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

R

readAlignmentFromFASTA(String) - Static method in class jgromacs.io.IOData

Reads an alignment from the given FASTA file

readArrayListFromFile(String) - Static method in class jgromacs.io.IOMath

Reads ArrayList from the given file

readDumpedTrajectory(Structure, String) - Static method in class jgromacs.io.IOData

Reads a trajectory from the given dumped XTC or TRR file

readFromFile(String) - Static method in class jgromacs.io.IOData

Reads a JGromacs object (Structure, IndexSetList, Trajectory or Sequence) from a file automatically identifying the type of the file

readIndexSetFromNDX(String) - Static method in class jgromacs.io.IOData

Reads an index set from the given NDX file

readIndexSetListFromNDX(String) - Static method in class jgromacs.io.IOData

Reads an index set list from the given NDX file

readMatrixFromFile(String) - Static method in class jgromacs.io.IOMath

Reads Matrix from the given file

readSequenceFromFASTA(String) - Static method in class jgromacs.io.IOData

Reads a sequence from the given FASTA file

readStructureFromGRO(String) - Static method in class jgromacs.io.IOData

Reads structure from the given GRO file

readStructureFromPDB(String) - Static method in class jgromacs.io.IOData

Reads structure from the given PDB file

readStructureFromPDB(String, int) - Static method in class jgromacs.io.IOData

Reads the given model from the given PDB file

readStructuresFromPDB(String) - Static method in class jgromacs.io.IOData

Reads an ensemble of structures from the given PDB file

readStructuresFromPDBsInDirectory(String) - Static method in class jgromacs.io.IOData

Reads an ensemble of structures from PDB files in the given directory

readTrajectory(Structure, String) - Static method in class jgromacs.io.IOData

Reads a trajectory from the given XTC or TRR file

reIndexPositions(int) - Method in class jgromacs.data.Sequence

Reindexes all positions in the sequence starting from a given index

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

Reindexes all positions in the sequence starting from 1

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

Removes atom #i from the residue

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

Removes the given atom from the residue

removeAtom(int) - Method in class jgromacs.data.Structure

Removes atom #i from the structure

removeAtom(Atom) - Method in class jgromacs.data.Structure

Removes the given atom from the structure

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

Removes atom of given index from the residue

removeAtomByIndex(int) - Method in class jgromacs.data.Structure

Removes the atom of given index from the structure

removeColumn(int) - Method in class jgromacs.data.Alignment

Removes column #i from the alignment

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

Removes a frame from the frame index set

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

Removes frame #i from the trajectory

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

Removes all gaps from the sequence

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

Removes an index from the index set

removeIndexSet(int) - Method in class jgromacs.data.IndexSetList

Removes index set of given index from the list

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

Removes the given index set from the list

removePoint(int) - Method in class jgromacs.data.PointList

Removes the point of index i from the point list

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

Removes the given point from the point list

removePosition(int) - Method in class jgromacs.data.Sequence

Removes sequence position #i

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

Removes the given sequence position

removePositionByIndex(int) - Method in class jgromacs.data.Sequence

Removes the sequence position of given index

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

Removes a residue from the structure

removeResidue(int) - Method in class jgromacs.data.Structure

Removes residue #i from the structure

removeSequence(int) - Method in class jgromacs.data.Alignment

Removes sequence #i from the alignment

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

Removes the given sequence from the alignment

Residue - Class in jgromacs.data

Objects of this class represent a single residue

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

Constructs a new Residue object

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

Constructs a new Residue object of given name

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

Constructs a new Residue object of given index, name and residue type

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

Constructs a new Residue object of given index, name, chainID and residue type

ResidueType - Class in jgromacs.db

Objects of this class represent a residue type

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

Constructs a new ResidueType object

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

Constructs a new ResidueType object of a given type

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

Constructs a new ResidueType object of given code

rotate(Matrix) - Method in class jgromacs.data.PointList

Rotates the points by a given 3x3 rotation matrix

runCore() - Method in class jgromacs.ui.TemplateApplication

runGromacsCommand(String, String[]) - Static method in class jgromacs.io.IOData

Executes Gromacs commands from within the Java code and reads the listed output files back into JGromacs objects.