GNM Application

Perform GNM calculations and output the results in plain text NMD, and graphical formats.

prody.apps.prody_apps.prody_gnm.prody_gnm(pdb, **kwargs)[source]

Perform GNM calculations for pdb.

Parameters:

  • altloc – alternative location identifiers for residues used in the calculations, default is 'A'

  • cutoff – cutoff distance (A), default is 10.0

  • 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

  • figbeta – save beta-factors figure, default is False

  • figcc – save cross-correlations figure, default is False

  • figcmap – save contact map (Kirchhoff matrix) 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

  • figmode – save mode shape figures for specified modes, e.g. “1-3 5” for modes 1, 2, 3 and 5, default is ''

  • figsf – save square-fluctuations figure, default is False

  • figwidth – figure width (inch), default is 8.0

  • gamma – spring constant, default is '1.'

  • kirchhoff – write Kirchhoff matrix, default is False

  • membrane – whether to include the explicit membrane model, default is False

  • model – index of model that will be used in the calculations, default is 1

  • 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

  • outbeta – write beta-factors calculated from GNM modes, 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

  • outscipion – write continuousflex modes directory and sqlite, default is False

  • outsf – write square-fluctuations, default is False

  • prefix – output file prefix, default is '_gnm'

  • select – atom selection, default is "protein and name CA or nucleic and name P C4' C2"

  • zeros – calculate zero modes, default is False