Uses of Package
org.strbio.mol

Packages that use org.strbio.mol

org.strbio.app	These classes are stand-alone applications.
org.strbio.local	These classes are for running or exchanging data with local programs (other programs installed on your computer).
org.strbio.mol	These classes represent objects or concepts useful to structural biologists.
org.strbio.mol.lib	These classes represent conceptual objects used in structural biology algorithms.
org.strbio.mol.lib.pred2ary	These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes.
org.strbio.net	These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page).
org.strbio.raf	These classes are related to the RAF file format used by the ASTRAL database.
org.strbio.util.db	These classes are a primitive interface to store and manipulate protein structure information from various commonly used databases.
org.strbio.util.ui	These classes are general purpose utility functions related to a program's user interface.

Classes in org.strbio.mol used by org.strbio.app

ProfilePSISet
Class to represent a set of profiles with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

ProfileSet
Class to represent a set of proteins with profile information.

Classes in org.strbio.mol used by org.strbio.local

Alignment
An Alignment is a simple representation of an alignment between two polymers.

PolymerSet
Class to represent a set of polymers to be acted on in a group.

PrimerSet
Class to represent a set of primers used to clone one gene

Profile
Class to represent a protein with profile information.

Protein
Class to represent a single protein.

ProteinSet
Class to represent a set of proteins to be acted on in a group.

Classes in org.strbio.mol used by org.strbio.mol

Alignment
An Alignment is a simple representation of an alignment between two polymers.

AlignmentSet
Class to represent a set of alignments (i.e. correct, calculated) between two polymers.

AlignmentStats
A class holding alignment statistics for a given alignment.

Atom
Class to represent an atom.

AtomNode
Class to represent a node in a list of atoms.

Molecule
Class to represent a molecule.

Monomer
Class to represent a single monomer in a linear polymer.

Nucleotide
Class to represent a single nucleotide Version 1.0, 8/17/01 - original version, based on org.strbio.mol.Residue

Polymer
Class to represent a linear, unbranched polymer.

PolymerSet
Class to represent a set of polymers to be acted on in a group.

Primer
Class to represent a single primer.

PrimerSet
Class to represent a set of primers used to clone one gene

Profile
Class to represent a protein with profile information.

ProfileSet
Class to represent a set of proteins with profile information.

ProfRes
Class to represent a single residue in a protein with profile information.

ProfResPSI
Class to represent a single residue in a profile, with position specific information (PSI) added.

Protein
Class to represent a single protein.

ProteinSet
Class to represent a set of proteins to be acted on in a group.

Residue
Class to represent a single residue in a protein.

ThreadSet
Class to keep track of two sets of proteins that are being used in threading algorithms.

Classes in org.strbio.mol used by org.strbio.mol.lib

Alignment
An Alignment is a simple representation of an alignment between two polymers.

Monomer
Class to represent a single monomer in a linear polymer.

Polymer
Class to represent a linear, unbranched polymer.

PolymerSet
Class to represent a set of polymers to be acted on in a group.

Profile
Class to represent a protein with profile information.

ProfilePSI
Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

ProfilePSISet
Class to represent a set of profiles with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

ProfileSet
Class to represent a set of proteins with profile information.

ProfResPSI
Class to represent a single residue in a profile, with position specific information (PSI) added.

Protein
Class to represent a single protein.

ProteinSet
Class to represent a set of proteins to be acted on in a group.

Residue
Class to represent a single residue in a protein.

Classes in org.strbio.mol used by org.strbio.mol.lib.pred2ary

Molecule
Class to represent a molecule.

Monomer
Class to represent a single monomer in a linear polymer.

Polymer
Class to represent a linear, unbranched polymer.

PolymerSet
Class to represent a set of polymers to be acted on in a group.

Profile
Class to represent a protein with profile information.

ProfilePSI
Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.

ProfileSet
Class to represent a set of proteins with profile information.

ProfRes
Class to represent a single residue in a protein with profile information.

ProfResPSI
Class to represent a single residue in a profile, with position specific information (PSI) added.

Protein
Class to represent a single protein.

ProteinSet
Class to represent a set of proteins to be acted on in a group.

Residue
Class to represent a single residue in a protein.

Classes in org.strbio.mol used by org.strbio.net

Profile
Class to represent a protein with profile information.

Protein
Class to represent a single protein.

Classes in org.strbio.mol used by org.strbio.raf

Molecule
Class to represent a molecule.

Polymer
Class to represent a linear, unbranched polymer.

Protein
Class to represent a single protein.

ProteinSet
Class to represent a set of proteins to be acted on in a group.

Classes in org.strbio.mol used by org.strbio.util.db

Protein
Class to represent a single protein.

Classes in org.strbio.mol used by org.strbio.util.ui

ProfileSet
Class to represent a set of proteins with profile information.

Protein
Class to represent a single protein.