cocoatree.io.export_sector_for_pymol¶
- cocoatree.io.export_sector_for_pymol(mapping, independent_components, axis, sector_pos_in_loaded_msa, sector_pos_in_filtered_msa, outpath)[source]¶
Export sector information for mapping on 3D structure in PyMOL.
Export numpy arrays of a sector’s residue positions and their contribution for coloring in PyMOL.
Arguments¶
- mappingnumpy.ndarray,
mapping between the unfiltered MSA and the PDB structure, output of cocoatree.msa.map_to_pdb() function
- independent_componentsnumpy.ndarray,
output of cocoatree.deconvolution.compute_ica() function
- axisint,
rank of the independent component associated with the desired sector
- sector_pos_in_loaded_msalist,
positions of the sector’s residues in the unfiltered MSA
- sector_pos_in_filtered_msanumpy.ndarray,
positions of the sector’s residues in the filtered MSA, output from cocoatree.deconvolution.icList() function
- outpathstr,
path to the output file as a binary in .npy format
Returns¶
binary file in .npy format containing an array with the positions of the sector’s residues and an array with their contribution to the independent component.
Examples using cocoatree.io.export_sector_for_pymol¶
Perform full SCA analysis on the S1A serine protease dataset