At 18:01 06/02/2006, Miguel wrote:
A few thoughts on jcamp, spectra, etc. which I hope are constructive.
> Hi Miguel,
>
> I have been checking the jmol forums and it seems that there may be some
> duplication of efforts on developing a jcamp display applet.
Perhaps
> Our original source code was from Henry Rzepa and I was led
> to believe it is open source.
I have copied in Henry in case he doesn't read jmol-dev.
> Shravan is still working on trying to integrate the spectra
> applet with jmol so we can pass a script to jmol. In addition
> he will be working on a "zoom" feature.
Very good.
> However, if Robert Lancashire already has a fully developed applet that
> interfaces with jmol already, perhaps we are wasting our time. It would be
> nice to know more about what he has already accomplished.
>
> Your thought?
My understanding (only from messages on the list) is that Robert's applet
is not currently released under an open source license, although he is
considering a license change that would make it open source.
I personally have had no recent contact with Robert.
I encourage you to coordinate with Bob Hanson and others on the
jmol-developers mailing list.
I think it's important to realise that "reading spectra" covers a
wide range of possibilities and Jmol should be careful it doesn't get
sucked into a tarpit. I have to declare an interest in that CML has,
with the Blue Obelisk/CDK/NMRShiftDB group at Koeln, developed
CMLSpect for managing spectra and their relationship to molecules. We
also have a funded project at Cambridge/Imperial for the capture of
spectra and archival in institutional repositories (SPECTRa (sic)).
* formats. Jcamp is an industry standard of many years' standard and
representing the thinking in informatics ca 25 years ago . It has
some extensibility, has some controlled vocabularies but has at least
6 and possibly more dialects. I have hacked most of these and they
are horrible. There would be continuing pressure to support all
these. There is the library at Cubic/Koeln for reading them, and this
would certainly have to be integrated into Jmol.
* manufacturers. By no means all manufacturers support Jcamp and what
comes off the machine initially is likely to be a binary file which
is manufacturer-specific. You will certainly get requests to support
these. They *are* a tarpit!
* FID spectra. You may well get FID spectra which require Fourier
transformation. If you don't understand FID spectra I suggest you
don't undertake to support them
* types of spectrum. These include 1H, 13C other nuclei, IR, UV, CD,
ESR and variants, Moessbauer, two-electron fluorescence, etc. These
include all variants of upside down, right-to-left, left to right,
variable units, etc.
My personal view is that Jmol, like all Blue Obelisk adopters, should
concentrate on doing its core activities excellently. IMO these are:
* molecular display
* other graphical objects (isosurfaces)
* animation
* scripting
* event models for molecules
* a limited amount of geometry analysis
Many of us are working towards a component-based community, under the
BO and others. These will be integrated in modern Open frameworks
such as workflows (Taverna) and application environments
(Eclipse/Bioclipse). The Koeln group (Tobias and Miguel) have been
visiting this week and have shown some very impressive
implementations in Bioclipse. It can display spectra (Spok, Koeln),
2D molecules, validate CML, interact with information systems, etc.
We see Jmol as a component that runs under Taverna, Bioclipse, etc.
and communicates with other components such as Spok. Spectra can be
done by Spok, by whatever comes from Robert, from any appropriate
open source tool. This avoids jar-hell, distribution problems, etc.
HTH
P.
Miguel
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Peter Murray-Rust
Unilever Centre for Molecular Sciences Informatics
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