locuaz

Looping Uniquely Catered Amino Acid Sequences

• Free software: MIT license
• Documentation: https://locuaz.readthedocs.io.

Install

Create a conda environment YAML file named, for example, usr_deps.yaml:

name: locuaz
channels:
  - conda-forge
dependencies:
  - conda-forge::python>=3.10
  - conda-forge::ambertools>=22.0.0
  - conda-forge::tensorflow
  - conda-forge::openbabel
  - conda-forge::pygraphviz

by running:

mamba env create -f usr_deps.yaml

Then, activate the environment and install the protocol through pip:

pip install locuaz

Check the Installation section on the docs for more info.

Post-Install

Using DLPacker based mutators

If you wish to used DLPacker based Mutators (dlp and dlpr), DLPacker weights have to be downloaded. Get them here or here. These weights have to be extracted to a dedicated folder and its path has to be specified in the input config under the paths key, on the mutator option. Check the docs for more info.

Running

After that, running locauz is as simple as:

# Activate your environment
mamba activate locuaz
# Point locuaz to your config file
locuaz config.yaml

Check the tutorials for info on how to write this config file.

Citing

Credits

• Biobb
• MDAnalysis
• FreeSASA