reading multiple PDB files with Bio3D

[sanvi]

I would like to read the multiple PDB files from a folder and would like to calculate the radius of gyration of each PDB file.

I calculated the radius of of gyration for a single file using the following program.

data<- read.pdb("/home/sanvi/Desktop/4q21.pdb")
mass <- rep(12, length(data$xyz)/3)
rgyr(data, mass)

For multiple files, I used the following code.

list <-  list.files(path="/home/sanvi/Desktop/pdbs", pattern=".pdb")
for(i in 1:length(list)){

  d2 = read.pdb(list[i])
  mass <- rep(12, length(d2$xyz)/3

  rgyr(d2,mass)}

Error: unexpected symbol in:
"                
                rgyr"

How can I calculate the radius of gyration for multiple PDB files?

[Xinqiu Yao]

Hi,

Please check your codes carefully and make sure they are free of bugs. For example, you may need full.names=TRUE in list.files(). Also, you have missed a ")" in "mass <- ...".

Another (faster) way is using lapply to loop over all pdb files. For example,

files <- list.files('/home/sanvi/Desktop', '.*\\.pdb$', full.names=TRUE)
rgs <- lapply(files, function(x) {
    data <- read.pdb(x)
    mass <- rep(12, length(data$xyz)/3)
    rgyr(data, mass)
})

[Barry Grant]

See duplicated issue #337

[Xinqiu Yao]

Sorry Barry, I've closed issue #337 for the same reason and replied in this issue...

[sanvi]

Thank you Xin-Qiu Yao for your help!

[sanvi]

Hi Xin-Qiu Yao,

Thank you very much for your help! When I tried your code, I get the following error.

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  scan() expected 'a real', got '3-0.52' 

[Xinqiu Yao]

Hi,

Make sure the files contains the pdb files you want. The code I showed above was just an example and you need to check e.g. the path is exactly where you stored your pdb files!