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

T

TemplateApplication - Class in jgromacs.ui
Template JGromacs application
TemplateApplication() - Constructor for class jgromacs.ui.TemplateApplication
 
toString() - Method in class jgromacs.data.Alignment
Returns the String representation of alignment
toString() - Method in class jgromacs.data.Angle
Returns the String representation of angle
toString() - Method in class jgromacs.data.Atom
Returns the String representation of atom
toString() - Method in class jgromacs.data.FrameIndexSet
Returns the String representation of frame index set
toString() - Method in class jgromacs.data.IndexSet
Returns the String representation of index set
toString() - Method in class jgromacs.data.IndexSetList
Returns the String representation of index set list
toString() - Method in class jgromacs.data.Point3D
Returns the String representation of point
toString() - Method in class jgromacs.data.PointList
Returns the String representation of point list
toString() - Method in class jgromacs.data.Residue
Returns the String representation of residue
toString() - Method in class jgromacs.data.Sequence
Returns the String representation of sequence
toString() - Method in class jgromacs.data.SequencePosition
Returns the String representation of sequence position
toString() - Method in class jgromacs.data.Structure
Returns the String representation of structure
toString() - Method in class jgromacs.data.Trajectory
Returns the String representation of trajectory
toString() - Method in class jgromacs.db.AtomType
Returns the String representation of atom type
toString() - Method in class jgromacs.db.ResidueType
Returns the String representation of residue type
toString1Letter() - Method in class jgromacs.data.Sequence
Returns a String representation in which each residue is represented by its 1 letter code
toString1Letter(int) - Method in class jgromacs.data.Sequence
Returns a String representation in which each residue is represented by its 1 letter code and the string is split to lines of the given length
toString3Letter() - Method in class jgromacs.data.Sequence
Returns a String representation in which each residue is represented by its 3 letter code
toString3Letter(int) - Method in class jgromacs.data.Sequence
Returns a String representation in which each residue is represented by its 3 letter code and the string is split to lines of the given length
toStringAsGRO() - Method in class jgromacs.data.Structure
Returns the String representation of structure in GRO format
toStringAsPDB() - Method in class jgromacs.data.Structure
Returns the String representation of structure in PDB format
toStringInfo() - Method in class jgromacs.data.Alignment
Returns summary information about the alignment
toStringInfo() - Method in class jgromacs.data.FrameIndexSet
Returns summary information about the frame index set
toStringInfo() - Method in class jgromacs.data.IndexSet
Returns summary information about the index set
toStringInfo() - Method in class jgromacs.data.IndexSetList
Returns summary information about the index set list
toStringInfo() - Method in class jgromacs.data.PointList
Returns summary information about the point list
toStringInfo() - Method in class jgromacs.data.Residue
Returns summary information about the residue
toStringInfo() - Method in class jgromacs.data.Sequence
Returns summary information about the sequence
toStringInfo() - Method in class jgromacs.data.Structure
Returns summary information about the structure
Trajectory - Class in jgromacs.data
Objects of this class represent a single trajectory
Trajectory() - Constructor for class jgromacs.data.Trajectory
Constructs a new Trajectory object
Trajectory(String) - Constructor for class jgromacs.data.Trajectory
Constructs a new Trajectory object of given name
Trajectory(Structure) - Constructor for class jgromacs.data.Trajectory
Constructs a new Trajectory object of given structure
Trajectory(Structure[]) - Constructor for class jgromacs.data.Trajectory
Constructs a new Trajectory object made from an ensemble of structures
transformByMatrix(Matrix) - Method in class jgromacs.data.Point3D
Returns the resulting vector of a matrix transformation
translate(Point3D) - Method in class jgromacs.data.PointList
Translates the points by a given vector

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