xyz2svg

Lightweight script to make vector images of molecules

Requirements

• python>=3.6
• briling/v or something capable of printing atom positions and connectivity

Basic usage

v mol/caffeine.xyz | ./mol2svg.py > caffeine.svg

Open an xyz file with v, rotate the molecule as you like and press p, then x to exit

Input file modification

For a water dimer

v mol/kj-H2O_1--H3O+.xyz > input/kj-H2O_1--H3O+.inp

prints

atom   8   -1.1697501   -0.1527130    0.0202511
atom   1   -1.8639331    0.4812310   -0.1588469
atom   1   -1.6335311   -0.9640680    0.2263131
atom   8    1.1960949    0.3707430   -0.0773079
atom   1    0.2351029    0.2036530   -0.0496909
atom   1    1.6046709    0.2360230    0.7985351
atom   1    1.6313459   -0.1748690   -0.7592539
bond   1   2
bond   1   3
bond   4   5
bond   4   6
bond   4   7

This file contains atomic numbers and coordinates in Å and list of bonds (base 1). We can add a hydrogen bond between atoms 1–5:

bond 1 5 -1

(see input/kj-H2O_1--H3O+.inp). Then

./mol2svg.py < input/kj-H2O_1--H3O+.inp > figures/kj-H2O_1--H3O+.svg

gives

One can also add (positive or negative) bond orders (input/caffeine_v2.inp):

Drawing options

Run

./mol2svg.py --help

to get help:

  --num                                                 add atom numbers
  --canvas-size CANVAS_SIZE                             basic canvas size (default 80)
  -wa ATOM_BORDER, --atom-border ATOM_BORDER            atom border width (default 5.0)
  -wb BOND_WIDTH, --bond-width BOND_WIDTH               bond width (default 5.0)
  -db BOND_DISTANCE, --bond-distance BOND_DISTANCE      line distance in multiple bonds (default 0.05)
  -rs ATOM_SIZE, --atom_size ATOM_SIZE                  scaling factor for atom radii
  -r%d ATOM_%d_RADIUS                                   sets basic radius for a specific element (in Å)
  -g, --gradient                                        fill atoms with radial gradients (pseudo-3D mode)

The same caffeine with options:

./mol2svg.py -rs 3.5 -wa 10 -wb 10 -db 0.1 < input/caffeine_v2.inp > figures/caffeine_v3.svg

@iribirii's pseudo-3D mode:

./mol2svg.py -rs 3.5 -wb 10 -g < input/caffeine.inp > figures/caffeine_v4.svg

Extended input

Add values to atoms, e.g.

label 1     0.009

to add them as text:

./mol2svg.py < input/C3-7-6-7_v2.inp > figures/C3-7-6-7_v2.svg

Add ghost atom coordinates and corresponding values, e.g.

value   4.3721492    1.2190677   -0.9878959    0.009

to add circles representing them:

./mol2svg.py -rs 2.5  --value-gradient '#00FF00' '#FF0000' < input/C3-7-6-7_v3.inp > figures/C3-7-6-7_v3.svg