3D Molecule on 2D

3D Molecule on 2D Plugin for MoleditPy

CI Test Coverage GitHub tag GitHub Downloads

Repo: https://github.com/HiroYokoyama/moleditpy_3d-molecule-on-2d/

This plugin enhances MoleditPy with integrated 3D depth cues, interactive 3D rotation within the 2D view, and 3D-aware data export.

Plugin Preview Plugin Preview 2 With Reaction Sketcher

Features

Integrated 3D Depth Cues

  • Atoms and bonds are automatically colored with a “distance fade” (brighter/whiter for distant parts) to provide a clear sense of 3D depth.
  • Adjustable depth cue strength in the settings.
  • Depth cues adapt to both individual molecules and the entire scene.

Interactive 3D Rotation

  • Rotate molecules in 3D directly on the 2D canvas.
  • Molecule-wise Rotation: Drag an atom or bond to rotate that specific molecule around its center of gravity.
  • Integrated with the main application’s tool system for mode exclusivity.

Smart 3D Synchronization (Clean Up 3D)

  • Synchronize your 2D layout back to the 3D geometry.
  • Automatically detects if the molecule’s topology has changed.
  • If only positions moved, it performs a fast alignment.
  • If bonds or atoms were edited, it triggers a fresh 3D coordinate generation.

3D-Aware Mol Export

  • The standard Mol file export is enhanced to include the 3D Z-coordinates.
  • Exported .mol files preserve the 3D structure seen in MoleditPy, making them compatible with other 3D modeling and analysis software.

Installation

  1. Copy 3d_molecule_on_2d.py into your MoleditPy plugins directory.
  2. Restart MoleditPy.
  3. Access the tools via the plugin toolbar.

Usage

  • Rotate 3D: Activate the tool and drag any atom/bond to rotate the molecule.
  • Clean Up 3D: Click to snap the 2D layout to the underlying 3D structure.
  • Settings: Adjust the fade strength and 3D projection scale.

Implementation Details

  • Monkey Patching: The plugin non-destructively patches AtomItem and BondItem paint methods and the MolecularData export logic.
  • Z-Coord Persistence: Z-coordinates are stored as part of the plugin state and restored across sessions.
  • RDKit Integration: Uses RDKit for 3D coordinate generation and Mol block handling.

Licensing scope

First-party code in this migration is LGPL-3.0-or-later. See LICENSE, COPYING and dependency/provenance terms. Third-party components and historical releases retain their own terms.