Esra is a scriptable, scalable, and highly hackable molecular mechanics library for Java. Its primary purpose is the statistical analysis of trajectory data generated with packages such as GROMOS, GROMACS, or AMBER, but it can also be used as a standalone package for performing simple molecular dynamics and Monte-Carlo simulations. It can be scripted with Jython, Mathematica, or Matlab.
|Tags||Scientific/Engineering Bioinformatics Chemistry education|
|Operating Systems||OS Independent|
|Implementation||Scheme Java Other Scripting Engines Python|
Release Notes: Bugfixes were made. Preliminary support for gromacs-formatted coordinate files was added.
Release Notes: Lots of bugfixes, extra unit tests, and documentation were introduced. All the remaining functionality needed to perform simple molecular dynamics and Monte-Carlo simulations was added.
Release Notes: The package system was cleaned up. Minor bugfixes were done.
Release Notes: This stable version features a pure Java classical force field (a simplistic version of the GROMOS96 force field), a (non-periodic)Poisson-Boltzmann solver, Dssp secondary structure assignment, limited support for SYBYL/MOL2 and X-PLOR file formats, and large amounts of documentation.
Release Notes: This is the first stable release. It features the basic building blocks for the analysis of molecular mechanics data. Its IO routines support formats that include GROMOS96, PDB, vmd/AMBER, and SYBYL/mol2. It has a Java linear algebra library, basic (geometric) analysis tools such as rmsds, fitting procedures, distance/angle/dihedral measurements, and hydrogen bond analysis.