Formatting list of SMILES with bash scripting

2 minute read


Here is a fun text manipulation exercise using bash you can do in less than an hour. Given that I have this text file, file.smi:

smiles1 some_id_abc
smiles2 some_id_xyz

I want to have it like this:

smiles1 C00000001
smiles2 C00000002

This was my real-world need of converting a list of SMILES to a format that is accepted by a conversion programme. Looks easy right?

Here was what I did: First I need to generate a sequence ending in total number of lines is file.smi:

# count lines in file.smi
wc -l < file.smi
# print sequence (1,2,3,...)
seq $(wc -l < file.smi)
# Add zero padding up to 8 characters (0000000x, 000000xx) 
seq -f "%08g" $(wc -l < file.smi)
# Add 'C' in the beginning (C0000000x, C000000xx) 
seq -f "%08g" $(wc -l < file.smi) | sed 's/^/C/' > new_ids_tempfile

Zero padding is the tricky part; the rest is just column manipulation:

# Put together smiles and new ids, change delimiter from tab to space
paste -d ' ' file.smi new_ids_tempfile
# file.smi may or may not have old ids, so just output first and last columns 
# to make sure only smiles and new ids are printed
paste -d ' ' file.smi new_ids_tempfile | awk '{print $1, $NF}'

Finally we can eliminate the intermediary tempfile by generating it on the fly:

paste -d ' ' file.smi <(seq -f "%08g" $(wc -l < file.smi) | sed 's/^/C/') | awk '{print $1, $NF}'

As with many one-liner text manipulation scripts, this is is pretty unintelligible at first glance. To do my future self a favour, I add extensive comments:

paste -d ' ' file.smi <(seq -f "%08g" $(wc -l < file.smi) | sed 's/^/C/') | awk '{print $1, $NF}'
#                                       |--count lines in file.smi         
#                       |--make sequences up to count, pad with zero up to 8 char width                
#                                                         |--add 'C' at beginning
#                     |--put the new ids C00000001,... in a temp file             
#|--paste together smiles and new ids, delimiter is single space                
#                                                                         |--finally, only output 
#                                                                            first and last columns

Hopefully this still makes sense in the future \(“▔□▔)/ *cross fingers*

Update: I found a nice website ( which can parse complicated one-liner shell commands like the above. Here is the parsing of the above.

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