Going from a list of elements to chemical formula

Question

I have a list of elemental compositions, each element in it's own row. Sometimes these elements have a zero.

   C H N O S
1  5 5 0 0 0
2  6 4 1 0 1
3  4 6 2 1 0

I need to combine them so that they read, e.g. C5H5, C6H4NS, C4H6N2O. This means that for any element of value "1" I should only take the column name, and for anything with value 0, the column should be skipped altogether.

I'm not really sure where to start here. I could add a new column to make it easier to read across the columns, e.g.

   c C h H n N o O s S
1  C 5 H 5 N 0 O 0 S 0
2  C 6 H 4 N 1 O 0 S 1
3  C 4 H 6 N 2 O 1 S 0

This way, I just need the output to be a single string, but I need to ignore any zero values, and drop the one after the element name.

Answer 1

And here a base R solution:

df = read.table(text = "
C H N O S
5 5 0 0 0
6 4 1 0 1
4 6 2 1 0
", header=T)

apply(df, 1, function(x){return(gsub('1', '', paste0(colnames(df)[x > 0], x[x > 0], collapse='')))})
[1] "C5H5"    "C6H4NS"  "C4H6N2O"

paste0(colnames(df)[x > 0], x[x > 0], collapse='') pastes together the column names where the row values are bigger than zero. gsub then removes the ones. And apply does this for each row in the data frame.

Answer 2

Here's a tidyverse solution that uses some reshaping:

df = read.table(text = "
C H N O S
5 5 0 0 0
6 4 1 0 1
4 6 2 1 0
", header=T)

library(tidyverse)

df %>%
  mutate(id = row_number()) %>%                      # add row id
  gather(key, value, -id) %>%                        # reshape data
  filter(value != 0) %>%                             # remove any zero rows
  mutate(value = ifelse(value == 1, "", value)) %>%  # replace 1 with ""
  group_by(id) %>%                                   # for each row
  summarise(v = paste0(key, value, collapse = ""))   # create the string value

# # A tibble: 3 x 2
#      id v      
#   <int> <chr>  
# 1     1 C5H5   
# 2     2 C6H4NS 
# 3     3 C4H6N2O