Hi Geoff, Thank you. I think you're right that obrotate would be better suited to my needs if I removed the SMARTS matching feature. I can hack the .cpp myself and include an option for users to choose whether to use a SMARTS pattern or the existing atom numbers in the .xyz file.
Thanks, - Lee-Ping ----- Original Message ----- From: "Geoffrey Hutchison" <geo...@pitt.edu> To: "Lee-Ping Wang" <leep...@stanford.edu> Cc: openbabel-discuss@lists.sourceforge.net Sent: Friday, April 27, 2012 6:15:22 PM Subject: Re: [Open Babel] Questionable behavior in obrotate (or babel) > I believe that 'obrotate' is determining the atom numbers from the SMART > pattern, and this becomes a problem when the atom numbers in 'obrotate' don't > match the atom numbers from the XYZ generated by babel. In the first example > (isoleucine), there are two explicit hydrogens that obrotate is not counting. > In the second example, there are two identical CH3 groups; 'obrotate' will > rotate the second one even though I explicitly specified the first one. I apologize no one else responded to your message, I've been a bit busy finishing off the semester! > I am able to work around this manually by trial and error and 'guessing' > which atom numbers are requested by 'obrotate', but I think it would be much > more straightforward if the atom numbers could be taken from the XYZ file and > not determined from the SMART pattern. If the atom numbers must be > determined from the SMART pattern, then it should be done in a manner > consistent with the numbering scheme in 'babel'. If I understand, you actually really want a tool which changes the torsion of a set of bonded atoms defined by atom numbers you supply -- you really don't care about the SMARTS matching feature of obrotate at all, correct? If so, I'd suggest you just hack obrotate.cpp to your needs. I don't have time tonight, but it's not a huge ordeal. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
