fastmolwidget 0.9.2

A PyQt/PySide widget to display crystal structures

fastmolwidget

A PyQt/PySide6 widget to display crystal structures

fastmolwidget is a lightweight, embeddable Qt widget that renders molecular and crystal structures in both 2D projection and 3D OpenGL. It supports anisotropic displacement parameter (ADP) ellipsoids, ball-and-stick diagrams, and plain sphere representations. The 2D backend uses a pure-Python QPainter renderer (no OpenGL required); the 3D backend uses hardware-accelerated OpenGL with sphere and ellipsoid impostors.

Screenshots

2D (QPainter)	3D (OpenGL)
ORTEP-style crystal structure with ADP ellipsoids (2D QPainter backend)	Real-time 3D ball-and-stick view with depth-shaded spheres and cylinder bonds (OpenGL backend)

Features

• ADP ellipsoids at the 50 % probability level
• Ball-and-stick and isotropic sphere
• Real-time 3D rendering via MoleculeWidget3D — sphere impostors and tessellated cylinder bonds in hardware-accelerated OpenGL
• Interactive mouse controls: rotate (left-drag), zoom (right-drag), pan (middle-drag), scroll wheel to resize labels
• Atom and bond selection: single click or Ctrl+click for multi-selection; emits atomClicked / bondClicked Qt signals
• Hover labels: hovering over an atom shows its label; hovering over a bond shows the distance in Ångströms
• Hydrogen visibility toggle
• Atom label display toggle with adjustable font size
• Bond width adjustment via spin box
• Configurable bond color — set programmatically or via the control-bar color picker
• Multiple file formats: CIF, SHELX .res/.ins, and plain XYZ. More to come...
• Embeddable — both MoleculeWidget (2D) and MoleculeWidget3D (3D) are plain QWidget subclasses; drop either into any layout
• Ready-to-use viewers — MoleculeViewerWidget (2D) and MoleculeViewer3DWidget (3D) bundle the renderer with a full control bar
• Common protocol — MoleculeWidgetProtocol lets you write code that works with either widget interchangeably

Supported File Formats

Extension	Format	Notes
.cif	Crystallographic Information File	Reads atoms, unit cell, and ADPs
.res / .ins	SHELXL instruction file	Reads atoms and unit cell via shelxfile
.xyz	Standard XYZ coordinate file	Cartesian coordinates, no cell or ADPs

Installation

# with PySide6 (recommended)
uv add "fastmolwidget[pyside6]"

# or PyQt6
uv add "fastmolwidget[pyqt6]"

# add 3D OpenGL support (optional, requires Qt ≥ 6.7 and pyopenGL installed in the Python environment)
uv add "fastmolwidget[pyside6,gl3d]"

Optional C++ Acceleration (sdm_cpp)

The symmetry-growing step (SDM) has an optional C++ extension that uses pybind11 and OpenMP for a significant speed-up on large structures. The pure-Python fallback is always available.

uv pip install pybind11
uv pip install -e . --no-build-isolation

# macOS: optionally install libomp for multi-threaded acceleration
brew install libomp

Requirements: Python ≥ 3.12, NumPy, gemmi, shelxfile, qtpy, and either PySide6 or PyQt6.

Quick Start

Standalone 2D viewer

from qtpy.QtWidgets import QApplication
from fastmolwidget import MoleculeViewerWidget

app = QApplication([])
viewer = MoleculeViewerWidget()
viewer.load_file("structure.cif")
viewer.show()
app.exec()

Standalone 3D viewer

from qtpy.QtWidgets import QApplication
from fastmolwidget import MoleculeViewer3DWidget

app = QApplication([])
viewer = MoleculeViewer3DWidget()
viewer.load_file("structure.cif")
viewer.show()
app.exec()

Embedding the 3D widget in your own layout

from fastmolwidget import MoleculeWidget3D

mol = MoleculeWidget3D(parent=self)
mol.open_molecule(atoms, cell=cell)
layout.addWidget(mol)

```python
from fastmolwidget import MoleculeWidget, MoleculeLoader

mol = MoleculeWidget(parent=self)
loader = MoleculeLoader(mol)
# The loader recognizes the file format from the extension and populates `mol` accordingly
loader.load_file("structure.cif")

# drop `mol` into any QLayout
layout.addWidget(mol)

Loading a different file at runtime

viewer.load_file("new_structure.res")

Reacting to atom / bond clicks

mol.atomClicked.connect(lambda label: print(f"Clicked atom: {label}"))
mol.bondClicked.connect(lambda a, b: print(f"Clicked bond: {a}–{b}"))

Mouse Controls

Action	Effect
Left-drag	Rotate the molecule
Right-drag	Zoom in / out
Middle-drag	Pan the view
Middle-click	Recentre the rotation pivot on the clicked atom (3D only)
Alt/Option + Left-click	On systems without a middle mouse button, Alt/Option + Left-click recentres the rotation pivot on the clicked atom (same as Middle-click)
Scroll wheel	Increase / decrease label font size
Left-click	Select a single atom or bond
Ctrl + Left-click	Toggle multi-selection
Hover over atom	Show the atom label (enlarged when persistent labels are on)
Hover over bond	Show the bond distance (Å) in a rounded tooltip near the cursor

Keyboard Shortcuts

The widget must have keyboard focus (click on it once) for these shortcuts to work.

Key	Effect
F1	Align the view so that the reciprocal axis a* points towards the viewer (requires a unit cell)
F2	Align the view so that the reciprocal axis b* points towards the viewer (requires a unit cell)
F3	Align the view so that the reciprocal axis c* points towards the viewer (requires a unit cell)

Note: The F-key shortcuts are available in both the 2D (MoleculeWidget) and 3D (MoleculeWidget3D) renderers. They have no effect when no unit cell is loaded (e.g. plain XYZ files).

Control Bar Options

MoleculeViewerWidget (2D) and MoleculeViewer3DWidget (3D)

Both viewers expose the same two-row control bar:

Row 1 — structure toggles

Control	Default	Description
Open File…	—	Opens a file dialog to load a structure file
Grow	✗	Expand the asymmetric unit to complete molecules (mutually exclusive with Pack Unit Cell)
Pack Unit Cell	✗	Generate all symmetry-equivalent positions within one unit cell (mutually exclusive with Grow)
Show ADP	✓	Toggle ORTEP ellipsoid / isotropic sphere rendering
Show Labels	✗	Toggle non-hydrogen atom labels
Hide Hydrogens	✗	When checked, hydrogen atoms and their bonds are hidden

Row 2 — bond and view controls

Control	Default	Description
Bond Width	3	Stroke width / cylinder radius for bonds (2D: 1–15, 3D: 0–15)
Bond Color	—	Opens a colour picker to change the default bond colour
Reset Rotation Center	—	Restores the rotation pivot to the molecule's geometric centre (both 2D and 3D)
Save Image…	—	Opens a file-save dialog and writes the current view to a PNG or JPEG file

When Pack Unit Cell is active, a unit-cell axis indicator (a = red, b = green, c = blue) is drawn in the bottom-left corner of the widget and rotates with the view.

API Overview

MoleculeViewer3DWidget(parent=None)

A self-contained 3D viewer combining MoleculeWidget3D with the control bar.

• load_file(path) — load a structure file (format auto-detected from extension: .cif, .res, .ins, .xyz)
• grow() — expand the asymmetric unit to complete molecules using crystal symmetry; deactivates Pack Unit Cell if active; no-op for XYZ files or when no file is loaded
• set_bond_color(color) — set the default color for non-selected bonds
• render_widget — read-only property exposing the underlying MoleculeWidget3D

MoleculeWidget3D(parent=None)

Hardware-accelerated OpenGL renderer. A QOpenGLWidget (Qt ≥ 6) or QWidget subclass that can be dropped into any layout.

Rendering technique

Primitive	Technique
Atoms	Billboard sphere impostors — each atom is a quad; the fragment shader ray-casts a sphere and writes corrected depth values
ADP ellipsoids	Impostor quads — the fragment shader ray-casts an exact ellipsoid using the inverse U_cart tensor passed as a mat3 uniform
Bonds	Tessellated cylinder mesh (8-segment, 4-segment for angular style) built on the CPU and uploaded as a single VBO
Labels	QPainter overlay drawn after the OpenGL pass

All GLSL shaders target #version 120 (OpenGL 2.1 / GLSL 1.20) for maximum hardware compatibility.

Qt Signals

Signal	Signature	Emitted when
atomClicked	(label: str)	The user clicks on an atom
bondClicked	(label1: str, label2: str)	The user clicks on a bond

Data Methods

• open_molecule(atoms, cell=None, keep_view=False)
  Load a new set of atoms and redraw.

  • atoms — list of Atomtuple(label, type, x, y, z, part, adp=None) in Cartesian coordinates (Å); embed adp=(U11,U22,U33,U23,U13,U12) directly in the tuple for anisotropic atoms
  • cell — optional (a, b, c, α, β, γ) tuple; required for ADP rendering
  • keep_view — preserve current zoom, rotation, and pan when True

• grow_molecule(atoms, cell=None)
  Replace atoms while preserving the view. Equivalent to open_molecule(..., keep_view=True).

• clear()
  Remove all atoms and bonds.

Display Methods

• show_adps(value: bool) — toggle ADP ellipsoid rendering; falls back to isotropic spheres when False
• show_labels(value: bool) — show / hide atom labels
• show_hydrogens(value: bool) — show / hide hydrogen atoms and bonds
• set_visible_parts(parts: set[int] | None) — filter by disorder part; None shows all atoms; an empty set hides all atoms; e.g. set_visible_parts({0, 1}) shows only Part 0 and Part 1
• set_bond_width(width: int) — set cylinder radius scale (1–15)
• set_bond_color(color) — set the default color for non-selected bonds; accepts QColor, hex string, or an RGB tuple
• set_labels_visible(visible: bool) — alias for show_labels
• setLabelFont(font_size: int) — set label font pixel size
• set_background_color(color: QColor) — change background colour
• reset_view() — reset zoom, rotation, and pan to defaults
• align_best_view() — rotate the structure so the widest face points towards the viewer (PCA on visible atoms; H/D excluded when hydrogen visibility is off)
• reset_rotation_center() — restore the rotation pivot to the molecule's geometric center (undoes a middle-click recentring)
• save_image(filename: Path, image_scale: float = 1.5) — capture the current OpenGL framebuffer and write it to a PNG or JPEG file (format inferred from the file extension). The captured image is then scaled by image_scale using smooth bilinear filtering before saving. Labels appear in the saved image if they are active at the time of the call.

Example — feeding atom data directly to MoleculeWidget3D

from fastmolwidget import MoleculeWidget3D, Atomtuple

mol = MoleculeWidget3D(parent=self)

# Embed ADP tensors directly in each Atomtuple (None = isotropic / no ADP)
atoms = [
    Atomtuple(label="C1", type="C", x=0.0,  y=0.0,  z=0.0,  part=0,
              adp=(0.02, 0.02, 0.02, 0.0, 0.0, 0.0)),
    Atomtuple(label="O1", type="O", x=1.22, y=0.0,  z=0.0,  part=0,
              adp=(0.03, 0.03, 0.03, 0.0, 0.0, 0.0)),
    Atomtuple(label="H1", type="H", x=-0.5, y=0.94, z=0.0,  part=0),
]

cell = (5.0, 5.0, 5.0, 90.0, 90.0, 90.0)

mol.open_molecule(atoms=atoms, cell=cell)
mol.atomClicked.connect(lambda label: print(f"Selected: {label}"))

layout.addWidget(mol)

MoleculeViewerWidget(parent=None)

A self-contained 2D viewer combining MoleculeWidget with the control bar.

• load_file(path) — load a structure file (format auto-detected from extension)
• grow() — expand the asymmetric unit to complete molecules using crystal symmetry; deactivates Pack Unit Cell if active; no-op for XYZ files or when no file is loaded
• set_bond_color(color) — set the default color for non-selected bonds
• render_widget — read-only property exposing the underlying MoleculeWidget

MoleculeWidget(parent=None)

The 2D QPainter renderer. A plain QWidget subclass you can drop into any layout.

Qt Signals

Signal	Signature	Emitted when
atomClicked	(label: str)	The user clicks on an atom; label is the atom name (e.g. "C1")
bondClicked	(label1: str, label2: str)	The user clicks on a bond; both atom labels are passed

Data Methods

• open_molecule(atoms, cell=None, keep_view=False)
  Load a new set of atoms and reset (or optionally preserve) the view.

  • atoms — list of Atomtuple(label, type, x, y, z, part, adp=None) in Cartesian coordinates (Å); embed adp=(U11,U22,U33,U23,U13,U12) for anisotropic atoms
  • cell — optional (a, b, c, α, β, γ) tuple of unit-cell parameters (Å / °); required for ADP rendering
  • keep_view — when True, the current zoom, pan, and rotation are preserved (useful for live updates)

• grow_molecule(atoms, cell=None)
  Replace the atom set while always preserving the current view.
  Equivalent to calling open_molecule(..., keep_view=True).

• clear()
  Remove all atoms and bonds from the display.

Display Methods

• show_adps(value: bool)
  Toggle ORTEP-style ADP ellipsoid rendering. When False, atoms are drawn as isotropic spheres.

• show_labels(value: bool)
  Show or hide non-hydrogen atom labels.

• show_hydrogens(value: bool)
  Show or hide hydrogen / deuterium atoms and their bonds.

• set_visible_parts(parts: set[int] | None)
  Filter by disorder part number. None (the default) shows all parts. Pass a set of integers to restrict rendering to those parts; an empty set hides every atom. Example: widget.set_visible_parts({0, 1}) shows Part 0 and Part 1.

• set_bond_width(width: int)
  Set the stroke width for bonds in pixels (valid range: 1–15).

• set_bond_color(color)
  Set the default color for non-selected bonds. Accepts QColor, hex string (e.g. "#d1812a"), or an RGB tuple (floats in [0..1] or integers in [0..255]).

• set_labels_visible(visible: bool)
  Alias for show_labels.

• setLabelFont(font_size: int)
  Set the pixel size used for atom labels.

• set_background_color(color: QColor)
  Change the widget background color.

• reset_view()
  Reset zoom, pan, and rotation to their defaults.

• align_best_view()
  Rotate the structure to the orientation that maximises atom visibility for screenshots. Uses PCA on the currently visible atom positions: the thinnest axis of the atom cloud points towards the camera so the widest face faces the viewer. Hydrogen / deuterium atoms are excluded when their visibility is turned off.

• save_image(filename: Path, image_scale: float = 1.5)
  Render the current structure view to an image file.
  The widget is redrawn off-screen at widget_size × image_scale; the result is saved as PNG or JPEG (format inferred from the file extension).
  Labels appear in the saved image if they are active at the time of the call.

Example — feeding atom data directly to MoleculeWidget (2D)

from fastmolwidget import MoleculeWidget, Atomtuple

mol = MoleculeWidget(parent=self)

# Embed ADP tensors directly in each Atomtuple (omit or use None = isotropic)
atoms = [
    Atomtuple(label="C1", type="C", x=0.0,  y=0.0,  z=0.0,  part=0,
              adp=(0.02, 0.02, 0.02, 0.0, 0.0, 0.0)),
    Atomtuple(label="O1", type="O", x=1.22, y=0.0,  z=0.0,  part=0,
              adp=(0.03, 0.03, 0.03, 0.0, 0.0, 0.0)),
    Atomtuple(label="H1", type="H", x=-0.5, y=0.94, z=0.0,  part=0),
]

cell = (5.0, 5.0, 5.0, 90.0, 90.0, 90.0)  # optional

mol.open_molecule(atoms=atoms, cell=cell)
mol.atomClicked.connect(lambda label: print(f"Selected: {label}"))

layout.addWidget(mol)

Advanced API

MoleculeWidgetProtocol

The core rendering interface is defined by MoleculeWidgetProtocol. Both MoleculeWidget (2D) and MoleculeWidget3D (3D) satisfy this protocol, making them drop-in replacements for each other.

from fastmolwidget.molecule_base import MoleculeWidgetProtocol
from fastmolwidget import MoleculeWidget3D

def do_something_with_widget(widget: MoleculeWidgetProtocol):
    ...

3D Application Example

import sys
from qtpy.QtWidgets import QApplication
from fastmolwidget import MoleculeViewer3DWidget

app = QApplication(sys.argv)
viewer = MoleculeViewer3DWidget()
viewer.load_file("examples/test_molecule.res")
viewer.show()
sys.exit(app.exec_())

3D Generic Widget Example

import sys
from qtpy.QtWidgets import QApplication, QMainWindow, QVBoxLayout, QWidget
from fastmolwidget import MoleculeWidget3D
from fastmolwidget.loader import MoleculeLoader

app = QApplication(sys.argv)

main_window = QMainWindow()
central_widget = QWidget(main_window)
layout = QVBoxLayout(central_widget)

# Create and configure the 3D molecule widget
molecule_widget = MoleculeWidget3D()
molecule_widget.set_bond_color("#FF5733")  # Example: set bond color to a shade of orange

# Load a molecule file (CIF, RES, or XYZ format)
loader = MoleculeLoader(molecule_widget)
loader.load_file("examples/test_molecule.res")

layout.addWidget(molecule_widget)
main_window.setCentralWidget(central_widget)

main_window.show()
sys.exit(app.exec_())

Running the Examples

To run the provided examples, you can use the following commands:

# 2D Viewer example
python -m fastmolwidget.examples.viewer_2d_example

# 3D Viewer example
python -m fastmolwidget.examples.viewer_3d_example

# Generic 3D Widget example
python -m fastmolwidget.examples.generic_3d_widget_example