Feature List

available

• portable and scriptable

• common coordinate transformations, such as gathering, fitting.

• simple, hierarchical atom selection language ( AtomSpecifiers)

• wide range of energy routines (exist, but still under heavy development): harmonic, angle, dihedral, improper dihedral potentials, direct coulomb, cutoff/reactionfield, direct Lennard-Jones, Ewald summation, some continuum electrostatics

• common analyses such as RMSDs, dipole moments, radii of gyration, hydrogen bonding, dssp secondary structure assignment.

• surprisingly fast

• support for a range of standard molecular structure formats:

• clever, watertight argument parsing library.

• 100 % pure java linear algebra library for convenient vector/matrix manipulations.

• thorough API documentation, simple, flat data structures, generic algorithms, unit testing (still in the works).

• it's free and open.

upcoming

• Monte-Carlo propagator (minimizing and metropolis criteria)

• NOE distance upper bound analysis