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

C

centerPoints() - Method in class jgromacs.data.PointList

Centers the points (around the origin)

clone() - Method in class jgromacs.data.Alignment

Returns an identical Alignment object

clone() - Method in class jgromacs.data.Angle

Returns an identical Angle object

clone() - Method in class jgromacs.data.Atom

Returns an identical Atom object

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

Returns an identical FrameIndexSet object

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

Returns an identical IndexSet object

clone() - Method in class jgromacs.data.IndexSetList

Returns an identical IndexSetList object

clone() - Method in class jgromacs.data.Point3D

Returns an identical Point3D object

clone() - Method in class jgromacs.data.PointList

Returns an identical PointList object

clone() - Method in class jgromacs.data.Residue

Returns an identical Residue object

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

Returns an identical Sequence object

clone() - Method in class jgromacs.data.SequencePosition

Returns an identical SequencePosition object

clone() - Method in class jgromacs.data.Structure

Returns an identical Structure object

clone() - Method in class jgromacs.data.Trajectory

Returns an identical Trajectory object

clone() - Method in class jgromacs.db.AtomType

Returns an identical AtomType object

clone() - Method in class jgromacs.db.ResidueType

Returns an identical ResidueType object

CLOSEST - Static variable in class jgromacs.analysis.Distances

CLOSESTHEAVY - Static variable in class jgromacs.analysis.Distances

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

Returns the given sequence concatenated to this sequence

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

Returns true if the given subsequence is contained in this sequence

convertFrameIndexToTime(int) - Method in class jgromacs.data.Trajectory

Converts frame index to simulation time

convertIndicesToArrayListIndices(IndexSet) - Method in class jgromacs.data.Structure

Converts atomic indices into list indices

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

Converts simulation time to frame index

crossProduct(Point3D) - Method in class jgromacs.data.Point3D

Returns the cross product of this vector and another vector