Re: [Jmol-users] [JSmol] I am wondering why it takes so long to load a smiles string

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

Use the SMILES if you can. The 2D requires MMFF94 minimization, and that is
what is slowing it down so much.


On Thu, Aug 8, 2013 at 10:47 PM, 陈文瀚 <che...@gm...> wrote:

> >> Do you have the same trouble at
> http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm ?
> It runs really fast. So I downloaded the page and did some simple test
> locally and it worked quite well.
> I monitored the network usage, and saw the invoking cactus.nci, but mine
> didn't do that.
>
> Only then I realized instead of passing a SMILES string to the url, by
> using load SMILES, I used load INLINE to load a string generated by JME
> with 2D representation of the molecule with atoms and corresponding
> coordinates like this :
>     6 6 C 14.93 -4.45 C 14.93 -3.05 C 13.72 -2.35 C 12.51 -3.05 C 12.51
> -4.45 C 13.72 -5.15 1 2 1 2 3 2 3 4 1 4 5 2 5 6 1 6 1 2
> Seemed to me the parsing of the string takes ages to finish, then the JME
> format string returned from cactus.nci. However still I will prefer to
> parse of the 2D coordinates into 3D. So I am wondering is there a way to
> make it parse faster?
>
> Cheers,
>
>
>
> _________________________________
> Wenhan Chen
> School of Chemistry and Molecular Biosciences
> The University of Queensland
>
>
>
> 2013/8/8 Robert Hanson <ha...@st...>
>
>> Wenhan Chen,
>>
>> If you are transferring a SMILES string to Jmol, it will have to go
>> through the NCI Resolver to get the structure. It's probably that
>> connection. Do you have jsmol.php set up on your server? Without that, some
>> browsers won't work at all, because you are doing an AJAX all in JSmol to a
>> remote server. If you can open a developer console in the browser, check
>> the network usage and see if it is hanging on a call to NCI.
>>
>> Do you have the same trouble at
>> http://chemapps.stolaf.edu/jmol/jsmol/jsmetest.htm ?
>>
>> Bob
>>
>>
>>
>> On Wed, Aug 7, 2013 at 11:11 PM, 陈文瀚 <che...@gm...> wrote:
>>
>>> Hi all,
>>>
>>> I am trying to shift my old Jmol routines to Jsmol as a way to avoid the
>>> disturbing warnings using Applet.
>>>
>>> I have long smiles string generated from JME for a relatively larger
>>> molecule(60 atoms) for unknown reasons it takes ages to get it loaded into
>>> Jsmol. And the browser kept poping up the warning of script not responsive.
>>> I am wondering if anyone else experience this before and how to solve it?
>>>
>>> Cheers,
>>>
>>>
>>> _________________________________
>>> Wenhan Chen
>>> School of Chemistry and Molecular Biosciences
>>> The University of Queensland
>>>
>>>
>>>
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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
>>
>>
>>
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>>
>
>
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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