# pyFASPR
A python wrapper of FASPR, a fast and accurate protein sidechain builder
## Install
#### via PyPI
``` bash
pip install pyfaspr
```
#### via GitHub
``` bash
pip install git+https://github.com/ShintaroMinami/pyFASPR.git
```
## Usage as python module
``` python
from pyfaspr import run_FASPR
# PDB file input
pdb_text_out = run_FASPR(pdb="pdb/file/path.pdb")
# PDB string input
pdb_text_in = "
ATOM 1 N GLY A 1 -12.034 2.689 10.030 1.00 0.00
ATOM 2 CA GLY A 1 -11.462 3.121 8.735 1.00 0.00
ATOM 3 C GLY A 1 -10.273 2.258 8.357 1.00 0.00
....
"
pdb_text_out = run_FASPR(pdb=pdb_text_in)
# Override sequence
seq_update = "GTILIFLDKNKEQAEKLAKEVGVTEIYESDN..."
pdb_text_out = run_FASPR(pdb=pdb_in, sequence=seq_update)
```
## Usage of pyfaspr script
``` bash
# To build sidechains
pyfaspr input.pdb
# Build sidechains with overriding new sequence
pyfaspr input.pdb -s GTILIFLDKNKEQAEKLAKEVGVTEIYESDN...
# To build sidechains and save a new PDB file
pyfaspr input.pdb -o output.pdb
```
### Option details
``` bash
usage: pyfaspr [-h] [--sequence SEQUENCE] [--output_pdb OUTPUT_PDB] [--verbose] pdb
Run FASPR to build sidechains for a PDB file.
positional arguments:
pdb Input PDB file path
options:
-h, --help show this help message and exit
--sequence SEQUENCE, -s SEQUENCE
Amino acid sequence to be overridden (optional) (default: None)
--output_pdb OUTPUT_PDB, -o OUTPUT_PDB
Output PDB file path (optional) (default: None)
--verbose, -v Enable verbose output (default: False)
```
## Original GitHub reopository
This code includes [tommyhuangthu](https://github.com/tommyhuangthu)'s excellent open source software, FASPR. The original repository is available on MIT license here, https://github.com/tommyhuangthu/FASPR.git.
The author of this repo appreciate to the FASPR team for making such great methods and software available!
## Citations
``` bibtex
@article{huang2020faspr,
title={FASPR: an open-source tool for fast and accurate protein side-chain packing},
author={Huang, Xiaoqiang and Pearce, Robin and Zhang, Yang},
journal={Bioinformatics},
volume={36},
number={12},
pages={3758--3765},
year={2020},
publisher={Oxford University Press}
}
```
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