Thursday 16 June 2016

More molecular depiction in Vim

The reception for my previous blog post on ASCII depiction in Vim was somewhat muted even, dare I say, lukewarm. Buoyed by this response, I updated that script to handle quoted SMILES strings (as found in my Python scripts, for example). And here I provide similar depiction support for SDF files ("\a" and "\A" for small and big depictions).

Disclaimer: Due to my use of complex regular expressions, this script is not suitable for use by Andrew Dalke, nor for any SDF file provided by same. If this script is used on a SDF file provided by Andrew Dalke, it may result in the summoning of Cthulhu. You have been warned.

function! SDFToAscii(width)
  let prev = search("$$$$", "nbW") + 1
  let end = search("$$$$", "nW")
  if end == 0
    let end = line('$')
  silent execute prev.",".end."yank"
  let output = system("obabel -isdf -oascii -d -xa 2.0 -xw ".a:width, @")
  botright new
  setlocal buftype=nofile bufhidden=wipe nobuflisted noswapfile nowrap
  put =output
  setlocal nomodifiable
noremap <silent> <leader>a :call SDFToAscii(79)<CR>
noremap <silent> <leader>A :call SDFToAscii(189)<CR>

Monday 13 June 2016

SMILES depiction in Vim

I spend a lot of time scrolling through files of SMILES in Vim, and copying and pasting SMILES into viewers. This is now a thing of the past. I bring you (from the depths of time) molecule depiction within Vim.

Using the script below (paste it into your .vimrc), I just hit "\s" with the cursor on a SMILES string, and up pops its ASCII depiction (":q" to close). Need a bigger image? "\S" is your friend. This is my first Vim script ("and I hope it's your last" sez you) so if you have any improvements, let me know.

[Update 16/06/2014]: Script updated to handle quoted SMILES strings and those with escaped backslashes.
noremap <silent> <leader>s :call SmiToAscii(79)<CR>
noremap <silent> <leader>S :call SmiToAscii(189)<CR>
function! SmiToAscii(width)
  let smiles = expand("<cWORD>")
  " Strip quotation marks and commas
  let smiles = substitute(smiles, "[\"',]", "", "g")
  " Handle escaped backslashes, e.g. in C++ strings
  let smiles = substitute(smiles, "\\\\", "\\", "g")
  botright new
  setlocal buftype=nofile bufhidden=wipe nobuflisted noswapfile nowrap
  execute '$read ! obabel -:'.shellescape(smiles, 1). ' -o ascii -d -xa 2.0 -xw '. a:width
  setlocal nomodifiable