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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.
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