Key Capabilities

• Interactive 3D Structure Viewer (``py3Dmol`` & WebGL): Encapsulated in the ModelViewer class (orochi.view.model_viewer), this component enables high-performance WebGL rendering of atomic lattices, unit cell boundaries, bonds, and coordination envelopes. Inheriting directly from orochi.base.core.OrochiBase, the viewer dynamically syncs with structural parameters defined in orochi.phase, allowing immediate visual updates in Gradio web interfaces when parameters are adjusted.

• Dynamic Total Scattering & PDF Plots (``Plotly``): Through orochi.view.pdf, users can render interactive, responsive Plotly figures comparing observed and simulated data (G(r), F(Q), S(Q)). Features include real-time fit difference profiles ($Delta G(r)$), synchronized zoom and hover tooltips, and customizable plotting layouts optimized for both standalone notebooks and web GUIs.

• Optimization & Bayesian Parameter Landscape Diagnostics (``Optuna`` & ``Plotly``): Diagnostic plots for Bayesian global optimization and least-squares refinement, including hyperparameter importance rankings, slice diagrams, and optimization objective histories (orochi.view.optuna.plots).

Package Status & Future Roadmap

Installation

Using pip:

pip install orochi.view

From source:

git clone https://github.com/Tominaka-Laboratory/orochi.view.git
cd orochi.view
pip install -e .

To confirm the installation was successful, run:

python -c "import orochi.view; print(orochi.view.__version__)"

Quick Start

1. 3D Atomic Structure Visualization with ModelViewer

from orochi.phase import Phase
from orochi.view.model_viewer import ModelViewer

# Load crystallographic structure
phase = Phase()
phase.read_cif("CeO2.cif")

# Render interactive 3D WebGL model
viewer = ModelViewer()
html_output = viewer.view_model(phase)

2. Interactive PDF Comparison with Plotly

from orochi.view.pdf import interactive

# Plot experimental vs. simulated G(r)
fig = interactive.plot(
    r_obs, g_obs,
    r_sim, g_sim,
    title="CeO2 PDF Refinement"
)
fig.show()

Support and Contribute

The orochi.view project welcomes your expertise and enthusiasm! If you see a bug or want to request a feature, please report it as an issue and/or submit a fix as a PR.

Before contributing, please read our Code of Conduct.

License

This project is licensed under the GNU General Public License v3.0 (GPLv3). See the LICENSE.rst file for details.

Citation

If you use Orochi in your research, please cite:

@article{tominaka2026orochi,
  title   = {Orochi: A Physics-Grounded Python Package for Pair Distribution Function Analysis of Crystalline and Low-Dimensional Materials},
  author  = {Tominaka, Satoshi},
  journal = {ChemRxiv},
  year    = {2026},
  url     = {https://chemrxiv.org/doc/d84591ff-85b9-489c-839a-4f7170dcc1c4}
}

Contact

For questions or feedback, please open a GitHub issue or contact Dr. Satoshi Tominaka at tominaka.satoshi@nims.go.jp.