Compiling structures to pdf-file (linux)

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:

for i in $(ls -1 .|grep .cdx)
~/marvin/bin/molconvert smiles $i -o tmp.smi
cat tmp.smi >> smiles.smi

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:

The final result


Author: Slava Bernat

I did my PhD in medicinal chemistry/chemical biology of G protein-coupled receptors and then explored some chemical biology of non-coding RNA as a postdoc. Currently I'm working in a small biotech company in San-Francisco Bay area as a research chemist. I'm writing about science, which catches my attention in rss feed reader and some random thoughts or tutorials.

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