R/visualizeprot-package.r

In zalperst/visualizeprot: Visualize the Protein Chemical Property Landscape

#' visualizeprot: Get a quick chemical representation of the protein
#'
#' Although the gold standard for understanding is usually thought to be through imagery in the spatial domain, such an endeavour becomes impossible as complexity increases. Therefore it may be a useful alternative to reduce the 3 spatial dimensions into a linear coordinate and plot a chemical property on the y-axis. I have chosen to plot logP values across an atom coordinate. LogP is a measurement of the affinity of a compound for octanol over water (more negative means more hydrophilic). I have chosen to process a pdb object rendered by the package "Rpdb" into a tibble, assign logPs and a acidity class (acidic, basic or neutral) based on the amino acid sequence. The logP values have been calculated and can be found at http://www2d.biglobe.ne.jp/~chem_env/amino/amino2j_e.html and are also commented in the function assign_params(). The typical work flow is as follows, first one reads in a pdb file with Rpdb, followed by processing with the pdb_dataframe() function from this package. After this one assigns logP and acidity categories with assign_params() and finally one chooses their plot of interest which is either categorical (acidity_landscape(), discriminate based on color), or numeric (with polar_landscape()). Alternatively, one can plot each on the same plot with full_landscape to match up the two. Interesting questions one might try to answer with this package are: "can I identify functional regions based on patterns of high polarity amino acids/ functional amino acids", " what are the structural/ functional differences between regions that are polar but not acidic? could this represent a protein:protein interaction region?"
#'
#' @name visualizeprot
#' @docType package
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