Displaying Molecules and Spectra For Electronic Conferences in Organic Chemistry
Department of Chemistry, Imperial College, London, SW7 2AY.
This short poster demonstrates1 how 3D molecule and IR and NMR spectral data can be inserted
into an article or poster designed for discussion at an electronic conference, using
downloadable programs called Java applets.
1. Molecules displayed using the ChemSymphony Applets
- HTML Code to display a molecule
- Display the Molecule
- Size of download: Code 339505 bytes, Molfile 933 bytes
There is much debate whether molecular information should be displayed using
so-called plug-ins, which in effect chemically enhance your browser, or whether
an alternative procedure based on Java should be used. Whereas the former
requires the user to go through the actions of installing software on their
computer, the latter makes no such demand on the user. To a large extent, it
depends what the user expects to do with the information. If they wish to have
the best possible performance, and to perhaps save 3D molecule coordinates on
their own computer, then plug-ins are the way to go. If they wish the
convenience of not having any local software to install or de-install, the Java
route is preferable. It may also be the only route available if an appropriate
(platform specific) version of the plug-in is not available for your favourite
computer (e.g Unix systems).
Note in the above example that whilst the code size is significant, the actual
molecule coordinate file size is trivial. Thus on a slow Internet link, the user
will have to wait significantly for the display of a small molecule. For this
reason, this page has been designed not to force such download upon loading the
page, but to specifically request the use to invoke the action themselves at
their convenience. This page itself contains no images or other
download-intensive data, and so should be displayed rapidly even when the
Internet connection is a relatively slow one.
2. Spectra displayed using the jSPEC Applet
- HTML code to display a spectrum
- Display the Spectra: UV/IR-Netscape | UV/IR-Internet Explorer |NMR (p-tolualdehyde)-Netscape | NMR (p-tolualdehyde)-Internet Explorer
- Size of download: Code 32153 bytes, UV, 2508, IR, 48162, 1H NMR 262972, 13C NMR, 131908 bytes.
Spectral display is a much less CPU intensive procedure than 3D molecule
display and rotation. This in turn means that the code for invoking such display
can be kept very small and compact. In this case, it is the spectral data that is
far larger in size than the jSPEC code used to display it. In this case as well,
we have chosen to keep the Applet displaying the spectra quite separate from the
mechanism used to display molecules. Some programs (e.g. Chime V 2.0) can
support both types of display, as well as other properties such as molecular
surfaces. The jSPEC code can in fact be also used to communicate with
Chime-based objects, although introducing this feature also makes the
Java-based jSPEC code much more browser specific; one of the undesirable features
that the use of Java was meant to avoid. Thus the Netscape version of the jSPEC
viewer contains Java classes that are only supported in Netscape, and hence will
fail using Internet Explorer. These classes are the ones that support communication
with Netscape plug-ins, a feature not (yet) supported in Internet Explorer.
3. The Future of Internet-based Chemical Object Display
The current HTML standard widely implemented is level 3.2. Data destined for
display using a plug-in is invoked using an <embed src=molecule.mol>
style tag. In contrast, data which will be displayed using a Java applet must be
invoked using <applet code=Visua2.class ...><param
value="Fluor.spc"></applet>. In effect, its the author who is
apparently deciding how the data will be displayed, in making a choice between
these two methods. Ideally, that choice should be left to the reader, not the
author. The proposal for HTML 4.0 will replace both these methods with a single
method <object data="molecule.mol"
type="chemical/x-mdl-molfile"></object> which could be passed
to either a plug-in or a Java applet.
This poster illustrates some of the ways in which structured and high value
chemical information can be displayed using Internet technologies developed over
the last five years. One issue facing us over the next two years is whether we
should now move directly to the use of a higher level of markup such as CML
(Chemical Markup language), rather than using what are described as the legacy
files that current generations of plug-ins and applets support (e.g MDL
Molfiles). Some two million Internet-based documents contain chemical
information, and the task of migrating this chemistry to more highly structured
forms will be one of the challenges facing us in the near future.
- H. S. Rzepa, "A History of Hyperactive Chemistry on the Web: From Text and Images to Objects,
Models and Molecular Components", Chimia, 1998, to be published in November issue.
(c) ECHET98. May 1998