Package ProGAL

ProGAL is a library containing geometric datastructures and algorithms with special emphasis on supporting representation and analysis of protein structures.

See:
Description

Class Summary

AllTests
Benchmark

Package ProGAL Description

ProGAL is a library containing geometric datastructures and algorithms with special emphasis on supporting representation and analysis of protein structures. TODO index

Goals

TODO write goals and outline of ProGAL

Section title

Implementation conventions

Composite geometric objects

The geometric object such as planes and lines are defined by other geometric objects such as points and vectors. The user has full control of these defining objects and changing the defining object also changes the dependent. For example, a plane is defined by a point and a normal vector that is typically passed to the plane upon construction. The reference of the point used to construct the plane is retrievable at any later time, and changing the properties of that reference also changes the plane.

toString and toConsole methods

All classes supplies four methods: toString(), toString(int dec), toConsole() and toConsole(int dec). The toString methods returns a string representation of an object that clearly specifies the class-type and defining parameters with two decimals precision. The dec parameter is used to adjust the precision. The toConsole-methods prints the object to System.out using the toString methods.

Various minor conventions

• Whereever it can be relevant equals methods should be supplied. An equals-method should only return true if the argument is of the same class-type.

References

Throughout this documentation references are made to the following literature

• [Ericsson 05] Christer Ericsson, Real-time Collision Detection, Elsevier, 2005.