colors etc

.xyz

@@ -0,0 +1,17 @@
+15
+
+N     -1.9997737     0.2248998     0.0000000    
+C     -1.8902337    -1.1433002     0.0000000    
+C     -0.8943837     1.0293398     0.0000000    
+C      0.3497463     0.4090598     0.0000000    
+C      0.4321763    -0.9418902     0.0000000    
+N     -0.6604037    -1.7419602     0.0000000    
+N      1.5839363     0.9436498     0.0000000    
+C      2.4005863    -0.1441302     0.0000000    
+N      1.7162263    -1.3147602     0.0000000    
+N     -1.0273937     2.4370398     0.0000000    
+H     -2.7833637    -1.7527702     0.0000000    
+H      3.4806763    -0.0808802     0.0000000    
+H     -1.9629337     2.8682998     0.0000000    
+H     -0.1966537     3.0466298     0.0000000    
+H      2.1045263    -2.2838602     0.0000000    

app.py

@@ -31,17 +31,31 @@ function(atom,viewer) {
     }
 }"""
 
-def get_qm_atom_features(gfn2_output, checked_features):
+#def get_qm_atom_features(gfn2_output, checked_features):
+#    qm_atom_features = {}
+#    qm_atom_features['atom type'] = gfn2_output["fetchatomicprops"]["atmlist"]
+#    for checked_feature in checked_features:
+#        if checked_feature == 'Charge':
+#            qm_atom_features['Charge'] = gfn2_output["fetchatomicprops"]["charges"]
+#        if checked_feature == 'Polarizability':
+#            qm_atom_features['Polarizability'] = gfn2_output["fetchatomicprops"]["polarisabilities"]   
+#    return qm_atom_features
+
+def get_qm_atom_features(gfn2_output):
     qm_atom_features = {}
-    qm_atom_features['atom type'] = gfn2_output["fetchatomicprops"]["atmlist"]
-    for checked_feature in checked_features:
-        if checked_feature == 'Charge':
-            qm_atom_features['Charge'] = gfn2_output["fetchatomicprops"]["charges"]
-        if checked_feature == 'Polarizability':
-            qm_atom_features['Polarizability'] = gfn2_output["fetchatomicprops"]["polarisabilities"]   
+    atom_list = gfn2_output["fetchatomicprops"]["atmlist"]
+    charge = gfn2_output["fetchatomicprops"]["charges"]
+    pol = gfn2_output["fetchatomicprops"]["polarisabilities"]
+    #atom_list = atom_list.append('Molecule')
+    #charge = charge.append("")
+    #pol = pol.append(gfn2_output["totalpol"])
+    qm_atom_features['atom type'] = atom_list
+    qm_atom_features['Charge'] = charge
+    qm_atom_features['Polarizability'] = pol 
     return qm_atom_features
 
-def get_qm_mol_features(gfn2_output, checked_features):
+
+def get_qm_mol_features(gfn2_output):
     qm_mol_features = {}
     qm_mol_features['Total Energy'] = gfn2_output["etotal"]
     qm_mol_features['Total Polarizability'] = gfn2_output["totalpol"]
@@ -70,16 +84,17 @@ def get_basic_visualization(input_f,input_format):
     return visualization_html
 
 def add_spheres_feature_view(view, feature,xyz, viewnum, sizefactor, spec_color):
+    normalization = max(max(feature),abs(min(feature)))
     for i in range(len(feature)):
         if feature[i]<0:
-            color="red"
+            color="#a0210f"
         else: 
             color=spec_color
         view.addSphere({'center':{
         'x':xyz[i][0], 
         'y':xyz[i][1],
         'z':xyz[i][2]},
-        'radius':abs(feature[i])*sizefactor,'color':color,'alpha':1.00}, viewer=viewnum) 
+        'radius':abs(feature[i])/normalization*sizefactor,'color':color,'alpha':1.00}, viewer=viewnum) 
     return view
 
 def add_densities(view, dens, color, viewnum):
@@ -88,23 +103,24 @@ def add_densities(view, dens, color, viewnum):
 
 
 def get_feature_visualization(input_f,input_format, features, xyz):
-    view = py3Dmol.view(width=600, height=400, viewergrid=(2,2))
+    view = py3Dmol.view(width=620, height=620, viewergrid=(2,2))
     view.setBackgroundColor('white')
     view.addModel(input_f, input_format, viewer=(0,0))
-    view.addModel(input_f, input_format, viewer=(0,1))
-    view.addModel(input_f, input_format, viewer=(1,0))
+    #view.addModel(input_f, input_format, viewer=(0,1))
+    #view.addModel(input_f, input_format, viewer=(1,0))
     view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,0))
-    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,1))
-    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(1,0))
     #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,1))
-    add_spheres_feature_view(view, features["fetchatomicprops"]["charges"], xyz, (0,1), 20, 'blue')
-    add_spheres_feature_view(view, features["fetchatomicprops"]["polarisabilities"], xyz, (1,0), 0.2, 'orange')
-    add_densities(view, open('dummy_struct_dens.cub', "r").read(), 'green', (1,1))
+    #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(1,0))
+    #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,1))
+    print('features', features)
+    add_spheres_feature_view(view, features["fetchatomicprops"]["charges"], xyz, (0,1), 1.0, '#4c4e9e')
+    add_spheres_feature_view(view, features["fetchatomicprops"]["polarisabilities"], xyz, (1,0), 1.0, '#809BAC')
+    add_densities(view, open('dummy_struct_dens.cub', "r").read(), '#F7D7BE', (1,1))
     #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}},'cartoon': {'color': '#4c4e9e', 'alpha':"0.6"}})
     view.zoomTo(viewer=(0,0))
     output = view._make_html().replace("'", '"')
     x = f"""<!DOCTYPE html><html> {output} </html>"""  # do not use ' in this input
-    visualization_html = f"""<iframe  style="width: 100%; height:420px" name="result" allow="midi; geolocation; microphone; camera; 
+    visualization_html = f"""<iframe  style="width: 100%; height:620px" name="result" allow="midi; geolocation; microphone; camera; 
     display-capture; encrypted-media;" sandbox="allow-modals allow-forms 
     allow-scripts allow-same-origin allow-popups 
     allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" 
@@ -113,7 +129,7 @@ def get_feature_visualization(input_f,input_format, features, xyz):
 
 
 
-def predict(checked_features, input_file, temperature):
+def predict(input_file):
     input_f = open(input_file.name, "r").read()
     input_format = input_file.name.split('.')[-1]
     
@@ -124,11 +140,11 @@ def predict(checked_features, input_file, temperature):
     gfn2_input = ["filename","geom=dummy_struct."+input_format, 'calcdens=1']
     gfn2_output = run_gfn2(gfn2_input)
 
-    qm_atom_features = get_qm_atom_features(gfn2_output, checked_features)
-    qm_mol_features = get_qm_mol_features(gfn2_output, checked_features)
+
+    #qm_mol_features = get_qm_mol_features(gfn2_output, checked_features)
     #basic_visualization_html = get_basic_visualization(input_f,input_format)
     feature_visualization_html = get_feature_visualization(input_f,input_format, gfn2_output, gfn2_output['xyz'])
-
+    qm_atom_features = get_qm_atom_features(gfn2_output)
 
     return feature_visualization_html, pd.DataFrame(qm_atom_features)#, pd.DataFrame(qm_mol_features, index=[0])
 
@@ -144,18 +160,15 @@ with gr.Blocks() as demo:
     with gr.Row():
         input_file = gr.File(label="Structure file for input")
         charge = gr.Textbox(placeholder="Total charge", label="Give the total charge of the input molecule. (Default=0)")
-    checked_features = gr.CheckboxGroup(["Charge", "Polarizability", "Koopman IP", "Electronic Density"], label="QM features", info="Which features shall be calculated?")
-    temperature = gr.Slider(value=300,minimum=0, maximum=1000, label="Temperature for Thermodynamics evaluation in K", step=5)
-    #with gr.Row():
-    #    helix = gr.ColorPicker(label="helix")
-    #    sheet = gr.ColorPicker(label="sheet")
-    #    loop = gr.ColorPicker(label="loop")
+    #checked_features = gr.CheckboxGroup(["Charge", "Polarizability", "Koopman IP", "Electronic Density"], label="QM features", info="Which features shall be calculated?")
+    #temperature = gr.Slider(value=300,minimum=0, maximum=1000, label="Temperature for Thermodynamics evaluation in K", step=5)
+
     single_btn = gr.Button(label="Run")
     with gr.Row():
         basic_html = gr.HTML()
-        gr.HighlightedText(value=[("Positive Charge","blue"),("Negative charge","red"),("Polarizability","orange"), ("Electronic Densities", "Green")], color_map={"red":"red", "blue":"blue", "orange":"orange", "Green":"green"})
-    #with gr.Row():    
-    #    basic_html = gr.HTML()
+
+    gr.HighlightedText(value=[("Positive Charge","Purple"),("Negative charge","red"),("Polarizability","Light blue"), ("Electronic Densities", "Beige")], color_map={"red":"#a0210f", "Light blue":"#809BAC", "Purple":"#4c4e9e", "Beige":"#F7D7BE"})
+
     with gr.Row():
         Dbutton = gr.Button("Download  calculated atom features")
         csv = gr.File(interactive=False, visible=False)
@@ -163,7 +176,7 @@ with gr.Blocks() as demo:
         df_atom_features = gr.Dataframe()
         #df_mol_features = gr.Dataframe()
 
-    single_btn.click(fn=predict, inputs=[checked_features, input_file, temperature], outputs=[basic_html, df_atom_features])
+    single_btn.click(fn=predict, inputs=[input_file], outputs=[basic_html, df_atom_features])
     Dbutton.click(export_csv, df_atom_features, csv)
 
         

dummy_struct.pdb

@@ -0,0 +1,52 @@
+CRYST1   81.052   81.052   81.052 109.47 109.47 109.47               1
+ATOM      1  N   GLU   199      36.081  39.009  29.686  1.00  0.00           N  
+ATOM      2  H1  GLU   199      35.429  38.796  30.426  1.00  0.00           H  
+ATOM      3  H2  GLU   199      36.154  38.207  29.076  1.00  0.00           H  
+ATOM      4  H3  GLU   199      35.853  39.916  29.303  1.00  0.00           H  
+ATOM      5  CA  GLU   199      37.432  39.167  30.291  1.00  0.00           C  
+ATOM      6  HA  GLU   199      38.116  38.436  29.860  1.00  0.00           H  
+ATOM      7  CB  GLU   199      37.982  40.570  30.022  1.00  0.00           C  
+ATOM      8  HB2 GLU   199      38.901  40.671  30.598  1.00  0.00           H  
+ATOM      9  HB3 GLU   199      38.212  40.628  28.958  1.00  0.00           H  
+ATOM     10  CG  GLU   199      37.028  41.688  30.394  1.00  0.00           C  
+ATOM     11  HG2 GLU   199      36.079  41.510  29.887  1.00  0.00           H  
+ATOM     12  HG3 GLU   199      36.878  41.635  31.472  1.00  0.00           H  
+ATOM     13  CD  GLU   199      37.549  43.062  30.023  1.00  0.00           C  
+ATOM     14  OE1 GLU   199      38.098  43.217  28.907  1.00  0.00           O  
+ATOM     15  OE2 GLU   199      37.394  43.992  30.847  1.00  0.00           O  
+ATOM     16  C   GLU   199      37.378  38.880  31.790  1.00  0.00           C  
+ATOM     17  O   GLU   199      36.391  39.196  32.464  1.00  0.00           O  
+ATOM     18  N   ASP   200      38.421  38.232  32.294  1.00  0.00           N  
+ATOM     19  H   ASP   200      39.166  37.937  31.679  1.00  0.00           H  
+ATOM     20  CA  ASP   200      38.512  37.883  33.705  1.00  0.00           C  
+ATOM     21  HA  ASP   200      37.703  38.355  34.262  1.00  0.00           H  
+ATOM     22  CB  ASP   200      38.401  36.370  33.871  1.00  0.00           C  
+ATOM     23  HB2 ASP   200      39.160  35.871  33.269  1.00  0.00           H  
+ATOM     24  HB3 ASP   200      38.581  36.162  34.926  1.00  0.00           H  
+ATOM     25  CG  ASP   200      37.030  35.856  33.483  1.00  0.00           C  
+ATOM     26  OD1 ASP   200      36.116  35.958  34.323  1.00  0.00           O  
+ATOM     27  OD2 ASP   200      36.851  35.393  32.334  1.00  0.00           O  
+ATOM     28  C   ASP   200      39.827  38.407  34.256  1.00  0.00           C  
+ATOM     29  O   ASP   200      40.869  37.761  34.126  1.00  0.00           O  
+ATOM     30  N   LEU   201      39.771  39.607  34.828  1.00  0.00           N  
+ATOM     31  H   LEU   201      38.893  40.106  34.850  1.00  0.00           H  
+ATOM     32  CA  LEU   201      40.950  40.261  35.373  1.00  0.00           C  
+ATOM     33  HA  LEU   201      41.853  39.729  35.075  1.00  0.00           H  
+ATOM     34  CB  LEU   201      41.025  41.684  34.837  1.00  0.00           C  
+ATOM     35  HB2 LEU   201      40.080  42.153  35.112  1.00  0.00           H  
+ATOM     36  HB3 LEU   201      41.851  42.260  35.254  1.00  0.00           H  
+ATOM     37  CG  LEU   201      41.150  41.645  33.318  1.00  0.00           C  
+ATOM     38  HG  LEU   201      40.848  40.661  32.961  1.00  0.00           H  
+ATOM     39  CD1 LEU   201      40.276  42.692  32.696  1.00  0.00           C  
+ATOM     40 HD11 LEU   201      40.578  43.677  33.052  1.00  0.00           H  
+ATOM     41 HD12 LEU   201      40.375  42.652  31.612  1.00  0.00           H  
+ATOM     42 HD13 LEU   201      39.237  42.509  32.972  1.00  0.00           H  
+ATOM     43  CD2 LEU   201      42.612  41.790  32.919  1.00  0.00           C  
+ATOM     44 HD21 LEU   201      43.189  40.972  33.350  1.00  0.00           H  
+ATOM     45 HD22 LEU   201      42.697  41.762  31.833  1.00  0.00           H  
+ATOM     46 HD23 LEU   201      42.997  42.740  33.289  1.00  0.00           H  
+ATOM     47  C   LEU   201      40.979  40.272  36.891  1.00  0.00           C  
+ATOM     48  O   LEU   201      42.089  40.361  37.458  1.00  0.00           O  
+ATOM     49  OXT LEU   201      39.891  40.190  37.498  1.00  0.00           O  
+TER      50      LEU   201 
+END   

dummy_struct.xyz

@@ -1,20 +1,17 @@
-18
-
-C         1.1681569 -0.2550550  0.8756595 
-C         1.3484628  0.1965789 -0.5826021 
-C        -0.1630149  0.2550556  1.4507918 
-C        -1.3484630 -0.1965791  0.5826038 
-C        -1.1681567  0.2550548 -0.8756576 
-C         0.1630149 -0.2550556 -1.4507899 
-H        -1.4440620 -1.2992544  0.6239080 
-H        -2.2954881  0.2017985  0.9917659 
-H        -0.2922653 -0.1016823  2.4895446 
-H        -0.1446071  1.3607175  1.5133326 
-H         1.4440620  1.2992544 -0.6239060 
-H         2.2954880 -0.2017985 -0.9917640 
-H         2.0131366  0.1016836  1.4934968 
-H         1.2010813 -1.3607168  0.9319297 
-H         0.2922653  0.1016827 -2.4895433 
-H         0.1446071 -1.3607176 -1.5133316 
-H        -2.0131365 -0.1016835 -1.4934950 
-H        -1.2010813  1.3607168 -0.9319277 
+15
+test structure for adenine
+N         -3.34715        2.34204       -0.00000
+C         -3.23761        0.97384        0.00000
+C         -2.24176        3.14648        0.00000
+C         -0.99763        2.52620       -0.00000
+C         -0.91520        1.17525       -0.00000
+N         -2.00778        0.37518        0.00000
+N          0.23656        3.06079        0.00000
+C          1.05321        1.97301        0.00000
+N          0.36885        0.80238        0.00000
+N         -2.37477        4.55418        0.00000
+H         -4.13074        0.36437       -0.00000
+H          2.13330        2.03626       -0.00000
+H         -3.31031        4.98544       -0.00000
+H         -1.54403        5.16377       -0.00000
+H          0.75715       -0.16672       -0.00000

qm_atom_features.csv

@@ -1,19 +1,16 @@
-,atom type
-0,6
-1,6
-2,6
-3,6
-4,6
-5,6
-6,1
-7,1
-8,1
-9,1
-10,1
-11,1
-12,1
-13,1
-14,1
-15,1
-16,1
-17,1
+,atom type,Charge,Polarizability
+0,7,-0.2927107,7.9022415
+1,6,0.1330993,8.2041169
+2,6,0.162086,8.1111222
+3,6,0.0412075,8.3483554
+4,6,0.144987,8.0719558
+5,7,-0.3111943,7.9682014
+6,7,-0.2861547,7.8825044
+7,6,0.0893093,8.1131044
+8,7,-0.0936049,7.1331855
+9,7,-0.2467183,7.6358162
+10,1,0.0567793,2.3388726
+11,1,0.0466292,2.4035132
+12,1,0.1834568,1.7122248
+13,1,0.1898361,1.6868968
+14,1,0.1829925,1.7143291