Description

The Molecular Biology Toolkit (MBT) provides a wide variety of example programs to help get you started creating your own custom programs using the toolkit. Each example is meant to demonsrate some specific feature of the toolkit. Though these examples provide enough detail to get you started on your way to writing a complete application using MBT, you may also want to refer to the more complete Applications as a guide for more complex and full-featured programs.

Example Programs

File	Description
BondSearch.java	An example program which demonsrates how to obtain derived bond pairs.
Elements.java	An example program which demonstrates the use of theElement and PeriodicTable utility classes.
Explorer.java	Implements an application which incorporates a more complete set ofMBT GUI layer components such as a menubar, TreeViewer, etc...
Filters.java	An example program which demonstrates StructureComponent Filters.
Fragments.java	An example program which walks chains-fragments-residues-atoms in orderto simulate the procesing of the secondary structure map.
Info.java	An example program which demonstrates how to access StructureInfo data.
InfoUtil.java	Prints the genetic code mapping with long amino acid name for allknown mRNA codons. Demonstrates some of the functionality of theNucleicAcidInfo, AminoAcidInfo, and CodonInfo utility classes.4 mRNA nucleic acids --> 64 mRNA Codons --> 20 Amino Acids--> 16000+ proteins
Ligands.java	An example program which demonstrates the use of the ligandclassification and traversal capabilities of the StructureMap class.
PrintDetails.java	An example program which demonstrates how to load data andprint out the detailed contents.
PrintDynamic.java	An example program which demonstrates how to load any structure usingthe StructureFactory class and then dynamically process all data typesavailable in that structure using the StructureComponentRegistry class.
PrintFasta.java	An example program which demonstrates how to directly instantiate anduse a StructureLoader class to read and print data.
RangeMapTest.java	An example program which exersises the RangeMap class.
Relations.java	An example program which demonstrates how to accessrelated structure components. In this example, we walk throughall of the Conformation objects and print each of theirrelated Atom objects.
RenderImage.java	This class is the main RenderImage application class.It is a command-line tool which loads a structure, optionally displaysa thumbnail using a StructureViewer, then saves the rendered image at arequested width and height to the specified image file.
SimpleViewer.java	This class is the main SimpleViewer application class.It provides a frame with a menubar and a StructureViewer.
Stats.java	An example program which gathers statistics about a structure.
StructureMapping.java	An example program which demonstrates the use of the StructureMap class.
Styles.java	An example program which demonstrates the use of theStructureStyles and related "viewables" classes.