Metadata-Version: 2.4
Name: aseview
Version: 0.0.2
Summary: A molecular viewer for ASE (Atomic Simulation Environment) data
Author-email: Mingi Kang <kangmg@kentech.ac.kr>
License: MIT License
        
        Copyright (c) 2024 Mingi Kang
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/kangmg/aseview
Project-URL: Repository, https://github.com/kangmg/aseview
Project-URL: Documentation, https://kangmg.github.io/aseview
Project-URL: Bug Tracker, https://github.com/kangmg/aseview/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: ase
Requires-Dist: ipywidgets
Requires-Dist: jupyter
Requires-Dist: typer>=0.9.0
Requires-Dist: rich>=13.0.0
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Requires-Dist: black; extra == "dev"
Requires-Dist: flake8; extra == "dev"
Dynamic: license-file

# aseview

Molecular structure viewer for ASE (Atomic Simulation Environment).

[![Docs](https://img.shields.io/badge/docs-online-blue)](https://kangmg.github.io/aseview) &nbsp;·&nbsp; [![DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/kangmg/aseview)

## Installation

```bash
pip install aseview
```

For development:

```bash
git clone https://github.com/kangmg/aseview.git
cd aseview
pip install -e .
```

## CLI Usage

```bash
# Basic usage
aseview molecule.xyz

# View trajectory (all frames)
aseview trajectory.xyz -i :

# View specific frames
aseview trajectory.xyz -i 0:10    # frames 0-9
aseview trajectory.xyz -i -1      # last frame
aseview trajectory.xyz -i ::2     # every 2nd frame

# Specify file format
aseview POSCAR -f vasp

# Custom port
aseview molecule.xyz -p 9000

# Overlay multiple structures
aseview reactant.xyz product.xyz

# Overlay with colormap
aseview trajectory.xyz -v overlay --cmap viridis

# Normal mode visualization with ORCA Hessian
aseview molecule.xyz --hess orca.hess

# Save as HTML file
aseview molecule.xyz -o output.html

# Kill existing server on port
aseview molecule.xyz -k

# Help
aseview -h
```

## SSH Port Forwarding

When running on a remote server (e.g., HPC cluster, Docker container):

```bash
# 1. On remote server
aseview molecule.xyz -p 8080

# 2. On local machine (separate terminal)
ssh -L 8080:localhost:8080 user@remote-server

# 3. Open in local browser
# http://localhost:8080
```

For Docker with custom SSH port:

```bash
# Connect with port forwarding
ssh user@localhost -p 10011 -L 8080:localhost:8080

# Then run aseview inside container
aseview molecule.xyz -p 8080
```

## Jupyter Notebook

### Quick Start

```python
from ase.io import read
from aseview import MolecularViewer

atoms = read('molecule.xyz')
viewer = MolecularViewer(atoms)
viewer.show()
```

### With Trajectory

```python
from ase.io import read
from aseview import MolecularViewer

# Read all frames
trajectory = read('trajectory.xyz', index=':')
viewer = MolecularViewer(trajectory)
viewer.show()
```

### Overlay Multiple Structures

```python
from ase.io import read
from aseview import OverlayViewer

reactant = read('reactant.xyz')
product = read('product.xyz')
viewer = OverlayViewer([reactant, product])
viewer.show()
```

### Overlay with Colormap

```python
from ase.io import read
from aseview import OverlayViewer

trajectory = read('optimization.xyz', index=':')
viewer = OverlayViewer(
    trajectory,
    colorBy='Colormap',
    colormap='viridis'  # viridis, plasma, coolwarm, jet, rainbow, grayscale
)
viewer.show()
```

### Align Molecules (RMSD Minimization)

```python
from ase.io import read
from aseview import OverlayViewer

structures = [read(f'conf{i}.xyz') for i in range(5)]
viewer = OverlayViewer(
    structures,
    alignMolecules=True,  # Kabsch rotation + Hungarian reordering
    colorBy='Molecule'
)
viewer.show()
```

### Normal Mode Visualization

#### From ASE Vibrations

```python
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import BFGS
from ase.vibrations import Vibrations
from aseview import NormalViewer

# Create or load molecule
atoms = Atoms('H2O', positions=[[0, 0, 0], [0.96, 0, 0], [-0.24, 0.93, 0]])
atoms.calc = EMT()

# Optimize structure
opt = BFGS(atoms)
opt.run(fmax=0.01)

# Calculate vibrations
vib = Vibrations(atoms, name='vib')
vib.run()
vib.summary()

# Visualize normal modes
viewer = NormalViewer(atoms, vibrations=vib)
viewer.show()
```

#### From ORCA Hessian File

```python
from ase.io import read
from aseview import NormalViewer

atoms = read('molecule.xyz')
viewer = NormalViewer.from_orca(atoms, 'orca.hess')
viewer.show()
```

Features:
- Mode selector dropdown with frequencies
- Sinusoidal animation of atomic displacements
- Amplitude slider to control displacement magnitude
- Show Vectors toggle to display mode displacement arrows
- Imaginary frequencies (transition states) shown in red

### Using view_molecule Helper

```python
from aseview.jupyter import view_molecule
from ase.io import read

atoms = read('molecule.xyz')
view_molecule(atoms, viewer_type='molecular', height=600)
```

### Custom Settings

```python
from aseview import MolecularViewer

viewer = MolecularViewer(
    atoms,
    style='neon',           # default, cartoon, neon, glossy, metallic, rowan, grey
    bondThreshold=1.2,      # bond detection scale factor
    atomSize=0.5,
    showCell=False,
    backgroundColor='#000000',
    showPolyhedron=True,    # coordination polyhedra (solid-state, CN >= 4)
    polyhedronOpacity=0.25,
    showRings=True,         # ring face highlighting (molecules, 4-8 atom rings)
    ringOpacity=0.35,
)
viewer.show(width='100%', height=800)
```

### Save to HTML

```python
viewer.save_html('output.html')
```

## Viewer Types

| Viewer | Description |
|--------|-------------|
| MolecularViewer | Single structure or trajectory animation |
| NormalViewer | Normal mode vibration visualization |
| OverlayViewer | Compare multiple structures overlaid |

## JavaScript Module

Use aseview in any web page without Python:

```html
<div id="viewer" style="width:100%; height:500px;"></div>

<script src="https://raw.githack.com/kangmg/aseview/main/aseview/static/js/aseview.js"></script>
<script>
    const viewer = new ASEView.MolecularViewer('#viewer');
    viewer.setData({
        symbols: ['O', 'H', 'H'],
        positions: [
            [0.0, 0.0, 0.117],
            [0.0, 0.757, -0.469],
            [0.0, -0.757, -0.469]
        ]
    });
</script>
```

See the [JavaScript Module documentation](https://kangmg.github.io/aseview/js-module/) for full API reference.

## Supported Formats

All formats supported by ASE: xyz, cif, pdb, POSCAR, extxyz, etc.

## License

MIT
