Package org.strbio.mol

These classes represent objects or concepts useful to structural biologists.

See:
Description

Class Summary

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.
PolymerProperties	Class containing all possible Polymer properties, in one place, rather than spreading them out among many files.
PolymerSet	Class to represent a set of polymers to be acted on in a group.
PolymerSet.PolymerEnumeration	An enumeration of Polymers, that gets them one by one out of a file.
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.
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.
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.

Package org.strbio.mol Description

These classes represent objects or concepts useful to structural biologists.