In zalperst/visualizeprot: Visualize the Protein Chemical Property Landscape

CYP

This is just a preloaded pdb for examples

Examples

pdb_dataframe

library(Rpdb)
library(tidyverse)
library(dplyr)
library(visualizeprot)
x <- Rpdb::read.pdb("~/trunc.pdb")
x$cryst1 <- NULL
y <- pdb_dataframe(x)

# Here is the dataframe
knitr::kable(head(x))

assign_params

library(Rpdb)
library(tidyverse)
library(dplyr)
x <- Rpdb::read.pdb("~/3cqz.pdb")
y <- pdb_dataframe(x)
z <- assign_params(y)
#Here is the dataframe
knitr::kable(head(z))

acidity_landscape

library(Rpdb)
library(tidyverse)
library(dplyr)
library(ggplot2)
x <- Rpdb::read.pdb("~/3cqz.pdb")
y <- pdb_dataframe(x)
z <- assign_params(y)
acidity_landscape(z)

polar_landscape

library(Rpdb)
library(tidyverse)
library(dplyr)
library(ggplot2)
x <- Rpdb::read.pdb("~/3cqz.pdb")
y <- pdb_dataframe(x)
z <- assign_params(y)
polar_landscape(z)

full_landscape

library(Rpdb)
library(tidyverse)
library(dplyr)
library(ggplot2)
library(mgcv)
x <- Rpdb::read.pdb("~/3cqz.pdb")
y <- pdb_dataframe(x)
z <- assign_params(y)
#there is some unexpected activity when tring to throw it diverse functions, works best with a polynomial function and just changing the order like so y~poly(x, degree)
full_landscape(z, y~x)

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