smi2png

Trivial smiles viewer. Uses RDKit to generate a .png depiction, which is sent to eog for viewing.

This is for use at the Linux command line when you want to see a depiction of the smiles in a file.

External dependencies are

• RDKit
• Abseil Python Common Libraries
• Eye of Gnome (eog)

Usage

smiles2png file.smi

converts the first 30 structures in file.smi to png and sends to eog.

smiles2png -

converts the first 30 structures in stdin to png and sends to eog.

smiles2png --smiles 'CN1C=NC2=C1C(=O)N(C(=O)N2C)C caffeine' --smiles 'c1ccccc1 benzene'

smiles strings are passed from the command line.

Options

• input: Name of smiles file(s) - or use positional arguments (argv)
• smiles: Smiles to be depicted, can be repeated.
• n: Number of molecules to display - default 30.
• f: If specified, skips the first f records in the input.
• align: A smiles that is used for aligning the structures.
• mols_per_row: number of molecules per row (number of columns).
• nrows: number of rows per .png file
• x and -y: dimensions of the .png
• smiles_col: the column in which the smiles is found (def 1)
• id_col: list of columns in which the name is found (def 2)
• sep: the column separator in the input file (def space)
• stem: File name stem for the .png files generated.
• verbose: verbose output
• keep: Do NOT remove the .png files after they are shown in eog.

Note that id_col can be a csv list of columns, so if you want to show columns 2 and 3 from a smiles file together with each structure, add --id_col 2,3.

Note too that input can be read from sys.stdin. So if you wish to view a particular record(s) from a smiles file, that can be done with something like

grep -E '(CHEMBL224048|CHEMBL449036)' somefile.smi | smiles2png <options> --input -

where - is used to signify use of stdin.