Protein Environment Graph Embeddings (PEGE)

Protein embeddings to describe local electrostic environments

Installation & Basic Usage

PEGE is installable from the Pypi repo:

python3 -m pip install pege

Pytorch Geometry also needs to be installed

In order for the structure preprocessing to work python2 and gawk need to installed.

apt install python2 gawk

Pege can be used to obtain protein embeddings as well as descriptors for specific atom_numbers from a pdb file:

from pege import Pege

protein = Pege(<pdb>)
protein_emb = protein.get_protein()
all_res_embs = protein.get_all_res_embs(chain="A")

Documentation

TBA

License

This source code is licensed under the MIT license found in the LICENSE file in the root directory of this source tree.

Contacts

Please submit a github issue to report bugs and to request new features. Alternatively, you may email the developer directly.