B Source Code

Finally, here is the source code. I had such great intentions of commenting the code and updating the API to be JDK 1.1 and 1.2 compliant, but I have fallen way behind, so I am hoping some others may be able to help (at least in terms of updating the API)...If not, feel free to help yourself and use what you can!


tar files
Biomer.tar
Biomer.tar.gz
Individual Files
About.java
Amber.java
Atom.java
Biomer.java
BiomerFrame.java
ConjugateGradient.java
ErrorDialog.java
ForceField.java
Fragments.java
GifEncoder.java
ImageButton.java
ImageEncoder.java
ImageLabel.java
IntHashtable.java
JpegEncoder.java
Matrix3D.java
MinimizeOptionsDialog.java
MolecularDynamics.java
MolecularDynamicsDialog.java
MolecularMechanics.java
Molecule.java
MoleculeCanvas.java
MoleculeCanvas3D.java
NucleicAcidDialog.java
NucleicAcidResidue.java
PDBChemModel.java
PeriodicTableDialog.java
PolyPeptideDialog.java
PolyPeptideResidue.java
PolySaccharideDialog.java
PolySaccharideResidue.java
PpmEncoder.java
PreferencesDialog.java
Residue.java
SaveMolecule.java
ShadeRef.java
SteepestDescent.java
Strand.java
SubImageButton.java
ThreeButtonDialog.java
XYZChemModel.java

Note: Biomer was written using the Java 1.0 event model to be compliant with most browsers. It was developed on a Linux machine running RedHat 5.1/5.2. The newer RedHat (notably, RedHat 6.0) systems come with a default JDK of kaffe - a GNU version of the JDK (you can test this by typing "cat `which java`"). Kaffe and the newer JDKs from Sun (e.g., JDK1.2) don't seem to adequately support the older event model. As such, it will be neccessary to update the Biomer event model APIs for these systems - something that I have been slow to get to...