trying to reverse changes
Browse files
app.py
CHANGED
|
@@ -159,6 +159,132 @@ 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 |
# -------- SPE --------
|
| 163 |
with gr.Tab("Single Point Energy"):
|
| 164 |
with gr.Row():
|
|
|
|
| 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):
|
| 177 |
+
gr.Markdown("""
|
| 178 |
+
**OMol** and **OMol-Direct**
|
| 179 |
+
- **Training dataset**: OMol25 (>100M calculations on small molecules, biomolecules, metal complexes, and electrolytes)
|
| 180 |
+
- **Level of theory**: ωB97M-V/def2-TZVPD with non-local dispersion; solvation treated explicitly
|
| 181 |
+
- **Inputs**: total charge & spin multiplicity
|
| 182 |
+
- **Applications**: biology, organic chemistry, protein folding, small-molecule drugs, organic liquids, homogeneous catalysis
|
| 183 |
+
- **Caveats**: trained only on aperiodic systems → periodic/inorganic cases may not work well
|
| 184 |
+
- **Difference**: OMol enforces energy–force consistency; OMol-Direct relaxes this for efficiency
|
| 185 |
+
|
| 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,
|
| 243 |
+
show_download_button=False,
|
| 244 |
+
show_label=False,
|
| 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 --------
|
| 289 |
with gr.Tab("Single Point Energy"):
|
| 290 |
with gr.Row():
|