It's just that I broke SMILES generation in Jmol. On Sun, Aug 8, 2010 at 11:39 PM, Otis Rothenberger <[email protected]>wrote:
> Bob, > > That's great, but see my note sent a few minutes ago. I don't think the > issue in my note creates a problem for your new compare function. It's > comparing internal Jmol SMILES. I think, however, I've encountered a problem > related to stereo SMILES via Jmol vs "absolute" SMILES. > > > Otis > > Otis Rothenbergerchemagic.com > > > On 8/9/2010 12:30 AM, Robert Hanson wrote: > > It works. > > On Sun, Aug 8, 2010 at 6:40 PM, Philip Bays <[email protected]> wrote: > >> Bob: >> >> If this works it is really great. In my stereochemistry tutorials, I have >> models randomly chosen and then have a data set so I know what the >> relationship is between the two structures chosen. Your compare function >> would obviate all of the data and do it automatically. Cool!! I know >> that one comparison in my data file is wrong, but I don't know which it is. >> This is the easy way to avoid trying to figure that out!! >> >> Phil >> >> On Aug 8, 2010, at 6:48 PM, Robert Hanson wrote: >> >> I've got the following: >> >> *x =compare({atomset1}, {atomset2}, "ISOMER")* Carries out a comparisons >> of atoms in the two atom sets and returns one of the following strings (Jmol >> 12.2): >> CONSTITUTIONAL ISOMERS having the same molecular formula but not the >> same connectivity ENANTIOMERS configurationally enantiomeric (mirror >> images) DIASTERIOMERS differing in one or more stereocenters >> (including double bonds) CONFORMATIONAL ISOMERS (x.xxxx) having the >> same constitution and configuration, but differing significantly in >> conformation (having root-mean-square deviations greater than 0.1; RMSD >> reported in parentheses IDENTICAL the same, constitutionally, >> configurationally, and conformationally NONE no relationship >> >> Conformational/Identical is tricky, because it's going to have to be based >> on some RMSD cut-off. I think we'll have to see how that works. Right now I >> have it reporting the RMSD with the result. >> >> But also I'm trying to fix that square planar geometry report. I know when >> I produced that bug -- just have to figure out how to remove it. >> >> On Sun, Aug 8, 2010 at 2:28 PM, Otis Rothenberger >> <[email protected]>wrote: >> >>> Bob, >>> >>> The constitutional part sounds tricky, but interesting. From a model kit >>> application perspective, I think incorporating the command in Jmol is a good >>> idea. >>> >>> Your script suggestions broke configurational into enantiomeric and >>> diastereomeric. Will that be part of the command? If not, the return from >>> the suggested compare command can be used to fish these types out as >>> needed. I know the term geometric isomer is dated, but I like the term. >>> From the logic of your script breakdown, I don't see a way to catch >>> geometric isomers. If you have any ideas on this, I'd love to hear them. >>> >>> Otis >>> >>> Otis Rothenbergerchemagic.com >>> >>> >>> On 8/8/2010 12:40 PM, Bob Hanson wrote: >>> >>> Otis, I'm integrating this into Jmol today. Should be able to distinguish >>> constitutional, configurational, and conformational isomers. >>> >>> Command will be: >>> >>> X=compare({1.1},{2.1},"ISOMER") >>> >>> Bob >>> >>> >>> On Aug 8, 2010, at 2:00 AM, Otis Rothenberger <[email protected]> >>> <[email protected]> wrote: >>> >>> >>> >>> Bob, >>> >>> I tacked your compare suggestions on to the end of our two model (same >>> frame) identity check. After a 1 second delay, your isomer type >>> comparison is displayed. In case users interested in this type of thing >>> missed your code in my previous verbose email chain re SMILES problems, >>> I'll post it in this separate note. All I can say is great and useful >>> toy. I've been playing with variations (2R,3R)-2-bromo-3-chlorobutane >>> and others way past bed time. >>> >>> Otis >>> >>> Bob Hanson Wrote: >>> >>> The way I was thinking to categorize two models is this: >>> >>> var m1 = {molecule=1} # or whatever >>> var m2 = {molecule=2} # or whatever >>> >>> # check molecular formulas >>> >>> var sameMF = (m1.find("MF") == m2.find("MF")) >>> >>> # get SMILES string for molecule 1 >>> >>> var smiles = m1.find("SMILES") >>> var smiles_enantiomer = >>> sm.replace("@@","!@").replace("@","@@").replace("!@@","@") >>> var smiles_nostereo = smiles.replace("@","") >>> >>> # note: we can't just compare SMILES strings like we can molecular formulas >>> # because SMILES strings here are not "cannonical" - but that is no >>> problem at all >>> # instead, we "find" the SMILES string for one model in the other. Using >>> "SMILES" >>> # here instead of "SMARTS" guarantees an exact search and not a >>> substructure search >>> >>> var identical = sameMF && (m2.find("SMILES",smiles)> 0) >>> var configurationalIsomers = sameMF && !identical && >>> (m2.find("SMILES",sm_nostereo) > 0) >>> var enantiomers = configurationalIsomers && >>> (m2.find("SMILES",smiles_enantiomer) > 0) >>> var diastereomers = configurationalIsomers && !enantiomers >>> var constitutionalIsomers = sameMF && !identical && !configurationalIsomers >>> >>> -- >>> Otis Rothenbergerchemagic.com >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by >>> >>> Make an app they can't live without >>> Enter the BlackBerry Developer Challengehttp://p.sf.net/sfu/RIM-dev2dev >>> _______________________________________________ >>> Jmol-users mailing >>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by >>> >>> Make an app they can't live without >>> Enter the BlackBerry Developer Challengehttp://p.sf.net/sfu/RIM-dev2dev >>> _______________________________________________ >>> Jmol-users mailing >>> [email protected]https://lists.sourceforge.net/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 >>> [email protected] >>> 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 >> >> ------------------------------------------------------------------------------ >> 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 >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> J. Philip Bays >> >> Professor of Chemistry >> >> Science Hall 172 >> >> Saint Mary's College >> >> Notre Dame IN 46556 >> >> (574) 284-4663 >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> [email protected] >> 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 > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challengehttp://p.sf.net/sfu/RIM-dev2dev > > > _______________________________________________ > Jmol-users mailing > [email protected]https://lists.sourceforge.net/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 > [email protected] > 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
------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
