Utilities used for faciliating development and avoiding to invent the wheel twice.
A memory efficient data structure to store flags for atoms and bonds; joelib.util.JOEBitVec mainly derived from java.util.BitSet. It's also used for SMARTS substructure search and ring search.
Comfortable logging framework with Log4J from http://jakarta.apache.org/log4j/docs/index.html
Well known scanff and printf formating classes from John E. Lloyd at http://www.cs.ubc.ca/\~lloyd/java/doc/cformat.html
Here a slightly modified version of the cformat.ScanfReader class is used, to take white spaces at the beginning of lines into account. To activate this modification call the useCstandard(false)-method.
Good matrix operation classes with Jama from http://math.nist.gov/javanumerics/jama/
Chemical Markup Language (CML) support based on the Chemical Data Object Programming Interface (CDOPI) (used as kernel for JOELib) http://www.openscience.org/~egonw/cdopi/.We extended the basic version for accepting descriptors and CML2 support.
Scientific Graphics Toolkit (SGT) http://www.epic.noaa.gov/java/sgt/
ACME Labs Java utilities for image creation (GIF, PPM) http://www.acme.com/java/
JpegEncoder of James R. Weeks and BioElectroMech. for image creation (JPEG)
BMPEncoder of Jean-Pierre Dube, Christian Ribeaud, and Egon Willighagen for image creation (BMP)