tycheleturner/alphafold_viewer_final.Rmd

## alphafold_viewer_final.Rmd
---
title: "AlphaFold Viewer Final"
author: "Tychele N. Turner, Ph.D."
date: "Created on October 30, 2022"
output:
  html_document: default
  pdf_document: default
abstract: This document contains the documentation for making the AlphaFold html.
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

### Set up of the environment
```{r}
library("NGLVieweR")

#run interactive
setwd("~/Desktop/pdb_AF")

#list the pdb files
pdb <- list.files(".", pattern="pdb")

#make a function out of the viewer
nglV <- function(x){
    NGLVieweR(x) %>% stageParameters(backgroundColor = "white", zoomSpeed = 1) %>% addRepresentation("cartoon",     param = list(name = "cartoon", colorScheme = "bfactor") ) %>% setSpin()
}

###list the output from your other file in here to make the final html###
"NP_000132.3.pdb"
nglV(pdb[1])
"NP_000133.1.pdb"
nglV(pdb[2])
"NP_000179.2.pdb"
nglV(pdb[3])
"NP_000255.2.pdb"
nglV(pdb[4])
"NP_000275.1.pdb"
nglV(pdb[5])
"NP_000305.3.pdb"
nglV(pdb[6])
"NP_000453.2.pdb"
nglV(pdb[7])
"NP_000480.3.pdb"
nglV(pdb[8])
"NP_000507.1.pdb"
nglV(pdb[9])
"NP_000710.5.pdb"
nglV(pdb[10])
```

## alphafold_viewer_prep.R
#!/bin/Rscript
#Tychele N. Turner, Ph.D.
#October 30, 2022

library("NGLVieweR")

#get pdb files
pdb <- list.files(".", pattern="pdb")

#loop to print out the name and the funtion running on the name of the file (this is the input to the viewer script)
for(i in 1:length(pdb)){
  cat(paste('"', pdb[i], '"', "\n", sep=""))
  cat(paste("nglV(pdb[", i, "])", "\n", sep=""))
}
	---
	title: "AlphaFold Viewer Final"
	author: "Tychele N. Turner, Ph.D."
	date: "Created on October 30, 2022"
	output:
	html_document: default
	pdf_document: default
	abstract: This document contains the documentation for making the AlphaFold html.
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = TRUE)
	```

	### Set up of the environment
	```{r}
	library("NGLVieweR")

	#run interactive
	setwd("~/Desktop/pdb_AF")

	#list the pdb files
	pdb <- list.files(".", pattern="pdb")

	#make a function out of the viewer
	nglV <- function(x){
	NGLVieweR(x) %>% stageParameters(backgroundColor = "white", zoomSpeed = 1) %>% addRepresentation("cartoon", param = list(name = "cartoon", colorScheme = "bfactor") ) %>% setSpin()
	}

	###list the output from your other file in here to make the final html###
	"NP_000132.3.pdb"
	nglV(pdb[1])
	"NP_000133.1.pdb"
	nglV(pdb[2])
	"NP_000179.2.pdb"
	nglV(pdb[3])
	"NP_000255.2.pdb"
	nglV(pdb[4])
	"NP_000275.1.pdb"
	nglV(pdb[5])
	"NP_000305.3.pdb"
	nglV(pdb[6])
	"NP_000453.2.pdb"
	nglV(pdb[7])
	"NP_000480.3.pdb"
	nglV(pdb[8])
	"NP_000507.1.pdb"
	nglV(pdb[9])
	"NP_000710.5.pdb"
	nglV(pdb[10])
	```
	#!/bin/Rscript
	#Tychele N. Turner, Ph.D.
	#October 30, 2022

	library("NGLVieweR")

	#get pdb files
	pdb <- list.files(".", pattern="pdb")

	#loop to print out the name and the funtion running on the name of the file (this is the input to the viewer script)
	for(i in 1:length(pdb)){
	cat(paste('"', pdb[i], '"', "\n", sep=""))
	cat(paste("nglV(pdb[", i, "])", "\n", sep=""))
	}