar.markdown('Original Author: José Manuel Nápoles ([@napoles3d](https://twitter.com/napoles3D)). Find original app in https://share.streamlit.io/napoles-uach/st_smiles/main/smiles.py')
+st.sidebar.write('Info about SMILES: https://archive.epa.gov/med/med_archive_03/web/html/smiles.html')