Otis, the updated applet is now in http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
"compare" examples can be found at http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm On Mon, Aug 9, 2010 at 10:00 AM, Robert Hanson <hans...@stolaf.edu> wrote: > Otis, it will take some getting used to and some careful documentation, but > I think you will find this SMILES/SMARTS "find" business extraordinarily > useful. It is a bit tricky. > > > On Mon, Aug 9, 2010 at 9:35 AM, Otis Rothenberger > <osrot...@chemagic.com>wrote: > >> Bob, >> >> I noticed that the return was either an array of all of the atomIndexes >> or null. The Boolean return for the statement was "on" or "off." >> >> I picked up on the fact that the find was not associative from your >> original discussion of the Jmol SMILES applet. I have to admit that I've >> been approaching this issue by trial and error. I have difficulty >> understanding who is to be searched by whom! Your specific example below >> may be putting me on the correct path on this issue. Am I on the right >> track with the following four search order assumptions? >> >> > I assume we are talking about "xxx".find("SMILES","yyy") here: > > > >> 1) If no stereo information is involved in either SMILES, it does not >> matter. >> > > > right > > >> 2) If both have stereo information, it does not matter??? >> > > right > > >> 3) If one SMILES has stereo information and one does not, then the >> stereo SMILES is the one to search??? >> > > if "xxx" has stereochemistry and "yyy" does not, then stereochemistry is > ignored > if "yyy" has stereochemistry and "xxx" does not, then the match will fail > > The idea is that when you "find" yyy "in" xxx if you have specified > stereochemistry in yyy, then it better be there in xxx because you are > explicitly looking for it; if you have not specified stereochemistry in > "yyy", then it doesn't matter what stereochemistry is indicated in xxx, > because -- apparently -- you don't care. > > The return from that will be as it was documented -- > 0 for a find, 0 for > no find, and -1 for error. > The array return business is now with "SMARTS" only. In that case, an error > just returns "?" > > > >> 4) In "XXXXX".find("SMILES","YYYYY"), "XXXXX" is being searched for >> "YYYYY." >> >> > right. Just like in "XXXXX".find("YYYY") the string "XXXXX" is being > searched for "YYYY". > > >> I'm assuming above that my intent is an identity check. I'm also >> assuming that 3 would return a match, but with stereo ambiguity. >> >> Ahh, didn't your vacation start yesterday? >> >> > Wednesday > > >> Best, Otis >> >> Otis Rothenberger >> chemagic.com >> >> >> On 8/9/2010 1:01 AM, Robert Hanson wrote: >> > SMILES generation is broken in 12.0. Let's take a look at this again >> > after I fix that. >> > >> > Note that find is not associative: >> > >> > "c...@h](Cl)F".find("SMILES","CC(Cl)F") >> > >> > and >> > >> > "CC(Cl)F".find("SMILES","c...@h](Cl)F") >> > >> > are not the same. In the first case, the result is TRUE; in the second >> > case it is FALSE. >> > >> > Also, I have just changed the output from that function. It now >> > returns an array of integers indicating which atoms of the initial >> > string were part of the match >> > et/lists/listinfo/jmol-users >> >> >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by >> >> Make an app they can't live without >> Enter the BlackBerry Developer Challenge >> http://p.sf.net/sfu/RIM-dev2dev >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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