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 this repository, you must cite the following works:

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.

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