Dearomatizing smiles

Hi,

I'm trying to  use molconvert to dearomatize a file with smiles. This works in itself, using

molconvert smiles:-a inputfile.smi -o outputfile.smi

but the molecular indicatiors (Ids) in the inputfile are stripped out.

Is there a way to keep them in the dearomatized output?

Hi,

Could you attach an example input file which gives the failure? I don't really understand what a molecular indicator is.

All the best

Andras

Here are some examples. The ID is the number after the smiles.

 

O=Cc1c([nH]c2ccccc12)c1ccc(Cl)cc1 439896

O=Cc1c([nH]c2ccccc12)c1ccc(Br)cc1 439898

O=Cc1c([nH]c2ccccc12)c1ccc(F)cc1 439900

O=Cc1c([nH]c2ccccc12)c1ccc(C)cc1 439902

O=Cc1c([nH]c2ccc(Cl)cc12)c1ccccc1 439904

C1NCc2c(C1)[nH]c1ccccc21 439908

Cc1ccc2[nH]c3CCNCc3c2c1 439910

COc1ccc2[nH]c3CCNCc3c2c1 439912

Fc1ccc2[nH]c3CCNCc3c2c1 439914

Hi,

It is not supported by default to use the comment part of the SMILES line (anything after the SMILES string) as it  is ignored during input.

What you can easily do is to solve the problem with simple shell programms:

molconvert smiles:-a inputfile.smi -o outputfile.smi
cut -d' ' -f2- inputfile.smi > ids.txt
paste -d' ' outputfile.smi ids.txt > result.smi

see the manual page of cut and paste for details.

 

I hope this helps

Andras

Thanks, this was very helpful!