smiles2svg

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

Requirements

CairoSVG
numpy
rdkit
svgwrite

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 (default: none)
  -f SMILES_FILE, --smiles_file SMILES_FILE
                        Name of the file with all the SMILES codes (default: none)
  -n NAME, --name NAME  Name for the SVG (and PNG) image. Only available for 1 SMILES code, not for list of SMILES.
                        (default: SMILES)
  --style {plain,names_hetero,names_all,stroke}
                        Select the style for the atoms. (default: plain)
  --color COLOR         Select a color for all the molecule. If 'default', atoms will have different colors depending on
                        the element. (default: default)
  --png                 Saves the figure in png format as well. (default: False)
  --png_width PNG_WIDTH
                        Select the image width in pixels. (default: 900)
  --font FONT           Select the font for the atomic symbols. (default: Calibri)
  --bond_color BOND_COLOR
                        Select the color for the bonds format "#RRGGBB". (default: #717171)
  --add_hydrogens       Adds Hydrogen atoms to the HB-Donors. (default: False)

Examples

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

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'

Hydrogen addition

It is also possible to add the H atoms to the hetero atoms that needed it using the --add_hydrogens option

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

Future features

• Select font
• Center text properly
• Save as PNG
• Add option to custom name
• Add option to draw stroke to all atoms
• Add option to draw the bonds with a color gradient between the atoms
• Addition of Hydrogens in HB-donors
• Addition of LP orbitals