Chen's website for bioinfo

class06

Chen

PartA

df<-data.frame(a=1:10, b=seq(200,400, length=10),c=11:20,d=NA)


for (i in 1:ncol(df)){
  df_colname<-colnames(df)
  current_col<-df_colname[i]
  df[[current_col]]<-(df[[current_col]]-min(df[[current_col]]))/(max(df[[current_col]])-min(df[[current_col]]))
                                                                 }

Part B install.pacakges(“bio3d”)

library(bio3d)
FUN_proteinplot<-function(PDBID){
  pdblist<-list()
  for (i in 1:length(PDBID)){
    ID<-PDBID[i]
  s<-read.pdb(ID)
  s.chainA <- trim.pdb(s, chain="A", elety="CA")
  
  s.b <- s.chainA$atom$b
  plotb3(s.b, sse=s.chainA, typ="l", ylab="Bfactor")
    l<-list(
    PDBID   = PDBID,
    chainA  = s.chainA,
    bfactor = s.b
  )
    pdblist[[i]]<-l
    
  }
  return(pdblist)
}

Documentation: 1. input: should be a vector, with PDBID 2. function: for comparing Bfactor of protein in interest 3. output: a plot with Bfactor for Residue

lab06