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

S

Sequence - Class in jgromacs.data

Objects of this class represent a single amino acid sequence

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

Constructs a new Sequence object

Sequence(String) - Constructor for class jgromacs.data.Sequence

Constructs a new Sequence object of given name

SequencePosition - Class in jgromacs.data

Objects of this class represent a single sequence position

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

Constructs a new SequencePosition object

SequencePosition(int, ResidueType) - Constructor for class jgromacs.data.SequencePosition

Constructs a new SequencePosition object of given index and residue type

SequencePosition(int, String) - Constructor for class jgromacs.data.SequencePosition

Constructs a new SequencePosition object of given index and annotation

SequencePosition(ResidueType, String) - Constructor for class jgromacs.data.SequencePosition

Constructs a new SequencePosition object of residue type and annotation

SequencePosition(int, ResidueType, String) - Constructor for class jgromacs.data.SequencePosition

Constructs a new SequencePosition object of given index, residue type and annotation

setAllAtomCoordinates(PointList) - Method in class jgromacs.data.Residue

Sets the coordinates of all atoms

setAllAtomCoordinates(PointList) - Method in class jgromacs.data.Structure

Sets the coordinates of all atoms

setAnnotation(String) - Method in class jgromacs.data.SequencePosition

Sets the annotation of sequence position

setAtom(int, Atom) - Method in class jgromacs.data.Residue

Replaces atom #i of the residue with the given atom

setAtomCoordinates(int, Point3D) - Method in class jgromacs.data.Residue

Sets the coordinates of atom #i

setAtomCoordinates(int, Point3D) - Method in class jgromacs.data.Structure

Sets the coordinates of atom #i

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

Replaces atom #j of residue #i with a new atom

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

Replaces atom #i of the residue of given index with a new atom

setAtomOfIndexCoordinates(int, Point3D) - Method in class jgromacs.data.Residue

Sets the coordinates of atom of given index

setAtomOfIndexCoordinates(int, Point3D) - Method in class jgromacs.data.Structure

Sets the coordinates of atom of given index

setAtomType(AtomType) - Method in class jgromacs.data.Atom

Sets the type of atom

setBvalue(double) - Method in class jgromacs.data.Atom

Sets the B-value of atom

setChainID(String) - Method in class jgromacs.data.Residue

Sets the chain ID of residue

setCoordinates(Point3D) - Method in class jgromacs.data.Atom

Sets the coordinates of atom

setFrame(int, PointList) - Method in class jgromacs.data.Trajectory

Replaces frame #i with a new frame

setInDegrees(double) - Method in class jgromacs.data.Angle

Sets the value of angle in degrees

setIndex(int) - Method in class jgromacs.data.Atom

Sets the index of atom

setIndex(int) - Method in class jgromacs.data.Residue

Sets the index of residue

setIndex(int) - Method in class jgromacs.data.SequencePosition

Sets the index of sequence position

setIndexSet(int, IndexSet) - Method in class jgromacs.data.IndexSetList

Replaces index set of given index with a new index set

setInRadians(double) - Method in class jgromacs.data.Angle

Sets the value of angle in radians

setName(String) - Method in class jgromacs.data.Atom

Sets the name of atom

setName(String) - Method in class jgromacs.data.FrameIndexSet

Sets the name of frame index set

setName(String) - Method in class jgromacs.data.IndexSet

Sets the name of index set

setName(String) - Method in class jgromacs.data.Residue

Sets the name of residue

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

Sets the name of sequence

setName(String) - Method in class jgromacs.data.Structure

Sets the name of structure

setName(String) - Method in class jgromacs.data.Trajectory

Sets the name of trajectory

setOccupancy(double) - Method in class jgromacs.data.Atom

Sets the occupancy of atom

setPoint(int, Point3D) - Method in class jgromacs.data.PointList

Replaces the point of index i with a given point

setPointFromArrayList(ArrayList<Point3D>) - Method in class jgromacs.data.PointList

Loads points from an ArrayList

setPosition(int, SequencePosition) - Method in class jgromacs.data.Sequence

Replaces position #i with the given sequence position

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

Replaces position #i with the a sequence position of given residue type and annotation

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

Replaces position #i with the a sequence position of given index and residue type

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

Replaces position #i with the a sequence position of given index, residue type and annotation

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

Replaces the position of given index with the a sequence position of given residue type and annotation

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

Replaces the position of given index with the a sequence position of given residue type

setResidue(int, Residue) - Method in class jgromacs.data.Structure

Replaces residue #i with a new residue

setResidueType(ResidueType) - Method in class jgromacs.data.Residue

Sets the type of residue

setResidueType(ResidueType) - Method in class jgromacs.data.SequencePosition

Sets the residue type of sequence position

setSequence(int, Sequence) - Method in class jgromacs.data.Alignment

Replaces sequence #i of the alignment with a new sequence

setStartTime(double) - Method in class jgromacs.data.Trajectory

Sets the start time of trajectory

setStructure(Structure) - Method in class jgromacs.data.Trajectory

Sets the structure described by the trajectory

setTimeStep(double) - Method in class jgromacs.data.Trajectory

Sets the time step of trajectory

setX(double) - Method in class jgromacs.data.Point3D

Sets the X coordinate of point

setXCoordinate(double) - Method in class jgromacs.data.Atom

Sets the X coordinate of atom

setY(double) - Method in class jgromacs.data.Point3D

Sets the Y coordinate of point

setYCoordinate(double) - Method in class jgromacs.data.Atom

Sets the Y coordinate of atom

setZ(double) - Method in class jgromacs.data.Point3D

Sets the Z coordinate of point

setZCoordinate(double) - Method in class jgromacs.data.Atom

Sets the Z coordinate of atom

Similarity - Class in jgromacs.analysis

Collection of methods for measuring structural similarity

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

Structure - Class in jgromacs.data

Objects of this class represent a single structure

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

Constructs a new Structure object

Structure(String) - Constructor for class jgromacs.data.Structure

Constructs a new Structure object of given name

subtract(FrameIndexSet) - Method in class jgromacs.data.FrameIndexSet

Returns the subtraction of another frame index set from this frame index set

subtract(IndexSet) - Method in class jgromacs.data.IndexSet

Returns the subtraction of another index set from this index set

superposeTo(PointList, PointList) - Static method in class jgromacs.analysis.Superposition

Calculates the superposition of a point list to another

superposeTo(Structure, Structure) - Static method in class jgromacs.analysis.Superposition

Calculates the superposition of a structure to another

superposeTo(Structure, IndexSet, Structure, IndexSet) - Static method in class jgromacs.analysis.Superposition

Calculates the superposition of a structure to another using a subset of atoms for fitting

superposeTo(Trajectory, PointList) - Static method in class jgromacs.analysis.Superposition

Calculates the superposition of each frame of a trajectory to a common reference frame

superposeTo(Trajectory, Structure) - Static method in class jgromacs.analysis.Superposition

Calculates the superposition of each frame of a trajectory to a common reference frame

superposeTo(Trajectory, Structure, IndexSet) - Static method in class jgromacs.analysis.Superposition

Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting

Superposition - Class in jgromacs.analysis

Collection of methods for superposing structures

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