holeclustersplot

Description

It can be used to plot radius of cavity/channel for clusters separately. It reads radius file from hole and cluster-id file from cluster, and extract radius of each cluster separately and plot them in one plot. This plot could be extremely useful to compare radius along the channel/cavity in all clusters.

Command summary

gmx_clusterByFeatures holeclustersplot  [-h] [-i radius.dat]
                                        [-clid clid.xvg] [-o output.png]
                                        [-csv output.csv] [-xmin XMIN]
                                        [-xmax XMAX] [-endrad ENDRAD]
                                        [-ax Z] [-gap 1] [-b 0] [-e -1]
                                        [-do 90] [-stdbar] [-dl 0]
                                        [-ymin YMIN] [-ymax YMAX]
                                        [-rmargin 0.15] [-lcols 1]
                                        [-fs 18] [-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.

-clid clid.xvg, --clid clid.xvg

Input file containing cluster-id as a function of time. The number of frames in this file should be same as in input radius file.

-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 holeclustersplot -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.

-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.

-stdbar, --stddev-bar

To show standard deviation as error-bar If it is supplied, standard deviation will be shown as an error-bar in the plot.

-dl 0, --discard-lasts 0

Number of smallest clusters to discard from the plotting. It can be useful to filter out few smallest clusters because these may contain small number of frames.

-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.

-rmargin 0.15, --right-margin 0.15

Margin at right side of the plots. If legends overflow into the plot area, margin can be increased to fit the legend.

-lcols 1, --legend-cols 1

Number of legend columns If legend overflow into the plot area, legends can be made of more than one column to accommodate all legends.

-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