read.pdb() converts chain 'F' to FALSE

[Mark Sun]

Reading in a PDB file that has a chain value of 'F' gets converted to FALSE

eg. use pdbid 5C6B R version: 3.3

[Xinqiu Yao]

Can you download and install the latest development version (either master or releases branch in this repository)? This is a fixed bug but hasn't been released to CRAN.

Check this page about how to install development version bio3d.

Bests

[Lars Skjærven]

Absolutely. Thanks for reporting

> pdb = read.pdb("5C6B")
  Note: Accessing on-line PDB file
  HEADER    VIRAL PROTEIN                           22-JUN-15   5C6B               
Warning message:
In read.table(text = sapply(raw.atom, split.fields), stringsAsFactors = FALSE,  :
  not all columns named in 'colClasses' exist
> 
> 
> head(pdb$atom$chain)
[1] FALSE FALSE FALSE FALSE FALSE FALSE

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bio3d_2.2-3.9000

loaded via a namespace (and not attached):
 [1] R6_2.1.2        magrittr_1.5    parallel_3.3.0  tools_3.3.0    
 [5] withr_1.0.1     roxygen2_5.0.1  crayon_1.3.1    Rcpp_0.12.5    
 [9] memoise_1.0.0   stringi_1.1.1   grid_3.3.0      stringr_1.0.0  
[13] digest_0.6.9    testthat_1.0.2  devtools_1.11.1

[Lars Skjærven]

For now you're welcome to try out the new version of read.pdb() in branch feature_cpp. That resolves this issue. Although we have been using this version of read.pdb() for some time, it should still be considered to be under development.

> install.packages("devtools")
> library(devtools)
> install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/", ref="feature_cpp")

> library(bio3d)
> pdb = read.pdb("5C6B")
  Note: Accessing on-line PDB file
trying URL 'http://www.rcsb.org/pdb/files/5C6B.pdb'
downloaded 632 KB

> head(pdb$atom$chain)
[1] "F" "F" "F" "F" "F" "F"

[Lars Skjærven]

fixed with commit https://bitbucket.org/Grantlab/bio3d/commits/a0d603833c4199035980bf2c605823b73c6468a1

bugfix available from branch master

[Mark Sun]

Thanks for the fast update!