holeplot

Description

It can be used to generate plots for outputs generated from hole. It generates plot of average radius with standard deviation as a function of axis-points. It also shows the distribution of residues that outlines the channel/cavity.

Command summary

gmx_clusterByFeatures holeplot  [-h] [-i radius.dat] [-resplot]
                                [-o output.png] [-vplot]
                                [-csv output.csv] [-xmin XMIN]
                                [-xmax XMAX] [-endrad ENDRAD] [-ax Z]
                                [-gap 1] [-b 0] [-e -1] [-do 90]
                                [-rfreq 50] [-ymin YMIN] [-ymax YMAX]
                                [-fs 18] [-rlsize 10] [-wd 6] [-ht 6]
                                [-dpi 300]

Options

-i radius.dat, --input radius.dat

Name of input radius file. Radius file shoudl be obtained from hole as an output file.

-resplot, --residues-plot

Plot distributions of outlining residues to cavity/channel. By default, these distributions are not plotted. This option enables the plotting of distributions.

-o output.png, --output output.png

Name of the output plot file. The extension will be used to determine the output format.

Following output formats (system dependent) might be available:
  • ps : Postscript
  • eps : Encapsulated Postscript
  • pdf : Portable Document Format
  • pgf : PGF code for LaTeX
  • png : Portable Network Graphics
  • raw : Raw RGBA bitmap
  • rgba : Raw RGBA bitmap
  • svg : Scalable Vector Graphics
  • svgz : Scalable Vector Graphics
  • jpg : Joint Photographic Experts Group
  • jpeg : Joint Photographic Experts Group
  • tif : Tagged Image File Format
  • tiff : Tagged Image File Format

Note

To list the output formats, use gmx_clusterByFeatures holeplot -h.

-csv output.csv, --out-csv output.csv

Output csv file. The radius as a function of axis-points in csv formatted file. This file can be read in external data-plotting program.

-vplot, --violinplot

In place of normal line-plot, it plots radius distribution as violins. It is useful because this plot gives distribution of radius values over entire trajectory for each axis-points

-xmin XMIN, --axis-min XMIN

Minimum value of axis point after which radius value will be considered for plot.

If not supplied, minimum axis value will be extracted from input radius file.

-xmax XMAX, --axis-max XMAX

Maximum value of axis point after which radius value will be discarded from plot.

If not supplied, maximum axis value will be extracted from input radius file.

-endrad ENDRAD, --end-radius ENDRAD

End/Opening radius. If radius is larger than this value, radius will not considered for average calculation and features output. This option value might be equal or less than -endrad value supplied with hole sub-command.

-ax Z, --axis Z

Principal axis parallel to the channel or cavity.

-gap 1, --gap 1

Gap between axis-points in Angstroms It should be either equal to or larger than -sample value supplied with hole sub-command.

-b 0, --begin 0

First frame in time to read from the input file

-e -1, --end -1

Last frame in time to read from the input file. By default ( -e -1), all frames till the end will be read.

-do 90, --data-occupancy 90

Percentage of radius-data occupancy for axis-points. If an axis-point has radius-data less than this percentage of frames, the axis-point will not be considered for average calculation and features output.

This is critical for axis-points, which are at the opening of channel/cavity. In several frames, radius-value could be missing and therefore, dataOccupancy threshold could be used to discard those axis points with lots of missing radius values over the trajectories.

-rfreq 50, --residue-frequency 50

Frequency percentage of residue occurrence during the simulations at a given axis points. If frequency is less than this threshold, it will not considered for plotting.

-ymin YMIN, --y-axis-min YMIN

Minimum value at Y-axis. If not supplied minimum value from data will be used. It can be useful to minimum and maximum values of Y-axis when several plots are compared together.

-ymax YMAX, --y-axis-max YMAX

Maximum value at Y-axis. If not supplied maximum value from data will be used. It can be useful to minimum and maximum values of Y-axis when several plots are compared together.

-rlsize 10, --rlabel-size 10

Fontsize of residue label along Y-axis

-fs 14, --font-size 14

Font-size of all texts in plot

-wd 8, --width 8

Width of plot in inch

-ht 8, --height 8

Height of plot in inch

-dpi 300, --dpi 300

Resolution of plot