Adding a row to a dataframe - r

Question

I am reading a file line by line and then adding specific lines to a dataframe. Here is an example of a line I would add to a dataframe:
ATOM 230 CA GLU A 31 66.218 118.140 2.411 1.00 31.82 C
I have verified that my checks are ok, I think it has specifically to do with my rbind command. Thanks for your help!
Edit: The error is as follows, the output of the dataframe is:
Residue AtomCount SideChain XCoord YCoord ZCoord
2 MET 1 A 62.935 97.579 30.223
21 <NA> 2 A 63.155 95.525 27.079
3 <NA> 3 A 65.289 96.895 24.308
It seems like it stops picking up the name of the residue..
The code I am using is:
get.positions <- function(sourcefile, chain_required = "A"){
positions = data.frame()
visited = list()
filedata <- readLines(sourcefile, n= -1)
for(i in 1: length(filedata)){
input = filedata[i]
id = substr(input,1,4)
if(id == "ATOM"){
type = substr(input,14,15)
if(type == "CA"){
#if there are duplicates it takes the first one
residue = substr(input,18,20)
type_of_chain = substr(input,22,22)
atom_count = strtoi(substr(input, 23,26))
if(atom_count >=1){
if(type_of_chain == chain_required && !(atom_count %in% visited) ){
position_string = trim(substr(input,30,54))
position_string = lapply(unlist(strsplit(position_string," +")),as.numeric)
positions<- rbind(positions, list(residue, atom_count, type_of_chain, position_string[[1]], position_string[[2]], position_string[[3]]))
}
}
}
}
}
return (positions)
}

Answer 1

When I ran your code with that data I got type=="LU" (so it failed the type=="CA" test) and the rest of processing never got accomplished. I think you may need to change the indices to
type = substr(input,10,11)
Fixing that problem brings up others, and its going to be very difficult to fix all the problems since the goal is not clearly stated, but it suggests that you edit your code and data so it's reproducible. This could be a reproducible input/execution method:
get.positions(textConnection("ATOM 230 CA GLU A 31 66.218 118.140 2.411 1.00 31.82 C") )

Answer 2

In, the end, the following worked. First I made a much larger data frame, and then just replace specific rows (thank you Joran who linked me to the R inferno).
For the user that asked why I am splitting on a plus, your assumption is incorrect. The syntax is actually " +", that's a space-plus so that it's splitting on multiple spaces.Finally, as for the incorrect indices, I've finally figured out how to show the extra spaces on the form. Here is the correct original line, you will see the indices match.
ATOM 2 CA MET A 1 62.935 97.579 30.223 1.00 37.58 C
The R code that works, is as follows.
get.positions <- function(sourcefile, chain_required = "A"){
N <- 10^5
AACount <- 0
positions = data.frame(Residue=rep(NA, N),AtomCount=rep(NA, N),SideChain=rep(NA, N),XCoord=rep(NA, N),YCoord=rep(NA, N),ZCoord=rep(NA, N),stringsAsFactors=FALSE)
visited = list()
filedata <- readLines(sourcefile, n= -1)
for(i in 1: length(filedata)){
input = filedata[i]
id = substr(input,1,4)
if(id == "ATOM"){
type = substr(input,14,15)
if(type == "CA"){
#if there are duplicates it takes the first one
residue = substr(input,18,20)
type_of_chain = substr(input,22,22)
atom_count = strtoi(substr(input, 23,26))
if(atom_count >=1){
if(type_of_chain == chain_required && !(atom_count %in% visited) ){
visited <- c(visited, atom_count)
AACount <- AACount + 1
position_string = trim(substr(input,30,54))
position_string = lapply(unlist(strsplit(position_string," +")),as.numeric)
#print(input)
positions[AACount,]<- c(residue, atom_count, type_of_chain, position_string[[1]], position_string[[2]], position_string[[3]])
}
}
}
}
}
positions<-positions[1:AACount,]
return (positions)
}