On 24/03/2015 05:05, Geoffrey Hutchison wrote: > Please don't write to me directly. There are many other users and developers > and in most cases, your message will simply get buried in my e-mail box.
Thanks, I use obabel very occasionally, was not aware of the existence of the mailing list. > > Without hydrogen atoms on the PDB file, the bond perception algorithm must > "guess" (i.e. perceive) bond orders. > > If you know something about the bonding topology, I would not use the PDB. A > quick search on Google turned up PubChem: > https://pubchem.ncbi.nlm.nih.gov/compound/5288494?from=summary#section=3D-Conformer > > This gives SMILES: > OC(=O)/C=C/c1ccc(/C(=C(/CC)\c2ccccc2)/c2ccccc2)cc1 > > It seems perhaps you do not want stereochemical information? > Thanks again for the hint, will take a look at it. Best regards, lina > Best regards, > -Geoff > > >> On Mar 23, 2015, at 1:41 AM, zhao li na <zh...@bii.a-star.edu.sg> wrote: >> >> Dear Geoff, >> >> When I used obabel to convert either mol2 or pdb into smi format, the >> generated smiles in not what I expected. >> >> Here I attach an example, >> >> the command I used is >> >> obabel -ipdb 1R5K_ligand.pdb -osmi -O 1R5K_ligand.smi >> >> I expect something like this. >> :::::::::::::: >> CCC(C(c1ccccc1)c1ccc(CCC(O)=O)cc1)c1ccccc1 >> >> But the output is something like this, >> :::::::::::::: >> CC[C@@H]([C@H](c1ccccc1)c1ccc(/C=C/C($O)$O)cc1)c1ccccc1 >> >> THanks ahead for your suggestions, >> >> Best regards, lina >> <1R5K_ligand.pdb><1R5K_ligand_prot.mol2> > -- zhao li na ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
