PCA Application

Perform PCA/EDA calculations and output the results in plain text, NMD, and graphical formats.

prody_pca(coords, **kwargs)

Perform PCA calculations for PDB or DCD format coords file.

Parameters:

• aligned – trajectory is already aligned, default is False
• altloc – alternative location identifiers for residues used in the calculations, default is 'A'
• 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
• membrane – whether to include the explicit membrane model, default is False
• nmodes – number of non-zero eigenvectors (modes) to calculate, default is 10
• nproc – number of processors, default is 0
• npzmatrices – write matrix to compressed ProDy data file, default is False
• 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
• outscipion – write continuousflex modes directory and sqlite, 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"