README.md

In zalperst/visualizeprot: Visualize the Protein Chemical Property Landscape

Visualizeprot

This package is meant to be used for a quick visualization of the polar landscape across the protein coordinate

Notes

5kyo.pdb is provided for testing (a CYP protein)

Installation.

devtools::install_github("zalperst/visualizeprot")

Quick Demo

Let's see what we can do: we will get our files formatted, then check out the logP/ acidity landscape across the atomic coordinate

library(Rpdb)
#> Loading required package: rgl
#> 
#> Attaching package: 'Rpdb'
#> The following objects are masked from 'package:base':
#> 
#>     norm, replicate, unsplit
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(tidyverse)
#> Loading tidyverse: ggplot2
#> Loading tidyverse: tibble
#> Loading tidyverse: tidyr
#> Loading tidyverse: readr
#> Loading tidyverse: purrr
#> Conflicts with tidy packages ----------------------------------------------
#> filter(): dplyr, stats
#> lag():    dplyr, stats
library(visualizeprot)
#CYP is a pre-loaded pdb just for testing
# to use your own pdb, use x <- Rpdb::read.pdb("/pathtopdb/xxx.pdb")
y <- pdb_dataframe(CYP)
z <- assign_params(y)
full_landscape(z)

zalperst/visualizeprot documentation built on May 4, 2019, 9:08 p.m.