awacke1 commited on
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7ba12a8
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1 Parent(s): 7d1b551

Update app.py

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  1. app.py +1 -64
app.py CHANGED
@@ -74,6 +74,7 @@ def smi2viewer(smi='CC=O'):
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  except:
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  return None
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  smi = 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=O)C(F)(Cl)Br'
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  conf = smi2conf(smi)
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  viewer = MolTo3DView(conf, size=(600, 300), style='sphere')
@@ -135,68 +136,4 @@ with c1:
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  with c2:
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  components.html(source_code, height = 400,width=400)
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- ################ Sidebar ####################
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- with st.sidebar.expander('Rule One (Atoms and Bonds)'):
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- st.markdown('''
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- ## Atoms
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- |If |then |
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- |----|----|
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- | Non-aromatic atoms |Uper case letters |
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- | Aromatic atoms |lower case letters |
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- |Atomic symbols has more than one letter | The second is lower case |
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- ## Bonds
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- | Bond type| Bond symbol |
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- |---|---|
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- |Simple | - |
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- |Double|=|
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- |Triple|#|
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- |Aromatic|*|
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- | Disconnected structures|. |
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- ### Example:
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- CC 👉 There is a non-aromatic carbon attached to another non-aromatic carbon by a single bond.
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- 🛑 A bond between two lower case atom symbols is *aromatic*.
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- ''')
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-
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- with st.sidebar.expander('Rule Two (Simple Chains)'):
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- st.markdown('''
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- ## Simple chains
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- * Structures are hydrogen suppresed (Molecules represented without hydrogens)
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- * If enough bonds are not identified by the user, the system will assume that connections
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- are satisfied by hidrogens.
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- * The user can explicitly identify hydrogen bonds, but if so the interpreter will assume that all of them are fully identified.
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- Note:
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-
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- *Because SMILES allows entry of all elements in the periodic table,
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- and also utilizes hydrogen suppression, the user should be aware of chemicals with two letters
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- that could be misinterpreted by the computer. For example, 'Sc' could be interpreted as a **sulfur**
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- atom connected to an aromatic **carbon** by a single bond, or it could be the symbol for **scandium**.
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- The SMILES interpreter gives priority to the interpretation of a single bond connecting a sulfur atom and an aromatic carbon.
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- To identify scandium the user should enter [Sc]*.
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- ''')
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-
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- with st.sidebar.expander('Rule Three (Branches)'):
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- st.markdown('''
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- ## Branches
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- * A branch from a chain is specified by placing the SMILES symbol(s) for the branch between parenthesis.
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- * The string in parentheses is placed directly after the symbol for the atom to which it is connected.
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- * If it is connected by a double or triple bond, the bond symbol immediately follows the left parenthesis.
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- ''')
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-
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- with st.sidebar.expander('Rule Four (Rings)'):
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- st.markdown('''
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- ## Rings
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- * SMILES allows a user to identify ring structures by using numbers to identify the opening and closing ring atom.
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- 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'.
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- The resulting structure is cyclohexane. Chemicals that have multiple rings may be identified by using different numbers for each ring.
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- * If a double, single, or aromatic bond is used for the ring closure, the bond symbol is placed before the ring closure number.
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- ''')
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-
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- with st.sidebar.expander('Rule Five (Charged atoms)'):
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- st.markdown('''
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- ## Charged atoms
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- Charges on an atom can be used to override the knowledge regarding valence that is built into SMILES software.
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- The format for identifying a charged atom consists of the atom followed by brackets which enclose the charge on the atom.
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- The number of charges may be explicitly stated ({-1}) or not ({-}).
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- ''')
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- 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')
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  st.sidebar.write('Info about SMILES: https://archive.epa.gov/med/med_archive_03/web/html/smiles.html')
 
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  except:
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  return None
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+
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  smi = 'COc3nc(OCc2ccc(C#N)c(c1ccc(C(=O)O)cc1)c2P(=O)(O)O)ccc3C[NH2+]CC(I)NC(=O)C(F)(Cl)Br'
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  conf = smi2conf(smi)
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  viewer = MolTo3DView(conf, size=(600, 300), style='sphere')
 
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  with c2:
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  components.html(source_code, height = 400,width=400)
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  st.sidebar.write('Info about SMILES: https://archive.epa.gov/med/med_archive_03/web/html/smiles.html')