Merge pull request #22 from avrabyt/master

🚀 demo app added,Article requirements ❇️

README.md

@@ -39,7 +39,7 @@ ipywidgets(==7.6.3)
 
 ## Quickstart
 
-##### Protein visualization using `showmol()`function 
+##### 1. Protein visualization using `showmol()`function 
 
 - **Using `py3Dmol object`**
 
@@ -60,14 +60,19 @@ The `render_pdb()` function accepts any PDB ID and returns a py3Dmol object.
 from stmol import *
 showmol(render_pdb(id = '1A2C'))
 ```
-![Quickstart-1](https://github.com/avrabyt/stmol/blob/master/Resources/Quickstart-1.png)
+![Quickstart-1](https://github.com/napoles-uach/stmol/blob/master/Resources/Quickstart-1.png)
 
-##### Labelling protein using `render_pdb()`function 
+##### 2. Labelling protein using `render_pdb()`function 
 Inorder to mark the residues, we can use the `render_pdb()` function, which in this example marks the *Alanine* [ALA] residues,
 ```python
 showmol(render_pdb_resn(viewer = render_pdb(id = '1A2C'),resn_lst = ['ALA',]))
 ```
-![Quickstart-1](https://github.com/avrabyt/stmol/blob/master/Resources/Quickstart-1.png)
+![Quickstart-1](https://github.com/napoles-uach/stmol/blob/master/Resources/Quickstart-2.png)
+
+###### Refer to the documentation [here](https://napoles-uach-stmol-home-pom051.streamlitapp.com/Documentation) 
+----------
+### Examples
+You can find several `stmol` examples [here](https://napoles-uach-stmol-home-pom051.streamlitapp.com/Examples).
 
 ----------------
 ## Dependencies
@@ -83,4 +88,8 @@ We appreciate contributions from the community! Every little bit helps, and cred
 - **Fix Bugs** - Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to help with it.
 - **Implement Features** - Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
 - **Submit Feedback** - The best way to send feedback is to file an issue at https://github.com/napoles-uach/stmol/issues
-
+--------------
+## Authors
+- J. M. N  ́apoles-Duarte <jnapoles@uach.mx>
+- Avratanu Biswas <avratanu.biswas@brc.hu>
+- Mitchell I. Parker <mip34@drexel.edu>

pages/2_Demo stmol.py

@@ -0,0 +1,66 @@
+
+### Step 1) Imports
+
+import streamlit as st
+import py3Dmol
+from stmol import showmol
+
+### Step 2) Streamlit
+
+st.sidebar.title("View Settings")
+
+pdb_code = st.sidebar.text_input(
+        label="PDB Code",
+        value="3K8Y",
+    )
+
+hl_resi_list = st.sidebar.multiselect(label="Highlight Residues",options=list(range(1,5000)))
+
+hl_chain = st.sidebar.text_input(label="Highlight Chain",value="A")
+
+label_resi = st.sidebar.checkbox(label="Label Residues", value=True)
+
+surf_transp = st.sidebar.slider("Surface Transparency", min_value=0.0, max_value=1.0, value=0.0)
+
+hl_color = st.sidebar.text_input(label="Highlight Color",value="red")
+
+bb_color = st.sidebar.text_input(label="Backbone Color",value="lightgrey")
+lig_color = st.sidebar.text_input(label="Ligand Color",value="white")
+
+st.markdown(f"## Stmol-App: PDB [{pdb_code.upper()}](https://www.rcsb.org/structure/{pdb_code}) (Chain {hl_chain})")
+
+### Step 3) Py3Dmol
+
+width = 700
+height = 700
+
+cartoon_radius = 0.2
+stick_radius = 0.2
+
+view = py3Dmol.view(query=f"pdb:{pdb_code.lower()}", width=width, height=height)
+
+view.setStyle({"cartoon": {"style": "oval","color": bb_color,"thickness": cartoon_radius}})
+
+view.addSurface(py3Dmol.VDW, {"opacity": surf_transp, "color": bb_color},{"hetflag": False})
+
+view.addStyle({"elem": "C", "hetflag": True},
+                {"stick": {"color": lig_color, "radius": stick_radius}})
+
+view.addStyle({"hetflag": True},
+                    {"stick": {"radius": stick_radius}})
+
+for hl_resi in hl_resi_list:
+    view.addStyle({"chain": hl_chain, "resi": hl_resi, "elem": "C"},
+                    {"stick": {"color": hl_color, "radius": stick_radius}})
+
+    view.addStyle({"chain": hl_chain, "resi": hl_resi},
+                        {"stick": {"radius": stick_radius}})
+
+if label_resi:
+    for hl_resi in hl_resi_list:
+        view.addResLabels({"chain": hl_chain,"resi": hl_resi},
+        {"backgroundColor": "lightgray","fontColor": "black","backgroundOpacity": 0.5})
+
+### Step 4) Stmol
+
+showmol(view, height=height, width=width)

pages/3_Examples.py

@@ -91,4 +91,6 @@
 
     with tab3 :
         with st.echo():
-            showmol(render_pdb_resn(viewer = render_pdb(id = '1A2C'),resn_lst = ['ALA',]))
+            showmol(render_pdb_resn(viewer = render_pdb(id = '1A2C'),resn_lst = ['ALA',]),height=700,width=700)
+
+