af2_analysis
is a python package allowing a simplified analysis of alphafold and colabfold results.
git clone https://github.com/samuelmurail/af2_analysis
cd af2_analysis
python setup.py install
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())