whitead/molcloud

Make a bunch of molecules

molcloud

This package draws molecules (or RNA, thanks to @Shunsuke-1994) in a big canvas packed together. See examples below.

Install

Make sure you have pygraphviz installed

pip install molcloud

Usage

molcloud [smiles-file]

and the output will go to cloud.png. You can specify a few things too:

molcloud [smiles-file] --output-file [output-file] --width 10 --node-size 25

To cut the resulting image in some custom shape, use the flag --template (thanks to @doncamilom)!

molcloud [smiles-file] --output-file [output-file] --template [template-file]

Use molcloud --help for complete options. smiles-file should contain smiles, one per line like:

O=C(OC)C=1C=CC2=NC=C(C(=O)OCC)C(NCC(O)C)=C2C1
O=C1C2=NC=CC3=C(OC)C=4OCOC4C(C=5C=C(OC)C(OC)=C(OC)C15)=C23

Adjust width as you add more molecules. The drawing is always square (sorry).

RNA Install

Thanks to @Shunsuke-1994! To install layout RNA, install the extra packages:

pip install molcloud[all]

RNA Usage

rnacloud [fasta-file]

where fasta-file should contain sequence and bracket notations, three lines per 1 sequence like:

>seq_0
UUCCAGCACCUGAUGUUCGAAUUUAAAUCGGCUCAACGAG
(((.((((.....)))).)))......(((......))).

Molecule Example

Example with template

molcloud tests/test.smi --template tests/shapes/beaker.png --width 15

RNA Example