[Open Babel] dbase filtering, then substructure search (in that order)

Dear all, I am trying to look for certain molecules in the sdf/fs database containing certain fragments as substructure. The problem is my fragments can be small (I am running a script to do multiple searches), so I can get "too many candidates in the fingerprint search phase". The simple solut

Re: [Open Babel] dbase filtering, then substructure search (in that order)

o: openbabel-discuss@lists.sourceforge.net Sent: Tuesday, November 20, 2012 11:42 AM Subject: Re: [Open Babel] dbase filtering, then substructure search (in that order) On 20/11/2012 08:03, Visvaldas K. wrote: > Dear all, > > I am trying to look for certain molecules in the sdf/fs database >

[Open Babel] how to add new hydrogens without readjusting existing ones?

How to add hydrogens without readjusting existing ones? Some programs like AutoDock  only have nonpolar hydrogens. If add also nonpolar hydrogens to the docked conformation, the existing polar hydrogens seem to be readjusted by openbabel. This is not good if I want to retain hydrogen bonds disco