smiles2svg

Script to make vector images of 2D-molecules from their SMILES code.

Requirements

numpy==1.24.3
rdkit==2023.3.2
svgwrite==1.4.3

Basic usage

smiles2svg -s 'Cn1cnc2n(C)c(=O)n(C)c(=O)c12' 

Creates a SVG image with the default parameters and produces the following image

A plain text file with all the SMILES codes written as individual lines can also be used as input. In this case the script with generate a SVG files for each individual SMILES code in the file.

smiles2svg -f 'smiles.txt'

An example file can be found in the example forlder with several SMILES codes.

Drawing options

Run

smiles2svg.py -h

to see help:

-h, --help            show this help message and exit
-s SMILES, --smiles SMILES
                      SMILES string of the mol
-f SMILES_FILE, --smiles_file SMILES_FILE
                      Name of the file with all the SMILES
                      codes
-n NAME, --name NAME  Name for the SVG image
--style {plain,names_hetero,names_all}
                      Select the style for the atoms.
                      (default='plain')
--color COLOR         Select a color for all the molecule.
                      If 'default', colors will the have
                      different colors depending on the
                      element. (default='default')

Examples

smiles2svg.py -s 'Cn1cnc2n(C)c(=O)n(C)c(=O)c12' --style 'names_hetero'

smiles2svg.py -s 'Cn1cnc2n(C)c(=O)n(C)c(=O)c12' --style 'names_hetero' --color '#468BFF'

smiles2svg.py -s 'Cn1cnc2n(C)c(=O)n(C)c(=O)c12' --style 'names_all'

Future features

• Change font
• Add stroke to all atoms
• Addition of Hydrogens in HB-donors
• Addition of LP orbitals