Java Applets for Displaying 3D Molecule Structures –
an Overview
Andreas Bohne-Lang1*, Elke Lang2 12/2004
1)
German Cancer Research Center, Molecular Modeling, Im Neuenheimer Feld 280,
D-69120 Heidelberg, Germany, a.bohne@dkfz.de
2)
University of Applied Sciences Darmstadt, Information and Knowledge Management,
Campus Dieburg, Max-Planck-Strasse 2, D-64807
Dieburg, Germany, lang@iuw.fh-darmstadt.de
Abstract: Nowadays,
the Web is one of the most intensively used information sources for scientific
and educational purposes. Unfortunately, standard web browsers are not capable
of displaying 3D molecular structures embedded in web pages. Other techniques
like plug-ins (e.g. Chime plug-in) show the disadvantage of being dependent on
operating systems and web browsers. Java applets do not show this disadvantage
- they can be run on either operating systems and web browsers. Thus they are
predestinated for visualization of 3D molecular structures in web pages. This
article will put a small spotlight on 14 of the most used Java applets used in
Web-based applications and will stress special features of the discussed
applets.
Key
words: General Chemistry /
Internet & Web-based Materials, Drugs & Pharmaceuticals, Distance
Learning, Writing in Chemistry
Introduction
Visualization of
three-dimensional (3D) molecular structures and their related properties is a
key feature for understanding the dynamics of molecules, of chemical reactions,
and the expression of macroscopic behavior determined by microscopic
properties. Thus, there is a long tradition of 3D model building and 3D
visualization by means of wooden or plastic models and by symbolizing 3D
structures using 2D means. Especially for educational purposes, simplification
and reduction are essential methods in order to get rid of complexity and of
properties that do not lie within the current focus. Hence, all aspects dealing
with the 3D structure have one fact in common: understanding the structure is
facilitated by selectively putting the emphasis on certain structural
components. Tools used for visualization should offer a broad range of
structure representation features, thus offering selective perspectives on
certain features.
The term ‘visualization of
molecules’ can be understood in different aspects [1,2,3]. On one hand it can
deal the question how a molecule is displayed: It can either be represented
using a two-dimensional structure graph composed of lines on a plane layout
ground, or it can be displayed by a three-dimensional model giving the user the
impression of space, relationships and even interaction of structural
components [4,5]. On the other hand, the focus of visualization can be put on
the molecular properties that should be highlighted according to relevance.
Relevant content or features could be structural components of a protein as
well as interaction of a protein and its ligand, or the style of coloring the
surface according to aspects like physico-chemical behavior, lipophilic or
hydrophobic properties or electrostatic potential [6].
Eric Martz, a pioneer of using
3D software for teaching students, outlines in his ‘BioMolecules in the
Classroom: Educational Molecular Visualization with Chime & RasMol’ [W32]
how visualization of molecules can help to understand complex biochemical
reactions.
Within the last years,
‘standard hardware’ has become well-suited for visualization purposes, and
visualization software is no longer expensive and cumbersome to install and
maintain. This opens a broad application field in realms where visualization is
valuable and desired, but cannot be maintained using
expensive resources.
This
article shows a series of 14 visualization tools that are well-suited for
educational purposes in three aspects: comfortable handling of technical
aspects (no difficult software installation needed), user surfaces are suitable
but simple, free access. The article mainly covers three technical aspects. The
fist concerns the efforts that are needed before being able to run a certain
applet for the first time. The second aspect deals with the display styles and
functions offered by the tools. The third aspects is related to the features of
using the mentioned applets within web pages that are programmed and/or
maintained by the users themselves.
A
brief introduction to Java technology
Modern
Web Browsers like Internet Explorer, Mozilla, and Opera cannot display chemical
structures without using additional software. They confine themselves to layout
of HTML (Hypertext Markup Language) and other text elements. Thus the user has
to install additional software components for visualizing 3D molecular
structures [W5]. In order to achieve graphical display of a molecule, the
browser has to retrieve a MIME (Multipurpose Internet
Mail Extensions) type indication [W4] from
the web server together with the molecule description data. The MIME type indicates the kind of data transmitted
and how data should be treated. There is a special
MIME type for molecule description data as
well as for movies or sounds.
In general, there are two different techniques
with different advantages and disadvantages (Tab. 1): External helper
applications and plug-ins. The group of plug-ins
should be divided up into native plug-ins like Chime and the Java plug-in that
is capable of executing the byte code of Java applets. In contrast to external
helper applications, the byte code of Java applets and programs is independent
of the operation system.
MDL`s Chime [W3] is
one of the most often used plug-ins for web-based display of chemical
structures, but Chime is not an open source project and the latest version only
supports Windows. Linux users can use Windows Chime by means of the CodeWeaver cross-over
plug-in[1].
Some words in
general concerning Java: In 1995 the Internet was becoming popular as a way of
moving media content - text, graphics, video - throughout a network of
heterogeneous devices using HTML. Java technology had been designed for parallel applications, e.g. to move media content across networks
of heterogeneous devices, but it also offered the capability to move ‘behavior’
in the form of applets along with the content. Sun’s molecule visualization
applet [W20] dates of this time. When Gosling, one of Sun’s first Java
developers, used this applet in a presentation for the first time, he impressed
the audience as they saw a molecule rotating in the middle of a static web
page. The initial idea of Java was writing programs in a programming language
that can be executed on each computer – independently from the operating
system. A program (compiler) translates the program code to a smaller
representation, the byte code. This byte code is transmitted over the Internet
and executed locally by the virtual machine that is part of the runtime
environment of Java. The Java plug-in provides web browsers with the virtual
machine for execution of the applet code. There are special Web security
features: E.g. generally, an applet is not allowed to access data from the
local hard disk of the user’s computer – it is running in a restricted
environment called sandbox. Later a mechanism was developed that enables
applets writing data to the local hard disk. In this case the applet needs a
security certificate that ensures the trustability of the data source. MolVie
uses this mechanism. Only the virtual machine that interprets the code is
highly system-dependent, but meanwhile Java virtual machines are available for
almost every computer system.
Java3D
Unfortunately,
the Java3D extension [W23a] abandons independency of the operating system. This
means the code cannot be executed on every computer as with normal Java
classes. At the moment, these special Java3D classes are only available for
Windows and Linux. A Mac version is in the beta phase. The Java3D extension has
to be installed on the client computer together with the Java runtime
environment. The 3D extension provides an interface to the DirectX or OpenGL
graphic layer of graphics cards in order to have fast access to the graphical
primitives. For a long time the main processor of a computer itself had to
calculate and render 3D objects. Today a dedicated graphics processor on the
graphics card does this job very fast. An extra layer (DirectX or OpenGL) has
been designed and implemented as an interface to this special processor. Thus
the main processor passes the description of an object to the graphics
processor which renders this object. The Java3D classes offer the advantage
that the programmer can easily use powerful functions to generate surfaces or
other complex objects.
One
of the most recent projects is JOGL (Java bindings for OpenGL) [W23b] that
needs at least Java 1.4.2 and provides full access to the APIs (Application Programming Interface) in
the OpenGL 1.5 specification as well as for nearly all vendor extensions.
|
Table 1: Advantages of different software techniques |
|||
|
|
Java
Applet |
Plug-in |
External
Helper Applications |
|
Installation by user |
(no)1 |
yes |
yes |
|
Simpleness of installation |
(-)1 |
easy |
medium |
|
Operating system dependencies |
low |
high |
high |
|
Browser dependencies |
low |
high |
no |
|
Interaction with other software components |
yes |
yes |
no |
|
Execution speed |
low-medium |
high |
high |
|
Data to
transfer |
Applet
code and molecule structure data |
only
molecule structure data |
only molecule structure data |
|
Parameter |
several |
several |
one |
|
Layout |
Browser
window |
Browser
window |
External
window |
|
User interaction |
possible |
possible |
possible |
|
Typical Implementation |
See
Table 2 |
Chime[W3],
canDo [W29], Flash
[W30,W31] |
RasMol[7,8,W1],
PyMol[W2], Swiss-PDB Viewer[9,W4] |
|
1) Windows XP is delivered without Java, and the
Java plug-in must be downloaded separately
from Sun’s Java page. The installation is done just by a click. |
|||
A brief explanation to the criteria listed in Table 1.
‘Installation’ and ‘Simpleness of installation’ describe if the user
needs to install software components separately on his computer. For a long
time, web browsers were delivered with Java and later with the Java plug-in.
Due to a dissent between the two companies Microsoft and Sun Inc, Microsoft’s
web browser Explorer is no longer delivered including Java. ‘Operating system
dependencies’ and ‘Browser dependencies’ indicate if the program can be used in
all environments or not. Unfortunately the native plug-ins like Chime are
highly operating-system and browser dependent. ‘Interaction with other software
components’ means that data transfer to e.g. a second applet or plug-in could
be established. Plug-ins can be interfaced by JavaScript from the HTML code of
the web page. Animated GIF images [W6] could not be controlled by other
software components. ‘Execution speed’ shows the difference in speed between
two principles: As well plug-ins as external helper tools are fast as they are
compiled into native code that can be directly executed. Java applets, in
contrast, have to interpret the Java byte code. ‘Data
to transfer’ lists the types of data needed. In
contrast to plug-ins and helper tools, the execution of a Java applet requires
its byte code in addition to the molecule structure file. Java applets and
plug-ins accept more than one parameter, thus it is possible to set parameters
in web pages or pass both a script and the molecule file to the applet.
‘Layout’ means the location where the molecule is displayed. ‘User interaction’
stresses that the user can interact with the molecule. Alternatively, animated
molecules can be shown in rotation without any interaction.
A spotlight focus on the most important applets
Table 2 lists different properties and features of the different
applets. ChemSymphony Lite and
DistMol are not listed in Table 2, as ChemSymphony
Lite is commercial and not longer available and DistMol is
too simple.
|
Figure
1: Jmol [W13] |
Jmol (Fig. 1) provides the maximum number of features. It can run Chime
scripts and in general is one of the most powerful developments. Jmol
supports small molecules as well as large ones. It can be divided up into one
or more menu applets and one visualization applet. This feature helps in
placing menu functions on suitable locations on the website. |
|
Figure
2: Chemis3D
[W12] |
Chemis3D (Fig. 2) has a menu which is quite similar to RasMol and thus users
who are used to work with RasMol will feel quite fast familiar with this tool.
|
|
|
WebMol [10,W14] (Fig 3) is primarily designed for proteins but can also
display medium and small molecules. Stereo view mode is a nice feature of
this applet. It runs on every Java virtual machine because it provides an
interface to Java version 1.0. |
|
Figure
4: Eric Harlow’s 3D Java Molecule Viewer [W16] |
Eric’s
3D Java molecule viewer [W16] (Fig 4) is only
useful for small molecules. Its advantage is its simplicity, and it runs on
every Java machine. It displays only atoms by their atom symbols and the
linkages between atoms. |
|
Figure
5: Anton Zamov’s Java 3D Molecule Viewer [W19] |
Anton Zamov’s Java 3D Molecule Viewer [W19] (Fig 5) just offers
basic functions like measuring angles and distances. |
|
Figure 6: Sun’s simple molecule viewer [W20] |
Sun’s xyz applet [W20] (Fig 6) was one of the first applets
displaying molecular structures. It uses an interesting trick to display the
molecules: pseudo-3-dimensionality is achieved by placing only balls
in z-direction from back to front one over the other.
This simple trick is only useful for molecules of maximally medium size. |
|
Figure
7: ChemSymphony |
The
old ChemSymphony Lite applet can still be
seen on the Internet. ChemSymphony is a commercial chemistry modeling
application business unit. ChemSymphony products have been sold to and used
successfully by several large pharmaceutical companies. ChemSymphony was sold
to Netgenics, Inc., now part of Lion Bioscience since summer 2000. A working
example of ChemSymphony Lite applet can be
found at [W22]. ChemSymphony Lite is restricted to displaying small
molecules. Its only functionality is molecule rotation. It is only mentioned for the sake of completeness. |
|
Figure
8: DistMol |
DistMol
(Fig. 8) [W21] is only suitable to display small
molecules, its main function is molecule rotation. It is only mentioned for the sake of completeness. |
|
Figure
9: ChemApplet [W15] |
ChemApplet [W15] (Fig 9) This applet is only mentioned
for the sake of completeness. Unfortunately the applet can only load the very
specific csf format. It seems that the applet is not longer enhanced – the
main developer page is lost. |
|
Figure
10: JaMM
[W18] |
The JaMM applet [W18] (Fig 10) has the nice feature of
stereo view but it is restrained by its non-standard input format. |
|
Figure 11: MolVie[W17] |
Molvie [11,W17,W25] (Fig
11) is mainly designed for protein structure
display. It is available without Java3D support (Fig. 11) or, as
Molvie3D (Fig 12), with Java3D support. Molvie
needs Java plug-in 1.3 or newer versions. It can handle and display
the protein sequence. If the applet has permission
it can save molecule structures locally. |
Figure
12 : MolVie3D [W25] |
|
Figure
13: JMV [W24] |
JMV [W24] (Fig 13) is the abbreviation for Java
Molecular Viewer. It can display small molecules as well as proteins and it
has all of the basic functions a molecule viewer needs. |
|
Figure 14: PDBjViewer [W26] |
PDBjViewer [12,W26]
(Fig 14) is one of the
most powerful resources in the field of Java3D molecule
viewers.Unfortunately, this applet needs at least the Java 1.4.2 plug-in and
thus it runs on very few machines. The advantage is that it can handle Rasmol
scripts and the texture mapping of surfaces is quite beautiful. |
Combining
applets and plug-ins: Sting Millennium [W27] and Protein Explorer [W28] should
be mentioned at this point. Both applets cannot display a molecule structure on
their own (they use Chime for display purposes), but they perform powerful
preprocessing of protein data. These tools could potentially be used to convert
molecular data to Jmol for displaying the molecule structure; this would avoid
the disadvantages of Chime or plug-ins in common.
Conclusion and Discussion
In
general, developers of web pages should prefer Java applets rather than native
browser plug-ins as Java applets are independent of the operation system of the
computer. Which of the numerous Java applets should be preferred, however, is
depending on the intention of the web page. Generally, Jmol can be recommended
as an open-source project that includes a lot of nice features and supports
many load routines for different molecular structure representation formats.
Furthermore, Jmol is characterized by its closeness
to Chime, as Chime scripts can be used in Jmol without any problems. Using
Chime scripts, complex molecule views or animations can be programmed in Jmol.
Especially for education purposes, it is important to have not only a static
view of a molecule, but to be able instead to provide a dynamic animation of
chemical reactions. If special features are needed, it is advisable to offer
more than one applet type, like the stereo view mode of WebMol. Java3D applets
have a brilliant graphical quality (see Fig 14), but at the moment applets
using the Java3D extension should be classified as experimental. Incorporating
this type of applets on a Web page should therefore involve the availability of
an alternative standard applet.
Acknowledgement: We want to
thank the DFG
(Deutsche Forschungsgemeinschaft [German Research Society]) for funding the
project: Konzeption und Entwicklung einer Web-basierten Arbeitsumgebung für
glykowissenschaftliche Fragestellungen und Bereitstellung von fachbasierten
Informationsangeboten. [Concept and development
of a web-based workbench for glycoscience research and information services.]
References:
- Bohne
A., Lang E., von der Lieth CW. Drugs of
the Future 2000, 25, 489-500
- Martz E; 3D
Molecular Visualization with Protein Explorer in Introduction to
Bioinformatics Krawetz SA, Womble
DD Eds.; Humana, 2003; chapter 32, 565-586
- Gasteiger
J., Sadowski J, Schuur J, et al. J. Chem. Inf. Comput. Sci. 1996, 36, 1000-8
- Vollhardt
H., Brickmann J. Pac. Symp. Biocomput. 1995, 663-73
- Ihlenfeld
W. J. Mol. Model. 1997, 3, 386-402
- Tate J Methods
Biochem Anal 2003, 44, 135-158
- Sayle R A,
Milner-White EJ Trends Biochem Sci, 1995, 20, 374
- Bernstein
HJ Trends Biochem Sci. 2000, 25, 453-5
- Kaplan W, Littlejohn TG Brief
Bioinform. 2001, 2, 195-7
- Walther D Trends
Biochem. Sci. 1997, 2, 274-5
- Sun H,
Li M, Xu Y. Comput Methods Programs Biomed. 2003, 71, 85-90.
- Kinoshita K,
Nakamura H. Bioinformatics, 2004, 20, 1329-1330
Apendix A1: Further
reading URLs (referenced in text with [Wxx])
|
1 |
Rasmol
derivatives Original |
|
|
2 |
PyMol |
|
|
3 |
CHIME |
|
|
4 |
SwissPDB Viewer |
|
|
4 |
MIME types in chemistry |
|
|
5 |
List of free molecule visu- alization programs |
|
|
6 |
PDB2Multigif |
|
|
7 |
PDB2VRML (ex.) |
http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml.html |
|
8 |
Protein
Data Base |
|
|
9 |
CML (Chemical Markup Language) |
|
|
10 |
X3D |
|
|
11 |
Open Babel project |
|
|
|
||
|
Java
|
||
|
12 |
Chemis3D |
|
|
13 |
Jmol |
|
|
14 |
WebMol |
|
|
15 |
ChemApplet |
http://www.dkfz-heidelberg.de/spec/mol_view_java/ChemApplet/ |
|
16 |
3d Java Molecule Viewer (Eric Harlow) |
|
|
17 |
MolVie |
|
|
18 |
JaMM |
|
|
19 |
Java
3D Molecule Viewer v2.0 (Anton Zamov) |
|
|
20 |
Sun’s molecule viewer (xyzApp) |
http://java.sun.com/applets/jdk/1.1/demo/MoleculeViewer/example1.html |
|
21 |
DisMol |
|
|
22 |
Chemsymphony Lite |
|
|
|
||
|
Java3D |
||
|
23a |
Java
3D API |
|
|
23b |
Java bindings for OpenGL (JOGL) |
|
|
24 |
JMV |
|
|
25 |
MolVie3D |
|
|
26 |
PDBjViewer |
|
|
|
||
|
Preprocessing Applets (using Chime for displaying) |
||
|
27 |
Sting Millennium |
|
|
28 |
Protein Explorer |
|
|
|
||
Shockwave / Flash -
Viewer
|
||
|
29 |
canDo |
|
|
30 |
Ebook 3D Modler |
|
|
31 |
Flash CML-Reader
/ CML: [W9] |
|
|
|
||
|
BioMolecules in the Classroom |
||
|
32 |
Eric Martz |
|