annabossler commited on
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1 Parent(s): 6d4df16

Update app.py

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  1. app.py +11 -80
app.py CHANGED
@@ -159,18 +159,15 @@ def relax_wrapper(structure_file, task_name, steps, fmax, charge, spin, relax_ce
159
  # ==== UI ====
160
  with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
161
  with gr.Tabs():
162
- # -------- HOME TAB --------
163
  with gr.Tab("Home"):
164
  with gr.Row():
165
- # Columna izquierda con acordeones
166
  with gr.Column(scale=1):
167
  gr.Markdown("## Learn more about OrbMol")
168
 
169
  with gr.Accordion("What is OrbMol?", open=False):
170
  gr.Markdown("""
171
  OrbMol is a suite of quantum-accurate machine learning models for molecular predictions. Built on the **Orb-v3 architecture**, OrbMol provides fast and accurate calculations of energies, forces, and molecular properties at the level of advanced quantum chemistry methods.
172
-
173
- The models combine the transferability of universal potentials with quantum-level accuracy, making them suitable for a wide range of applications in chemistry, materials science, and drug discovery.
174
  """)
175
 
176
  with gr.Accordion("Available Models", open=False):
@@ -186,57 +183,21 @@ The models combine the transferability of universal potentials with quantum-leve
186
  **OMat**
187
  - **Training dataset**: OMat24 (>100M inorganic calculations, from Materials Project, Alexandria, and far-from-equilibrium samples)
188
  - **Level of theory**: PBE/PBE+U with Materials Project settings; VASP 54 pseudopotentials; no dispersion
189
- - **Inputs**: No support for spin and charge. Spin polarization included but magnetic state cannot be selected
190
  - **Applications**: inorganic discovery, photovoltaics, alloys, superconductors, electronic/optical materials
191
- - **Caveats**: magnetic effects may be incompletely captured
192
  """)
193
 
194
  with gr.Accordion("Supported File Formats", open=False):
195
  gr.Markdown("""
196
- OrbMol supports the following molecular structure formats:
197
- - `.xyz` - XYZ coordinate files
198
- - `.pdb` - Protein Data Bank format
199
- - `.cif` - Crystallographic Information File
200
- - `.traj` - ASE trajectory format
201
- - `.mol` - MDL Molfile
202
- - `.sdf` - Structure Data File
203
-
204
- All formats are automatically converted internally for processing.
205
- """)
206
-
207
- with gr.Accordion("How to Use", open=False):
208
- gr.Markdown("""
209
- **Single Point Energy**: Upload a molecular structure and select a model to calculate energies and forces.
210
-
211
- **Molecular Dynamics**: Run time-dependent simulations to observe molecular behavior at different temperatures and conditions.
212
-
213
- **Relaxation/Optimization**: Find the minimum-energy configuration of your molecular structure.
214
-
215
- Each tab provides specific parameters you can adjust to customize your calculations.
216
- """)
217
-
218
- with gr.Accordion("Technical Foundation", open=False):
219
- gr.Markdown("""
220
- All models are based on the **Orb-v3 architecture**, the latest generation of Orb universal interatomic potentials.
221
-
222
- Key features:
223
- - Graph neural network architecture
224
- - Equivariant message passing
225
- - Multi-task learning across different quantum chemistry methods
226
- - Billions of training examples across diverse chemical spaces
227
- - Sub-kcal/mol accuracy on test sets
228
  """)
229
 
230
  with gr.Accordion("Resources & Support", open=False):
231
  gr.Markdown("""
232
  - [Orb-v3 paper](https://arxiv.org/abs/2504.06231)
233
  - [Orb-Models GitHub repository](https://github.com/orbital-materials/orb-models)
234
- - For issues/questions, please open a GitHub issue or contact the developers
235
-
236
- **Citation**: If you use OrbMol in your research, please cite the Orb-v3 paper and the relevant dataset papers (OMol25/OMat24).
237
  """)
238
 
239
- # Columna derecha con contenido principal
240
  with gr.Column(scale=2):
241
  gr.Image("logo_color_text.png",
242
  show_share_button=False,
@@ -245,47 +206,17 @@ Key features:
245
  show_fullscreen_button=False)
246
 
247
  gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
248
-
249
  gr.Markdown("""
250
- Welcome to the OrbMol demo! This interactive platform allows you to explore the capabilities of our quantum-accurate machine learning models for molecular simulations.
251
-
252
- ## Quick Start
253
-
254
- Use the tabs above to access different functionalities:
255
-
256
- 1. **Single Point Energy**: Calculate energies and forces for a given molecular structure
257
- 2. **Molecular Dynamics**: Run MD simulations using OrbMol-trained potentials
258
- 3. **Relaxation / Optimization**: Optimize molecular structures to their minimum-energy configurations
259
-
260
- Simply upload a molecular structure file in any supported format (`.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`) and select the appropriate model for your system.
261
 
262
- ## Model Selection Guide
 
 
263
 
264
- **Choose OMol/OMol-Direct for:**
265
- - Organic molecules and biomolecules
266
- - Drug-like compounds
267
- - Metal-organic complexes
268
- - Molecules in solution
269
- - Systems where you need to specify charge and spin
270
-
271
- **Choose OMat for:**
272
- - Inorganic crystals and materials
273
- - Periodic systems
274
- - Bulk materials and alloys
275
- - Solid-state compounds
276
-
277
- Explore the accordions on the left to learn more about each model's capabilities, training data, and limitations.
278
- """)
279
-
280
- gr.Markdown("## Try an Example")
281
- gr.Markdown("""
282
- To get started quickly, navigate to any of the calculation tabs above and try one of these examples:
283
- - **Single Point Energy**: Upload a small molecule to see energy and force predictions
284
- - **Molecular Dynamics**: Run a short simulation at 300K to observe thermal motion
285
- - **Relaxation**: Optimize a distorted structure to find its equilibrium geometry
286
  """)
287
 
288
- # -------- SPE -------- (SIN CAMBIOS)
289
  with gr.Tab("Single Point Energy"):
290
  with gr.Row():
291
  with gr.Column(scale=2):
@@ -333,7 +264,7 @@ To get started quickly, navigate to any of the calculation tabs above and try on
333
  [spe_out, spe_status, spe_viewer]
334
  )
335
 
336
- # -------- MD -------- (SIN CAMBIOS)
337
  with gr.Tab("Molecular Dynamics"):
338
  with gr.Row():
339
  with gr.Column(scale=2):
@@ -389,7 +320,7 @@ To get started quickly, navigate to any of the calculation tabs above and try on
389
  [md_status, md_traj, md_log, md_script, md_explain, md_viewer]
390
  )
391
 
392
- # -------- Relax -------- (SIN CAMBIOS)
393
  with gr.Tab("Relaxation / Optimization"):
394
  with gr.Row():
395
  with gr.Column(scale=2):
 
159
  # ==== UI ====
160
  with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
161
  with gr.Tabs():
162
+ # -------- HOME TAB (NUEVA) --------
163
  with gr.Tab("Home"):
164
  with gr.Row():
 
165
  with gr.Column(scale=1):
166
  gr.Markdown("## Learn more about OrbMol")
167
 
168
  with gr.Accordion("What is OrbMol?", open=False):
169
  gr.Markdown("""
170
  OrbMol is a suite of quantum-accurate machine learning models for molecular predictions. Built on the **Orb-v3 architecture**, OrbMol provides fast and accurate calculations of energies, forces, and molecular properties at the level of advanced quantum chemistry methods.
 
 
171
  """)
172
 
173
  with gr.Accordion("Available Models", open=False):
 
183
  **OMat**
184
  - **Training dataset**: OMat24 (>100M inorganic calculations, from Materials Project, Alexandria, and far-from-equilibrium samples)
185
  - **Level of theory**: PBE/PBE+U with Materials Project settings; VASP 54 pseudopotentials; no dispersion
186
+ - **Inputs**: No support for spin and charge
187
  - **Applications**: inorganic discovery, photovoltaics, alloys, superconductors, electronic/optical materials
 
188
  """)
189
 
190
  with gr.Accordion("Supported File Formats", open=False):
191
  gr.Markdown("""
192
+ OrbMol supports: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
193
  """)
194
 
195
  with gr.Accordion("Resources & Support", open=False):
196
  gr.Markdown("""
197
  - [Orb-v3 paper](https://arxiv.org/abs/2504.06231)
198
  - [Orb-Models GitHub repository](https://github.com/orbital-materials/orb-models)
 
 
 
199
  """)
200
 
 
201
  with gr.Column(scale=2):
202
  gr.Image("logo_color_text.png",
203
  show_share_button=False,
 
206
  show_fullscreen_button=False)
207
 
208
  gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
 
209
  gr.Markdown("""
210
+ Welcome to the OrbMol demo! Use the tabs above to access different functionalities:
 
 
 
 
 
 
 
 
 
 
211
 
212
+ 1. **Single Point Energy**: Calculate energies and forces
213
+ 2. **Molecular Dynamics**: Run MD simulations
214
+ 3. **Relaxation / Optimization**: Optimize structures
215
 
216
+ Supported formats: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
217
  """)
218
 
219
+ # -------- SPE (IDÉNTICA A LA QUE FUNCIONABA) --------
220
  with gr.Tab("Single Point Energy"):
221
  with gr.Row():
222
  with gr.Column(scale=2):
 
264
  [spe_out, spe_status, spe_viewer]
265
  )
266
 
267
+ # -------- MD (IDÉNTICA A LA QUE FUNCIONABA) --------
268
  with gr.Tab("Molecular Dynamics"):
269
  with gr.Row():
270
  with gr.Column(scale=2):
 
320
  [md_status, md_traj, md_log, md_script, md_explain, md_viewer]
321
  )
322
 
323
+ # -------- Relax (IDÉNTICA A LA QUE FUNCIONABA) --------
324
  with gr.Tab("Relaxation / Optimization"):
325
  with gr.Row():
326
  with gr.Column(scale=2):