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AF2 Analysis Logo

Alphafold2 Analysis

af2_analysis is a python package allowing a simplified analysis of alphafold and colabfold results.

Installation

git clone https://github.com/samuelmurail/af2_analysis
cd af2_analysis
python setup.py install

Usage

Create the Data object, giving the path of the directory containing the results of the alphafold2/colabfold run.

import af2_analysis
my_data = af2_analysis.Data('MY_AF2_RESULTS_DIR')

Extracted data are available in the df attribute of the Data object.

my_data.df
  • Compute pdockQ and pdockQ2:
my_data.compute_pdockq()
my_data.compute_pdockq2()
  • plot msa
my_data.plot_msa()
  • plot plddt:
my_data.plot_plddt([0,1])
  • plot PAE:
my_data.plot_pae(my_data.df['ranking_confidence'].idxmax())
  • show 3D structure (nglview required):
my_data.show_3d(my_data.df['ranking_confidence'].idxmax())