cite

app.py

@@ -79,6 +79,7 @@ def submitted():
         os.makedirs(job_dir)
 
 
+        pdb = None
         if 'pdb' in request.files:
             try:
                 f = request.files['pdb']

rnamigos_launcher.py

@@ -14,17 +14,20 @@ def launch(pdb_path, library_path, n_hits=30, run='rnamigos-ismb'):
         MASTER launcher.
     """
 
-    _,ext = os.path.splittext(pdb_path)
-
-    if ext == '.cif':
-        print(f"launcher path {pdb_path}")
-        G = get_graph(pdb_path)
-    elif ext == '.json':
-        with open(pdb_path) as f:
-            data = json.load(f)
-            G = nx.node_link_data(data)
+    if pdb_path is None:
+        G = nx.read_gpickle(os.path.join("static", "samples", "1aju_arg.nx"))
     else:
-        raise ValueError("Invalid input file type.")
+        _,ext = os.path.splittext(pdb_path)
+
+        if ext == '.cif':
+            print(f"launcher path {pdb_path}")
+            G = get_graph(pdb_path)
+        elif ext == '.json':
+            with open(pdb_path) as f:
+                data = json.load(f)
+                G = nx.node_link_data(data)
+        else:
+            raise ValueError("Invalid input file type.")
 
     print("LOADING MODEL")
     run = 'ismb-tune_0'
@@ -32,8 +35,6 @@ def launch(pdb_path, library_path, n_hits=30, run='rnamigos-ismb'):
     fp_pred,_ = inference_on_graph(model, G, meta['edge_map'])
 
     print("LOADING LIBRARY")
-    # library = pickle.load(open(os.path.join("static", "libraries", "pdb_rna.p"), 'rb'))
-
     if library_path is None:
         library = pickle.load(open(os.path.join("static", "library", "all_rna_pdb.p"), 'rb'))
     else:

templates/help.html

@@ -139,5 +139,5 @@ You can then download the full list of distances to each element in the library
 
 <h1>Contact </h1>
 
-<code>cgoliver[at][protonmail][dotcom]
+<code>rnamigos@cs.mcgill.ca</code>
 {% endblock body %}

templates/home.html

@@ -36,6 +36,15 @@ Carlos G. Oliver (cgoliver[at]protonmail(dotcom))<br>
       <input type="submit" id="query_submit" value="Find Ligands">
 	</form>
 </div>
+
+<h1>Citing</h1>
+
+Augmented base pairing networks encode RNA-small molecule binding preferences<br>
+Carlos Oliver, Vincent Mallet, Roman Sarrazin Gendron, Vladimir Reinharz, William L. Hamilton, Nicolas Moitessier, Jerome Waldispuhl<br>
+bioRxiv 701326; doi: https://doi.org/10.1101/701326
+
+
+
 </body>
 {% endblock body %}