Re: [Jmol-users] State and Triple Bond

[Robert H. <ha...@st...>]

I don't think so, Otis.

load smiles "C#C"
show state/sdf

  load /*file*/"
http://cactus.nci.nih.gov/chemical/structure/C%23C/file?format=sdf&get3d=True
";


It could be that somewhere in your processing.  I did that at Chemagic.com.


Bob



On Fri, Dec 13, 2013 at 9:25 AM, Otis Rothenberger <osr...@ch...>wrote:

> This is just an advisory about Jmol state that may save some other users
> some frustration. After the fact, I see that the frustrating situation is
> actually a design feature. I just missed it. If you want to save time on
> the issue, jump to the Bottom Line in my last sentence.
>
> I'm getting state with:
>
> 1) stateData = Jmol.getPropertyAsString(jmolApplet0, "stateInfo");
>
> If a triple bond containing model is loaded with a SMILES, then the state
> file contains something like the following after it's saved to server:
>
> 2) load model ({0}) /*file*/"http://chemagic.com/models.aspx?smi2sdf=CC#C
> ";
>
> That needs to be the following to communicate with Resolver:
>
> 3) load model ({0}) /*file*/"
> http://chemagic.com/models.aspx?smi2sdf=CC%23C";
>
> This is all well and good. You need to make these # URL conversions when
> you work with Resolver.
>
> Here's the advisory: When you go to make this change using replace on the
> state variable, you need to know that 1 above already has the value "%23"
> in place for triple bond #. This, however, gets written to server as #.
> Consequently, a replace statement on stateData would look something like
> this:
>
> 4) stateData = stateData.replace(/%23/g, "!HASH!");
>
> Not:
>
> 5) stateData = stateData.replace(/#/g, "!HASH!");
>
> Since the state variable is used directly in Jmol to RESTORE model state,
> I now see why this had to be handled this way. Bottom Line: If you're
> looking for a triple bond # in a state file variable, look for %23, not #.
>
> Otis
>
> --
> Otis Rothenberger
> ot...@ch...
> http://chemagic.com
>
>
>
>
>
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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