Uses of Class
org.proteinshader.structure.AminoAcid

Packages that use AminoAcid

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 AminoAcid in org.proteinshader.structure

Methods in org.proteinshader.structure that return AminoAcid

AminoAcid	Chain.addNewAminoAcid(AminoAcidEnum type, String residueID) Creates a new AminoAcid with the type and Residue ID given as arguments, adds the AminoAcid to the Chain's collection of AminoAcids, and returns a reference to the new AminoAcid.
AminoAcid	Segment.getAminoAcid() Returns the a reference to the AminoAcid that this Segment corresponds to.
AminoAcid	Chain.getAminoAcid(String residueID) Returns the AminoAcid with the residueID given as an argument.
AminoAcid	Region.getAminoAcidAfterRegion() Returns the AminoAcid after this Region (or null if it does not exist).
AminoAcid	Region.getAminoAcidBeforeRegion() Returns the AminoAcid before this Region (or null if it does not exist).

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

Iterator<AminoAcid>	Chain.iteratorAminoAcids() Returns an Iterator for the AminoAcids held by this Chain.
Iterator<AminoAcid>	Region.iteratorAminoAcids() Returns an Iterator for the AminoAcids referred to by this Region.

Constructors in org.proteinshader.structure with parameters of type AminoAcid

Segment(AminoAcid aminoAcid, Hermite hermite1, Hermite hermite2, Quaternion startRotation, Quaternion middleRotation, Quaternion endRotation, boolean alwaysCapStart, boolean alwaysCapEnd)
Creates a Segment.

Uses of AminoAcid in org.proteinshader.structure.visitor

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

void	FrenetFrameGeneratorVisitor.calculateRotation(AminoAcid prev, AminoAcid cur, AminoAcid next) Calculates the equivalent of a discrete Frenet frame (a rotation matrix [N B T]) and uses it to set the rotation attribute of the current AminoAcid.
void	Visitor.visit(AminoAcid aminoAcid) Traverses all Atoms owned by the AminoAcid if AAPortionMode is set to ENTIRE_AA.
void	SFWriterVisitor.visit(AminoAcid aminoAcid) Writes all information held by an AminoAcid.
void	FrenetFrameGeneratorVisitor.visit(AminoAcid aminoAcid) The AminoAcid being visited is considered as CA(i+1), while the last two AminoAcids are considered to be CA(i) and CA(i-1).
void	LoopGeneratorVisitor.visit(AminoAcid aminoAcid) Checks whether a start AminoAcid and an end AminoAcid for a Loop have been found, and creates a new Loop as needed.
void	AminoAcidLabelVisitor.visit(AminoAcid aminoAcid) Adds a residueID to the list of labels if it has not been seen before.
void	BondGeneratorVisitor.visit(AminoAcid aminoAcid) Uses Atom distances to generate Bonds within the AminoAcid, and also uses the memory of the last carbonyl carbon seen to check for a possible peptide Bond.