StericRender: Topographic Steric Mapping with Molecular Visualisation

StericRender computes topographic steric maps and buried volume (%VBur) for any molecular structure, producing publication-quality SVG figures from the command line. It implements the SambVca methodology and uses xyzrender for oriented molecular overlays.

What it produces

• Topographic steric maps (SVG, CSV, NPZ)
• Buried volume (%VBur) with quadrant breakdowns (JSON)
• Oriented molecular overlay SVG via xyzrender
• Multi-frame XYZ batch processing
• Three atomic radii sets: scaled-Bondi (default), Bondi, CSD
• Configurable sphere radius, map radius, mesh spacing, colour palettes

CLI

stericrender complex.xyz \
  --origin 1 \
  --toward 2,3 \
  --flip-z \
  --config pmol \
  --overlay-opacity 0.72 \
  --map-palette sambvca \
  --color-range -3 3 \
  --output-prefix results/complex

The origin atom is automatically excluded from the steric analysis. Use --include-origin to override.

Installation

pip install stericrender
# latest development version:
pip install --upgrade git+https://github.com/JamesOBrien2/StericRender.git

Or with uv:

uv tool install stericrender

From source:

git clone https://github.com/JamesOBrien2/StericRender.git
cd StericRender
pip install -e .

Python API

import numpy as np
from stericrender.io import load_structure_frames, atoms_to_arrays
from stericrender.orientation import orient_positions
from stericrender.radii import radii_for_symbols
from stericrender import compute_buried_volume, compute_steric_map

frames = load_structure_frames("complex.xyz")
symbols, positions = atoms_to_arrays(frames[0].atoms)

# orient: atom 1 at origin, +z toward atom 2
oriented = orient_positions(positions, center_index=0, axis_indices=[1])
selected = [i for i, s in enumerate(symbols) if s != "H" and i != 0]
radii = np.array(radii_for_symbols([symbols[i] for i in selected]))

volume = compute_buried_volume(oriented.positions[selected], radii)
print(f"%VBur = {volume.percent_buried:.2f}")

steric_map = compute_steric_map(oriented.positions[selected], radii)
# steric_map.x, steric_map.y, steric_map.z — topographic grid arrays

Sphere radius and map radius

--sphere-radius scales the analysis sphere; --map-radius sets the display extent independently.

--sphere-radius 2	--map-radius 5

Available flags

--include, --exclude, --include-origin, --frames, --radii, --include-hydrogens, --sphere-radius, --map-radius, --mesh, --config, --overlay-opacity, --overlay-all-atoms, --zoom, --stereo, --stereo-style, --no-contours, --no-colorbar, --no-vbur-label, --show-quadrants, --no-overlay

Gallery

Monocoordinated Ligands

PCy3	NHC-Ni	NHC-Ir

Dicoordinated Ligands

MeDuPhos	Box	Diphosphine

PHOX	Xantphos	Diimine

TADDOL	BINOL	Bipy

Tetracoordinated Ligands

Salen-Mn	Chiral salen-Mn	Zr-ONNO

Zirconocenes

C2 zirconocene	Substituted zirconocene	Cs zirconocene

Acknowledgements

• The SambVca group (Cavallo et al.) — the %VBur methodology and topographic steric map convention that StericRender implements
• morfeus-ml — reference implementation used for validation
• xyzrender by @aligfellow — molecular rendering and SVG overlay
• Jonathan Di Pietro (@jonathandip) — zoom and radius concept, testing

Citation

If you use StericRender in published research, please cite:

James O'Brien, StericRender: Topographic Steric Mapping with Molecular Visualisation, computer software, Zenodo, 2026, https://doi.org/10.5281/zenodo.21475425

Machine-readable citation metadata is available in CITATION.cff. GitHub also provides APA and BibTeX entries through the Cite this repository menu. This permanent DOI covers all StericRender releases and resolves to the latest archived version.

Please also cite the methodological works on which StericRender builds:

1. Laura Falivene, Raffaele Credendino, Albert Poater, Andrea Petta, Luigi Serra, Romina Oliva, Vittorio Scarano, and Luigi Cavallo,
   "SambVca 2. A Web Tool for Analyzing Catalytic Pockets with Topographic Steric Maps,"
   Organometallics 2016, 35, 2286–2293.
   DOI: 10.1021/acs.organomet.6b00371

2. Sílvia Escayola, Naeimeh Bahri-Laleh, and Albert Poater,
   "%VBur index and steric maps: from predictive catalysis to machine learning,"
   Chemical Society Reviews 2024, 53, 853–882.
   DOI: 10.1039/D3CS00725A

3. A. S. Goodfellow and B. N. Nguyen,
   "Graph-Based Internal Coordinate Analysis for Transition State Characterization", Journal of Chemical Theory and Computation 2026.
   DOI: 10.1021/acs.jctc.5c02073