README

Repo uploaded on github on: 10/16/2020
Scripts for post processing data in Rosetta scorefile generated for the work outlined in preprint:
Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2
Sai Pooja Mahajan , Yashes Srinivasan , Jason W Labonte , Matthew P DeLisa , and Jeffrey J. Gray 
doi:10.1101/2020.06.25.171371

Scripts may not work out of the box. Scripts are shared for transparency.

For data in the paper, contact first author or owner of this repository.

The script generate_heatmaps_criteria.py will generate all heatmaps in figures 2-5. 
   - This script requires scorefiles generated as outlined in the paper (over 361 sequons).
   - Scorefiles are available upon request.

For property based heatmaps, see generate_property_heatmaps.py
  - This script requires data from score files and additional properties such as shape complementarity
    available as pickled dataframes upon request.
  - The pickled/non-pickled dataframes can alternatively be generated from scorefiles with the 
    util functions in: functions_create_and_save_dataframes.py

Requirements:
pythion3.6 or higher
packages:
numpy
scipy
sklearn
matplotlib
seaborn
pandas
pickle
os
sys
glob
math
pyrosetta4 (python3 compatible)