histogram
Parameter distribution during simulation
This can be used to calculate distribution of a parameter of either a specific base-pair/step or over a DNA segment during the simulations.
Usage:
usage: dnaMD histogram [-h] [-i L-BP_cdna.dat] [-o output.dat]
[-tbp total-bp-number] [-bins bins] [-p parameter]
[-bs bp/s-start-number] [-be bp/s-end-number]
[-mm sum-or-mean] [-fbp 1]
Optional arguments:
-h, --help show this help message and exit
-i L-BP_cdna.dat, --input L-BP_cdna.dat
Name of input file (from do_x3dna or hdf5 file).
This file should contain the required parameters. It can be a file either
produced from do_x3dna or hdf5 storage file.
-o output.dat, --output output.dat
Name of output file.
The extracted output will be written in output file.
-tbp total-bp-number, --total-bp total-bp-number
Total number of basepair in DNA/RNA.
It is an essential input.
-bins bins, --bins bins
Number of bins in the histogram
Default value is 30.
-p parameter, --parameter parameter
Parameter name.
This parameter will be extracted from file. Ensure that parameter is present
in the file, otherwise wrong values will be extracted from file.
-bs bp/s-start-number, --bp-start bp/s-start-number
First BP/BPS of DNA after which parameter will be extracted.
If it is not given, first basepair or base-step will be considered.
-be bp/s-end-number, --bp-end bp/s-end-number
Last BP/BPS of DNA upto which parameter will be extracted.
If it is not given, parameter for only a single bp/s given with -bs/--bp-start
option will be extracted.
-mm sum-or-mean, --merge-method sum-or-mean
Method to merge the parameter of a DNA segment from local parameters
of all base-pairs/steps that are within the range given by '-bs' and '-be'.
Currently accepted keywords are as follows:
* mean : Average of local parameters
* sum : Sum of local parameters
When only "-bs" option is provided without "-be", then -mm/--merge-method is
not required.
-fbp 1, --first-bp 1 Basepair number of first base-pair.
Usually it is one. Therefore, if this option is not provided, base-pair
numbering will start from one.
In rare cases, base-pair numbering might start with other number. In those
cases, use this option to start numbering of basepair from other number than
one.
Example
dnaMD histogram -i pdna.h5 -o histogram.dat -tbp 60 -bs 20 -be 45 -p rise -mm sum -bins 20
Following output is obtained in histogram.dat
file.
# "rise" Density
84.082 0.0
84.278 0.00509694
84.474 0.0
84.67 0.00509694
84.866 0.00509694
85.062 0.0203878
85.258 0.0356786
85.454 0.107036
85.65 0.0560664
.
.
.
It can be plotted by xmgrace as following:
xmgrace histogram.dat
The obtained plot is similar to the histogram plot shown here for 20-45 bp length bound DNA.