Lightweight script to make vector images of molecules
python>=3.6- briling/v or something capable of printing atom positions and connectivity
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
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):
Run
./mol2svg.py --help
to get help:
--num add atom numbers
--elements add element symbols
--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)
--fog enable fog for depth perspective
--fog-strength FOG_STRENGTH fog strength (default 0.8, between 0.0 and 1.0)
--light-hydrogen use a lighter color for H
--hide-H hide C–H hydrogens (optionally specifying 1-indexed atom indices to keep, e.g. --hide-H 5 12)
--cpk use CPK coloring scheme
-fs FONT_SIZE, --font-size FONT_SIZE font size (default 24)
-fn FONT_NAME, --font-name FONT_NAME font name (default monospace)
--bond-color BOND_COLOR bond line color (default black - hex)
--atom-stroke-color ATOM_STROKE_COLOR atom stroke color (default black - hex)
--text-stroke-color TEXT_STROKE_COLOR text stroke color (default white - hex)
--text-color TEXT_COLOR text fill color (default black - hex)
--text-weight TEXT_WEIGHT text weight (default bold)
--text-style TEXT_STYLE text style (default normal)
--text-stroke-width TEXT_STROKE_WIDTH text stroke width (default 8)
--value-gradient VALUE_GRADIENT VALUE_GRADIENT starting and finishing colors for value gradient (default ["#000000", "#FF0000"]
--value-radius VALUE_RADIUS radius of value gradient circles (default 0.2 Å)
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
./mol2svg.py -rs 3.5 -wb 10 -g < input/caffeine.inp > figures/caffeine_v4.svg
./mol2svg.py -wb 10 --fog --fog-strength 0.8 -wa 4 < input/C60-Ih.inp > figures/C60-Ih.svg
- currently incompatible with gradiented 3D mode
./mol2svg.py -wb 10 --fog --fog-strength 0.9 -wa 4 --hide-H
with an optional list of relevant hydrogens to keep:
./mol2svg.py -wb 10 --fog --fog-strength 0.9 -wa 4 --hide-H 68
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