pymovis 0.1.0

Molecular Orbital Visualization System - A Python package for visualizing molecular orbitals from quantum chemistry calculations

PyMovis

PyMovis is a Python package for visualizing molecular orbitals from quantum chemistry calculations. It reads Gaussian formatted checkpoint files, cube files, and PySCF checkpoint files, then renders 3D orbital isosurfaces with PyVista.

Features

• Visualize molecular orbitals from fchk, cube, and chk files
• Select orbitals by index or by labels such as HOMO, LUMO, HOMO-1, LUMO+2
• Render atoms, bonds, and orbital isosurfaces in 3D
• Use automatic camera placement with axis-based views
• Specify camera center and camera axes from atom indices
• Save high-quality images with transparent backgrounds

Installation

From source

git clone https://github.com/YusukeSugenami/pymovis.git
cd pymovis
pip install -e .

Quick Start

Command line

The package installs a pymovis command.

pymovis test.fchk HOMO

Visualize multiple orbitals:

pymovis test.fchk HOMO LUMO

Save to specific output files:

pymovis test.fchk HOMO LUMO -o homo.png lumo.png

Python API

from pymovis import savemo

savemo("test.fchk", ["HOMO", "LUMO"])

Camera Control

PyMoVis supports three levels of camera control.

1. Manual camera settings

Use camera_pos, camera_focal, and camera_up directly:

pymovis test.fchk HOMO \
  -cp 10 10 10 \
  -cf 0 0 0 \
  -cu 0 1 0

2. Automatic axis-based camera

Use --camera_axis to place the camera so the molecule fits in the frame. The current renderer defaults are used for this calculation:

• window size: 1024 x 768
• aspect ratio: 4:3
• vertical field of view: 30 deg

pymovis test.fchk HOMO --camera_axis X

This option looks at the molecule from the negative side of the selected axis and uses the corresponding screen orientation:

• X view: right is +Y, up is +Z
• Y view: right is +X, up is +Z
• Z view: right is +X, up is +Y

You can invert the axis direction with prefix '-' (e.g. -X)

3. Atom-index based camera control

You can define the camera center and axes from atom indices. Indices are 0-based.

Camera center

Use --camera_focal_atoms.

• One atom index: the camera center is that atom position
• Two or more atom indices: the camera center is the centroid of those atoms

Example:

pymovis test.fchk HOMO --camera_focal_atoms 0
pymovis test.fchk HOMO --camera_focal_atoms 0 1 2

Camera axis and up direction

Use --camera_axis_atoms for the camera view axis and --camera_up_atoms for the screen up direction.

• Two atom indices: the axis is the line through those atoms
• Three or more atom indices: the axis is the normal vector of the best-fit plane through those atoms

Example:

pymovis test.fchk HOMO \
  --camera_focal_atoms 0 1 2 \
  --camera_axis_atoms 0 1 \
  --camera_up_atoms 0 1 3

Fixing axis sign with reference vectors

When using three or more atoms to define an axis (via best-fit plane normal), the sign of the resulting axis is ambiguous. You can fix this using --camera_axis_reference and --camera_up_reference.

Each reference option accepts:

• Two atom indices: [idx1 idx2] → the reference vector is coords[idx2] - coords[idx1]
• Three floats: [X Y Z] → the reference vector is given directly

The axis is flipped if its dot product with the reference vector is negative.

Example using atom indices:

pymovis test.fchk HOMO \
  --camera_axis_atoms 0 1 2 \
  --camera_up_atoms 3 4 5 \
  --camera_axis_reference 0 1 \
  --camera_up_reference 2 5

Example using direct coordinates:

pymovis test.fchk HOMO \
  --camera_axis_atoms 0 1 2 \
  --camera_up_atoms 3 4 5 \
  --camera_axis_reference 0 0 1 \
  --camera_up_reference 0 1 0

Camera precedence

The current behavior is:

• If --camera_axis_atoms and --camera_up_atoms are provided, those atom-based axes are used
• Otherwise, if --camera_axis is provided, the axis-based automatic camera is used
• If --camera_focal is provided, it becomes the camera center used by the automatic camera calculation
• If --camera_up is provided, it overrides the final up vector
• If none of the automatic options are provided, manual camera_pos, camera_focal, and camera_up are used as-is

CLI Options

Usage: pymovis input_file [mo ...] [options]

Positional arguments:
  input_file              Gaussian fchk or cube file to visualize
  mo                      MO indices to visualize
                          Use integer indices starting from 0 or labels such as HOMO/LUMO

Options:
  -o, --out               Output file names
  -i, --iso               Isosurface value
  -t, --transparent       Transparent background flag
  -cp, --camera_pos       Manual camera position
  -cf, --camera_focal     Manual camera focal point
  -cu, --camera_up        Manual camera up vector
  -ca, --camera_axis      Automatic camera axis: X / Y / Z. Use '-' prefix (e.g. -X) to invert the axis direction.
  --camera_focal_atoms    Atom indices used to define the camera focal point
  --camera_axis_atoms     Atom indices used to define the camera view axis
  --camera_up_atoms       Atom indices used to define the camera up axis
  --camera_axis_reference Reference vector for camera view axis sign (2 atom indices or 3 coordinates)
  --camera_up_reference   Reference vector for camera up axis sign (2 atom indices or 3 coordinates)
  -womo, --without_mo     Only render molecule structure without MO isosurface

Supported File Formats

Format	Extension	Description
Gaussian Formatted Checkpoint	.fchk	Gaussian MO and geometry data
Cube File	.cube	Cube grid data
PySCF checkpoint	.chk	PySCF SCF checkpoint

Python API

savemo

savemo(
    inp_file,
    mo_index,
    out_name=None,
    iso=0.03,
    camera_pos=None,
    camera_focal=None,
    camera_up=None,
    camera_axis=None,
    camera_focal_atoms=None,
    camera_axis_atoms=None,
    camera_up_atoms=None,
    camera_axis_reference=None,
    camera_up_reference=None,
    transparent_background=True,
    without_mo=False,
)

• inp_file: input file path
• mo_index: list of MO indices or labels
• out_name: output file names
• iso: isosurface value
• camera_axis: automatic axis-based view (X, Y, Z)
• camera_focal_atoms: atom indices for the camera focal point
• camera_axis_atoms: atom indices for the view axis
• camera_up_atoms: atom indices for the up axis
• camera_axis_reference: reference vector for camera axis sign (2 atom indices or 3D coordinates)
• camera_up_reference: reference vector for camera up axis sign (2 atom indices or 3D coordinates)
• transparent_background: save transparent background picture if True
• without_mo: save only molecular structure if True

load_inp

from pymovis import load_inp
mol = load_inp("test.fchk")

Returns a MoleculeData object with parsed geometry, basis, and MO data.

Camera Utilities

If you want to use the camera logic directly, the package exposes helper functions such as:

from pymovis import (
    infer_camera_from_coords,
    infer_axis_camera_fit_from_coords,
    infer_atom_axis_camera_fit_from_coords,
)

Configuration

Default rendering and parser settings are defined in pymovis/settings.py.

Important values include:

• PADDING
• GRID_SETTING
• GRID_SHAPE
• IMAGE_QUALITY
• BACKGROUND_COLOR
• PARSER_ARGS

Example Workflows

Visualize the HOMO from a file

pymovis water.fchk HOMO

Visualize HOMO and LUMO with automatic axis view

pymovis water.fchk HOMO LUMO --camera_axis Z

Visualize with atom-defined camera center and axes

pymovis water.fchk HOMO \
  --camera_focal_atoms 0 1 2 \
  --camera_axis_atoms 0 1 \
  --camera_up_atoms 0 1 3

Save transparent output

pymovis water.fchk HOMO --transparent True