Uses of Class
org.proteinshader.structure.Water

Packages that use Water

org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.

Uses of Water in org.proteinshader.structure

Methods in org.proteinshader.structure that return Water

Water	Chain.addNewWater(String residueID) Creates a new Water with the Residue ID given as an argument, adds the Water to the Chain's collection of Waters, and returns a reference to the new Water.
Water	Chain.getWater(String residueID) Returns the Water with the residueID given as an argument.

Methods in org.proteinshader.structure that return types with arguments of type Water

Iterator<Water>

Chain.iteratorWaters() Returns an Iterator for the Water molecules held by this Chain.

Uses of Water in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type Water

void	Visitor.visit(Water water) Traverses all Atoms owned by the Water.
void	SFWriterVisitor.visit(Water water) Writes all information held by a Water.
void	BondGeneratorVisitor.visit(Water water) If the Water includes hydrogen atoms, then Bonds will be created between the oxygen and each hydrogen (after checking that the Bond lengths are reasonable).