Table of Contents
Prerequisites:
Java 2 JDK (http://java.sun.com/)
Apache Ant (http://jakarta.apache.org/ant)
DocBook XSL (http://sourceforge.net/project/showfiles.php?group_id=21935)
Jmol source code
The Jmol source code can be either downloaded (see SourceForge project files) or checked out from the CVS repository (see SourceForge CVS access).
Once you have all the prerequisites, Jmol can be built from the top source directory with the following command:
On Unix,
/home/user/programming/Jmol> ant -Ddocbook.dir=/home/user/programming/docbook-xsl
On Windows,
h:\programming\Jmol> ant -Ddocbook.dir=h:\programming\docbook-xsl
where docbook.dir is set equal to the absolute path of the DocBook XSL.
The applet needs to be compiled with javac 1.2, to be compatible with most browsers. This can be done by doing:
h:\programming\Jmol> setenv JAVA_HOME /path/to/java1.2
h:\programming\Jmol> ant -Dbuild.compiler=classic
On Unix, the development version of Jmol is run by simply executing the jmol script in the Jmol development directory.
On Windows, the environment variable JMOL_HOME must be set to the development directory, and then the jmol.bat script can be executed. For example:
H:\programming\Jmol> set JMOL_HOME=h:\programming\Jmol
H:\programming\Jmol> jmol.bat
Jmol source code should be written in a style which adheres to "The Elements of Java Style" by Vermeulen, et al.
Table of Contents
Making releases is currently one of the core responsibilities of the project leader. A release primarily consists of the .zip and .tar.gz distributions. Binary packages are not part of the Jmol release, but the release manager will inform the packagers in time to make binary packages.
A Jmol release consists of both the application and the applet. Both must work as expected.
In the samples/ directory a number of test files are located for the input filters. All files in that directory must be checked to be readable before every release.
The following table names all files, the reader classes which should read it, and the Extra windows that should be available.
filename | reader | extra |
|---|---|---|
1crn.pdb | PDBReader | |
4-cyanopheylnitrene-Benzazirine-TS.g94.out | Gaussian94Reader | Vibrate |
ammonia.adf.out | ADFReader | Animate, Vibrate |
azt.xyz | XYZReader | |
bulk_Si.in | ABINITReader | Crystal |
caffeine.xyz | XYZReader | |
CdSe_nanocrystal.xyz | XYZReader | |
ch3oh_ace.out | Aces2Reader | Vibrate |
ch3oh_g94.out | Gaussian94Reader | Animate, Vibrate |
ch3oh_gam.out | GamessReader | Vibrate |
ch4-opt.out | JaguarReader | Animate |
cholesterol.xyz | XYZReader | |
Cl2O.log | GamessReader | Animate |
conformeren.cml | CMLReader | Animate, Graph |
cs2.xyz | XYZReader | |
cyclohexane_chair.xyz | XYZReader | |
cyclohexane_movie.xyz | XYZReader | Animate |
ddt.xyz | XYZReader | |
diels-alder_movie.xyz | XYZReader | Animate |
dna.xyz | XYZReader | |
estron.cml | CMLReader | Crystal |
ethanol.xyz | XYZReader | |
ethene.mm1gp | ChemicalMMReader | |
frame_1.res | ShelXReader | Crystal |
g98.out | Gaussian98Reader | Animate, Vibrate |
glycine-crystal.cml | CMLReader | |
HfO2_mol_opt.in | ABINITReader | Crystal |
HfO2_on_Si_relax.in | ABINITReader | Crystal |
met-enkaphalin_movie.xyz | XYZReader | Animate |
methanol1.cml | CMLReader | |
methanol2.cml | CMLReader | |
pdhch3.in | Jaguar Input is not yet supported | |
phenol-without-para-G.g98.out | Gaussian98Reader | Animate, Vibrate |
phenylnitrene.g92.out | Gaussian92Reader | Vibrate |
phenylnitrene.g94.out | Gaussian94Reader | |
slab_7Si_3Vac_2x.in | ABINITReader | Crystal |
slab_7Si_3Vac_2x_relax_2x1.out | ABINITReader | Crystal, Animate, Graph |
SN1_reaction.cml | CMLReader | Animate |
SN1_reaction.xyz | XYZReader | Animate |
SN2_reaction.xyz | XYZReader | Animate |
t54.in | ABINITReader | Crystal |
taxol.xyz | XYZReader | |
test.mol | MdlReader | |
tms.log | Gaussian94Reader | Animate, Chemical Shift |
toluene.pdb | PDBReader | |
viagra.xyz | XYZReader | |
zeolite_AFl.out | ABINITReader | Crystal, Graph, Animate |
zoloft.xyz | XYZReader |
Distribution packages will be made for any platform for which a developer promises to provide support. File used to create packages should be commited to CVS under the Jmol/packaging directory. Currently the following packages are available:
RPM (by Bradley Smith)
Debian (by Egon Willighagen)
MacOS (by Dan Gezelter)