Package org.strbio

The StrBio library is a set of Java classes useful for development of software for computational structural biology research.

See:
Description

Class Summary

IO	A class containing some useful IO functions which don't really merit their own classes.

Package org.strbio Description

The StrBio library is a set of Java classes useful for development of software for computational structural biology research. They are licenced under the LGPL.

The classes were developed by John-Marc Chandonia, jmc@strbio.org. The latest version should be available at http://www.strbio.org.

These classes are the basis for several published research projects, including the Pred2ary secondary structure prediction program and the ASTRAL database of protein domain sequences.

The most interesting structural biology applications included are:

• Pred2ary protein secondary structure prediction
• JThread protein fold prediction
• ConvertProtein for interconversion of protein file formats (FASTA, PDB, MSF, ALN, CASP, DSSP, HSSP, YAPF)
• Filters to exchange data with commonly used molecular biology applications (e.g., BLAST, MinArea, MODELLER)
• MakeRAF tool to create the Rapid Access Format sequence maps for the ASTRAL database.

Other more general-purpose functionality that is included:

• Neural network library, including Scaled Conjugate Gradient or Steepest Descent optimization
• Hooke and Jeeves derivative-free global optimization algorithm
• Misc mathematical objects and algorithms (vectors, matrices, etc)
• Efficient string formatting using Printf-based syntax (printf, atoi, atof, etc.)