moleditpy_nics_placer

MoleditPy NICS Placer Plugin

A MoleditPy plugin that detects rings in the loaded molecule and places ghost atoms at NICS(0) and NICS(1) probe positions for use in NICS (Nucleus-Independent Chemical Shift) calculations with ORCA or Gaussian.

Features

• Detects all rings (aromatic and non-aromatic) from the 3D structure
• Computes NICS probe positions:
  • NICS(0) — ring centroid (in-plane)
  • NICS(1)± — ±1 Å above and below the ring plane (SVD best-fit plane)

• Interactive 3-state sphere preview in the 3D viewport:

  Colour	Meaning	Interaction
  Yellow (semi-transparent)	Available, not staged	Click → turns red
  Red (semi-transparent)	Staged for placement	Click → turns yellow; Apply → places atom
  Green	Already placed in molecule	Clear All to remove

• Ghost atom symbol selector — choose per project or set a persistent default:

  Symbol	Software
  Bq	Gaussian; also valid in ORCA (default)
  H:	ORCA native ghost atom notation

• Table view with per-ring status (size, aromaticity, placed/staged count)
• Helper buttons: Stage NICS(0) / Stage NICS(1)± for selected rings, Place All, Clear All, Refresh
• Auto-refresh — when the molecule changes (load, undo/redo), rings and spheres update automatically
• Compatible with ORCA Input Generator Pro and Gaussian Input Generator Neo via the shared custom_symbol atom property

Workflow

1. Load a molecule with 3D coordinates in MoleditPy.
2. Open 3D Edit → NICS Placer…
3. Yellow spheres appear at all NICS(0), NICS(1)+, and NICS(1)− positions for every ring.
4. Click yellow spheres to stage them (turns red), or use the Stage buttons for bulk selection.
5. Select ghost atom symbol (Bq or H:) from the combo box.
6. Press Apply (place red Bq) to insert ghost atoms at all staged positions.
7. Open ORCA Input Generator Pro or Gaussian Input Generator Neo — ghost labels appear automatically in the coordinate block.
8. Run NICS calculation.

Settings & Persistence

Plugin setting (settings.json)

The selected ghost atom symbol is saved to nics_placer/settings.json whenever it is changed. This is the user default — it persists across all sessions and documents.

Project setting (.pmeprj project file)

When a project is saved, the current ghost symbol and all placed ghost atom indices are stored in the project file. Loading a project restores both, overriding the plugin default for that session. Closing the project (File → New) reverts to the plugin default from settings.json.

Installation

Copy the nics_placer/ folder into your MoleditPy plugins directory:

moleditpy_nics_placer/
    nics_placer/
        __init__.py      ← plugin entry point
        dialog.py        ← NicsPlacerDialog (PyQt6 + PyVista)
        nics_math.py     ← pure numpy ring geometry
        settings.json    ← auto-created on first symbol change (gitignored)

Requirements

• MoleditPy ≥ v3 (V3 plugin API)
• PyQt6
• RDKit
• PyVista
• numpy

Running Tests

The test suite runs fully headless (no Qt, RDKit, or PyVista required):

cd moleditpy_nics_placer
python -m pytest tests/ -v

Test file	Coverage
test_nics_math.py	Pure geometry: centroid, SVD normal, NICS point computation, ring extraction
test_plugin_integration.py	Plugin contract: save/load/reset handlers, ghost label persistence, symbol persistence

Implementation Notes

Ring plane (best-fit plane)

The ring normal is computed via SVD of the mean-centred atom positions:

centered = positions - mean(positions)
U, S, Vt = SVD(centered)
normal = Vt[-1]       # last singular vector = direction of minimum variance
normal /= ‖normal‖

This gives the least-squares best-fit plane normal, robust for all planar and near-planar rings.

Ghost atom convention

Ghost atoms are rdkit.Chem.Atom(0) (atomic number 0, dummy atom) with SetProp("custom_symbol", symbol). The custom_symbol property is the shared convention used by MoleditPy’s XYZ Editor, ORCA Input Generator Pro, and Gaussian Input Generator Neo.

Version

1.0.0 — HiroYokoyama

This site is open source. Improve this page.