locuaz 0.3.5

Antibody optimization protocol

Looping Uniquely Catered Amino Acid Sequences

• Free software: MIT license

• Documentation: https://locuaz.readthedocs.io.

Install

Check the Installation section on the docs.

Post-Install

If on MDAnalysis 2.4.3 or older, edit the file MDAnalysis/topology/tpr/utils.py line 330:

segid = f"seg_{i}_{molblock}"

replace it with:

segid = molblock[14:] if molblock[:14] == "Protein_chain_" else molblock

On scoring

Mutators

• DLPacker is included as a submodule. To download it:

  git submodule init
  git submodule update

Then, in

The first 2 can be copied from the recently downloaded directory (locuaz/DLPacker). The weights have to be downloaded. Then, the path to the dlpacker directory has to be specified in the input config under the paths key, on the mutator option.

Generators

• gmxmmpbsa based generators like SPM4gmxmmpbsa need a residue decomposition file from gmxmmpbsa, so the gmxmmpbsa script needs to include something along the lines of:

  /
  &decomp
  idecomp=2, dec_verbose=0,
  print_res="within 4"
  /

Credits

• Biobb

• MDAnalysis

• FreeSASA

MIT License

Copyright (c) [2023] [Patricio Barletta]

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.