Merge refactored Plantonic Solid module#98
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… structure not as expected previously; Removed ProAffinity legacy folder and fixed adfr path checking.
Handle "no data" error when processing transition matrices since this is not a standard output.
Fixed transition matrix parser; tutorial_6bno test passed!!!
## Overview
This high-level API provides convenient functions for:
- Creating hyperparameter configurations with sensible defaults
- Using preset configurations for common scenarios
- Enabling specific features (ODE, affinity prediction, etc.)
- Managing configurations (save, load, update, validate)
## Quick Start
```python
from ionerdss.model import pdb
# Create and use hyperparameters
params = pdb.create_hyperparameters(
interface_detect_distance_cutoff=0.8,
interface_detect_n_residue_cutoff=5
)
# Build model with configuration
builder = pdb.PDBModelBuilder("1ABC")
system = builder.build_system(
workspace_path="./workspace",
hyperparams=params
)
```
…how to use dynamic docstring (currently used in set_hyperparameters to directly inherit doc string from hyperparameters.py)
Successfully extended the ionerdss ODE module to support any molecular system topology (linear, cyclic, branched, complete graphs) by implementing NetworkX-based naming and integrating graph-based subcomplex generation.
Codecov Report❌ Patch coverage is 📢 Thoughts on this report? Let us know! |
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