During my job-searching campaign I was once asked to show all the structures that I have synthesized. Drawing 200+ molecules seemed no fun to me. Even opening all .cdx files generated in 3.5 years, to copy-paste in a single one, was too boring. So I’ve used openbabel for this job.
Once I had all the .cdx in one folder I’ve ran
babel *.cdx allStruc.svg -xe -xl -xC rsvg-convert -f pdf -o allStruc.pdf allStruc.svg
But the output was weird. All the charged molecules were assigned unrealistic charges over +2000, so all my potassium trifluoroborate and ammonium salts were crap.
Then I turned to molconvert tool from Chemaxon, which is free for academic non-commercial use. To convert all .cdx files to correct smiles I used a simple script:
#!/bin/bash for i in $(ls -1 .|grep .cdx) do ~/marvin/bin/molconvert smiles $i -o tmp.smi cat tmp.smi >> smiles.smi done
Followed by openbabel (I’ve decided to sort the molecules by molecular weight so the complexity will increase more or less steadily down the list):
babel smiles.smi allStruc.svg -xe -xl -xC --sort MW rsvg-convert -f pdf -o allStruc.pdf allStruc.svg
Still, the conversion wasn’t ideal. Particularly, BF3¯ groups were represented as BF2·F¯. Fortunately, simple replacement of SMILES code ‘B(F)F’ to ‘[B-](F)(F)F’ and removal of extra fluoride (‘[F-].’ in SMILES) solved the problem.
So, here we go, the work of 3.5 years as almost square matrix 15×14: