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.
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? 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> ------------------------------------------------------------------------------ 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
