We are intensively working on extensions focused on RMSD calculation, scripting possibilities, or advanced work with biomolecules containing standard residues.
Molecular volumes calculations of FPP and FPP analogues were performed using the volume calculation script from Schrodinger, version 9.3.
For calculation the script ANI.pl (by Jiapeng Chen) available at https://github.com/chjp/ANI was used taking one strain of a pair as query and the other one as reference and vice versa.
The VSOP system of codes has been used for PBR fuel utilization calculations and MATLAB script has been used to implement the PSO algorithm.
This paper focuses exclusively on precisely describing the conception of the algorithms, architecture and how geo-processing is done rather than providing line per line calculation details and scripts.
Sliding windows analysis, statistical calculation, and permutation scripts were written with the R package [74].
All operations and statistical calculations were performed by scripts in Perl and R languages.
Pasting bigWigs together makes it possible to perform many complex calculations with small auxiliary scripts.
For additional details on power calculations, please see analysis scripts and associated files on the Open Science Framework:■ https://osf.io/q3e4u/.
For additional details on power calculations, please see analysis scripts and associated files on the Open Science Framework: ■ https://osf.io/bjrpc/.
