Parameters: |
- aligned – trajectory is already aligned, default is False
- extend – write NMD file for the model extended to “backbone” (“bb”) or “all” atoms of the residue, model must have one node per residue, default is ''
- figall – save all figures, default is False
- figcc – save cross-correlations figure, default is False
- figdpi – figure resolution (dpi), default is 300
- figformat – figure file format, default is 'pdf'
- figheight – figure height (inch), default is 6.0
- figproj – save projections onto specified subspaces, e.g. “1,2” for projections onto PCs 1 and 2; “1,2 1,3” for projections onto PCs 1,2 and 1, 3; “1 1,2,3” for projections onto PCs 1 and 1, 2, 3, default is ''
- figsf – save square-fluctuations figure, default is False
- figwidth – figure width (inch), default is 8.0
- nmodes – number of non-zero eigenvectors (modes) to calculate, default is 10
- numdelim – number delimiter, default is ' '
- numext – numeric file extension, default is '.txt'
- numformat – number output format, default is '%12g'
- outall – write all outputs, default is False
- outcc – write cross-correlations, default is False
- outcov – write covariance matrix, default is False
- outdir – output directory, default is '.'
- outeig – write eigenvalues/vectors, default is False
- outhm – write cross-correlations heatmap file, default is False
- outnpz – write compressed ProDy data file, default is False
- outproj – write projections onto PCs, default is False
- outsf – write square-fluctuations, default is False
- prefix – output file prefix, default is '_pca'
- select – atom selection, default is "protein and name CA or nucleic and name P C4' C2"
|