A C D E F G H I J L M P R S T U W

A

addAtom(Atom) - Method in class jgromacs.data.Residue

Adds a new atom to the residue

addAtomToResidue(int, Atom) - Method in class jgromacs.data.Structure

Adds the given atom to residue #i

addAtomToResidueOfIndex(int, Atom) - Method in class jgromacs.data.Structure

Adds the given atom to the residue of given index

addFrame(int) - Method in class jgromacs.data.FrameIndexSet

Adds a new frame to the frame index set

addFrame(PointList) - Method in class jgromacs.data.Trajectory

Adds a new frame to the trajectory

addGap() - Method in class jgromacs.data.Sequence

Adds a new gap to the sequence

addIndex(int) - Method in class jgromacs.data.IndexSet

Adds a new index to the index set

addIndexSet(IndexSet) - Method in class jgromacs.data.IndexSetList

Adds a new index set to the list

addIndexSet(IndexSet, String) - Method in class jgromacs.data.IndexSetList

Adds a new index set of given name to the list

addPoint(Point3D) - Method in class jgromacs.data.PointList

Adds a new point to the point list

addPosition(SequencePosition) - Method in class jgromacs.data.Sequence

Adds a new position to the sequence

addPosition(ResidueType, String) - Method in class jgromacs.data.Sequence

Adds a new position of given residue type and annotation to the sequence

addPosition(int, ResidueType) - Method in class jgromacs.data.Sequence

Adds a new position of given index and residue type to the sequence

addPosition(int, ResidueType, String) - Method in class jgromacs.data.Sequence

Adds a new position of given index, residue type and annotation to the sequence

addPositionsFromString(String) - Method in class jgromacs.data.Sequence

Adds a series of new positions to the sequence taken from a String object

addResidue(Residue) - Method in class jgromacs.data.Structure

Adds a new residue to the structure

addSequence(Sequence) - Method in class jgromacs.data.Alignment

Adds a new sequence to the alignment

Alignment - Class in jgromacs.data

Objects of this class represent a sequence alignment

Alignment() - Constructor for class jgromacs.data.Alignment

Constructs a new Alignment object

ALPHACARBON - Static variable in class jgromacs.analysis.Distances

Angle - Class in jgromacs.data

Objects of this class represent an angle

Angle() - Constructor for class jgromacs.data.Angle

Constructs a new Angle object

Angle(double) - Constructor for class jgromacs.data.Angle

Constructs a new Angle object of given value in degrees

Angles - Class in jgromacs.analysis

Collection of methods for analysing angles

Angles() - Constructor for class jgromacs.analysis.Angles

Application - Class in jgromacs.ui

Parent class of JGromacs applications.

Application() - Constructor for class jgromacs.ui.Application

Constructor

Atom - Class in jgromacs.data

Objects of this class represent a single atom

Atom() - Constructor for class jgromacs.data.Atom

Constructs a new Atom object

AtomType - Class in jgromacs.db

Objects of this class represent an atom type

AtomType() - Constructor for class jgromacs.db.AtomType

Constructs a new AtomType object

AtomType(int) - Constructor for class jgromacs.db.AtomType

Constructs a new AtomType object of a given type

AtomType(String) - Constructor for class jgromacs.db.AtomType

Constructs a new AtomType object of given code