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``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
----------------
.. code-block:: bash
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