A19grey commited on
Commit
50f8f8c
·
1 Parent(s): 842b0e1

everything seems to work committing until I have more GPU credits

Browse files
Files changed (3) hide show
  1. app.py +3 -3
  2. molecules.json +1 -1
  3. visualization.py +7 -1
app.py CHANGED
@@ -215,7 +215,7 @@ def create_interface():
215
  # Molecule selection controls
216
  molecule_choice = gr.Dropdown(
217
  choices=list(molecules.keys()),
218
- value=list(molecules.keys())[0],
219
  label="Select Molecule",
220
  interactive=True,
221
  allow_custom_value=False
@@ -236,11 +236,11 @@ def create_interface():
236
  # Molecule parameters display
237
  params_display = gr.HTML(
238
  label="Molecule Parameters",
239
- value=format_molecule_params(default_molecule)
240
  )
241
 
242
  with gr.Column(scale=1):
243
- # 3D Molecule Viewer
244
  molecule_viz = MolGallery3D(
245
  columns=1,
246
  height=400, # Reduced height to match other elements
 
215
  # Molecule selection controls
216
  molecule_choice = gr.Dropdown(
217
  choices=list(molecules.keys()),
218
+ value=None, # Start with no selection
219
  label="Select Molecule",
220
  interactive=True,
221
  allow_custom_value=False
 
236
  # Molecule parameters display
237
  params_display = gr.HTML(
238
  label="Molecule Parameters",
239
+ value="<div>Select a molecule to view its parameters</div>"
240
  )
241
 
242
  with gr.Column(scale=1):
243
+ # 3D Molecule Viewer (starts empty)
244
  molecule_viz = MolGallery3D(
245
  columns=1,
246
  height=400, # Reduced height to match other elements
molecules.json CHANGED
@@ -50,7 +50,7 @@
50
  },
51
  "CH4": {
52
  "name": "Methane",
53
- "enabled": 1,
54
  "formula": "CH₄",
55
  "smiles": "C",
56
  "basis": "sto-3g",
 
50
  },
51
  "CH4": {
52
  "name": "Methane",
53
+ "enabled": 0,
54
  "formula": "CH₄",
55
  "smiles": "C",
56
  "basis": "sto-3g",
visualization.py CHANGED
@@ -147,6 +147,7 @@ def create_molecule_viewer(molecule_id: str, scale_factor: float) -> MolGallery3
147
  Create a 3D visualization of the molecule using MolGallery3D and RDKit.
148
  For better visualization, hydrogen atoms are replaced with nitrogen atoms in the display only.
149
  The actual quantum calculations still use the real molecule structure.
 
150
 
151
  Args:
152
  molecule_id: Molecule identifier (e.g., "H2")
@@ -294,7 +295,12 @@ def create_molecule_viewer(molecule_id: str, scale_factor: float) -> MolGallery3
294
  # Final sanitization check
295
  Chem.SanitizeMol(mol)
296
 
297
- return [mol] # Return the molecule as a list as expected by MolGallery3D
 
 
 
 
 
298
 
299
  except Exception as e:
300
  logger.error(f"Failed to generate 3D coordinates: {e}", exc_info=True)
 
147
  Create a 3D visualization of the molecule using MolGallery3D and RDKit.
148
  For better visualization, hydrogen atoms are replaced with nitrogen atoms in the display only.
149
  The actual quantum calculations still use the real molecule structure.
150
+ Atoms are displayed as spheres with explicit bonds between them.
151
 
152
  Args:
153
  molecule_id: Molecule identifier (e.g., "H2")
 
295
  # Final sanitization check
296
  Chem.SanitizeMol(mol)
297
 
298
+ # Set RDKit display properties for ball-and-stick appearance
299
+ for atom in mol.GetAtoms():
300
+ atom.SetProp('molAtomMapNumber', str(atom.GetIdx())) # This helps with atom visibility
301
+
302
+ # Return the molecule as a list as expected by MolGallery3D
303
+ return [mol]
304
 
305
  except Exception as e:
306
  logger.error(f"Failed to generate 3D coordinates: {e}", exc_info=True)