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https://github.com/whitead/molcloud
Make a bunch of molecules
https://github.com/whitead/molcloud
Last synced: 3 days ago
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Make a bunch of molecules
- Host: GitHub
- URL: https://github.com/whitead/molcloud
- Owner: whitead
- License: mit
- Created: 2022-07-01T21:22:05.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-11-22T16:05:30.000Z (about 1 month ago)
- Last Synced: 2024-12-24T12:14:52.459Z (10 days ago)
- Language: Python
- Size: 2.37 MB
- Stars: 94
- Watchers: 2
- Forks: 16
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# molcloud [](https://whitead.github.io/molcloud/)[](https://badge.fury.io/py/molcloud)
This package draws molecules (or RNA, thanks to [@Shunsuke-1994](https://github.com/Shunsuke-1994)) in a big canvas packed together. See examples below.
## Install
Make sure you have [pygraphviz installed](https://pygraphviz.github.io/documentation/stable/install.html)
```sh
pip install molcloud
```
## Usage
```sh
molcloud [smiles-file]
```
and the output will go to `cloud.png`. You can specify a few things too:
```sh
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](https://github.com/doncamilom))!
```sh
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:
```plain
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](https://github.com/Shunsuke-1994)! To install layout RNA, install the extra packages:
```sh
pip install molcloud[all]
```
## RNA Usage
```sh
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
```sh
molcloud tests/test.smi --template tests/shapes/beaker.png --width 15
```
## RNA Example
