Update app.py

app.py

@@ -164,10 +164,10 @@ class View3DmolCell(py3Dmol.view):
     def __init__(self, width=640, height=480):
         divid = "3dmolviewer_UNIQUEID"
         self.uniqueid = None
-        if type(width) == int:
-            width = '%dpx'%width
-        if type(height) == int:
-            height = '%dpx'%height
+        if isinstance(width, int):
+            width = '%dpx' % width
+        if isinstance(width, int):
+            height = '%dpx' % height
         self.startjs = '''<div id="%s"  style="position: relative; width: %s; height: %s;">
             </div>\n''' % (divid, width, height)
         self.startjs += '<script>\n'
@@ -192,15 +192,14 @@ def rgb_to_hex(rgb):
 def mol_to_pharm3d(mol, mode='html'):
     AllChem.Compute2DCoords(mol)
 
-    feat_factory = AllChem.BuildFeatureFactory(os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef'))
-    feats = feat_factory.GetFeaturesForMol(mol)
+    feats = FEAT_FACTORY.GetFeaturesForMol(mol)
 
     view = View3DmolCell(width=400, height=400)
     for feat in feats:
         pos = feat.GetPos()
         color = _featColors.get(feat.GetFamily(), (.5, .5, .5))
         view.addSphere({
-            'center': {'x': pos.x,'y': pos.y,'z': pos.z},
+            'center': {'x': pos.x, 'y': pos.y, 'z': pos.z},
             'radius': 0.5,
             'color': rgb_to_hex(color)
         })
@@ -210,9 +209,8 @@ def mol_to_pharm3d(mol, mode='html'):
     view.setStyle({'stick': {}})
     view.zoomTo()
 
-    match mode:
-        case 'html':
-            return view.write_html()
+    if mode == 'html':
+        return view.write_html()
         # case 'png':
         #     return view.png()
 
@@ -1208,7 +1206,7 @@ def create_html_report(df, file=None, task=None, opts=(), progress=gr.Progress(t
     else:
         if 'Exclude Pharmacophore 3D' not in opts:
             df_html['Pharmacophore'] = df_html['Compound'].parallel_apply(
-                lambda x: mol_to_pharm3d(x, mode='html') if not pd.isna(x) else x)
+                lambda x: mol_to_pharm3d(x) if not pd.isna(x) else x)
 
         image_zoom_formatter = HTMLTemplateFormatter(template='<div class="image-zoom-viewer"><%= value %></div>')
         uniprot_id_formatter = HTMLTemplateFormatter(
@@ -1931,7 +1929,11 @@ with gr.Blocks(theme=theme, title='DeepSEQreen', css=CSS, delete_cache=(3600, 48
                             csv_sep = gr.Radio(label='CSV Delimiter',
                                                choices=['Comma', 'Tab'], value='Comma')
                             html_opts = gr.CheckboxGroup(label='HTML Report Options',
-                                                         choices=['Exclude Molecular Graph', 'Exclude Scaffold Graph'])
+                                                         choices=[
+                                                             'Exclude Molecular Graph',
+                                                             'Exclude Scaffold Graph',
+                                                             'Exclude Pharmacophore 3D'
+                                                         ])
 
             with gr.Row():
                 report_clr_btn = gr.ClearButton(size='lg')
@@ -2111,6 +2113,7 @@ with gr.Blocks(theme=theme, title='DeepSEQreen', css=CSS, delete_cache=(3600, 48
         show_progress='hidden'
     )
 
+
     def example_fill(input_type):
         return {target_id: 'Q16539',
                 target_gene: 'MAPK14',
@@ -2537,6 +2540,7 @@ QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
         else:
             return preset
 
+
     def update_family(family, preset):
         if preset == 'Family-Specific Auto-Recommendation':
             return 'Family-Specific Auto-Recommendation'
@@ -2545,6 +2549,7 @@ QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
         else:
             return family
 
+
     target_identify_target_family.change(
         fn=update_preset, inputs=[target_identify_target_family, target_identify_preset],
         outputs=target_identify_preset, show_progress='hidden')
@@ -2727,7 +2732,6 @@ QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
     ).then(fn=create_html_report_file, inputs=[report_df, file_for_report, report_task, html_opts],
            outputs=html_download_file, show_progress='full')
 
-
 if __name__ == "__main__":
     pandarallel.initialize()