The Java BioComputing Library

Welcome to the Java BioComputing Library. These pages provide overview documentation on common task that can be solved by the package as well as detailed API documentation.

Table of Contents

• Introduction
• BioShell programs
• BioShell tutorials
• Common tasks
• Other notes, gotchas and howtos

Introduction

There are three ways how the package can be used:

• as a bunch of programs
• as a library for Jython.
• as a libary for Java In addition, many jbcl.* classes have main methods which occasionally do something useful. In general, these main methods are intended to test if a particular class works correctly, but they can be also helpful for an average user, e.g. DataTable.main() method reads a tabular text file with double values and computes basic descriptive statistics for desired columns. All the main methods are listed on this page.

BioShell programs

• All command-line BioShell tools are listed here The following pages provide a detailed list of all options parsed by each of the programs:
  • ACorr help page
  • BBQ help page
  • Clust help page
  • Hist help page
  • PRAline help page
  • PsiBlastAnalyse help page
  • PsiBlastSearch help page
  • RmsCalc help page
  • Seqc help page
  • StatPhys help page
  • StrAlign help page
  • StrCalc help page
  • Strc help page
  • Trac help page
  • WHAM help page

• BioShell command line option system page provides description of command-line option system used by BioShell programs. Uses may also use these options in his own programs or scripts.

BioShell tutorials

• Statistical Physics Calculations with BioShell Package.
• BioShell shortcuts for modeling with CABS tool

Common tasks

• Selecting residues and atoms document provides information how to pick up residues or atoms both by command-line tools and from scripts or programs

Other notes, gotchas and howtos

• This document explains some issues specific to Jython
• Git notes page reminds some basic commands in git version control software.