Uses of Class
jgromacs.db.ResidueType

Packages that use ResidueType

jgromacs.data

jgromacs.data is a collection of classes representing multiple levels of structural data

Uses of ResidueType in jgromacs.data

Methods in jgromacs.data that return ResidueType

ResidueType	Alignment.getMostFrequentResidueType(int i) Returns the most frequent residue type in column #i of the alignment
ResidueType	SequencePosition.getResidueType() Returns the residue type of sequence position
ResidueType	Residue.getResidueType() Returns the type of residue
ResidueType	Sequence.getResidueTypeOfPosition(int i) Returns the residue type of sequence position #i
ResidueType	Sequence.getResidueTypeOfPositionOfIndex(int index) Returns the residue type of sequence position of given index

Methods in jgromacs.data with parameters of type ResidueType

void	Sequence.addPosition(int index, ResidueType type) Adds a new position of given index and residue type to the sequence
void	Sequence.addPosition(int index, ResidueType type, java.lang.String annotation) Adds a new position of given index, residue type and annotation to the sequence
void	Sequence.addPosition(ResidueType type, java.lang.String annotation) Adds a new position of given residue type and annotation to the sequence
void	Sequence.insertPosition(int i, int index, ResidueType type) Inserts sequence position of given index and residue type to position #i Note that you may have to re-index sequence positions after using this method
void	Sequence.insertPosition(int i, int index, ResidueType type, java.lang.String annotation) Inserts sequence position of given index, residue type and annotation to position #i Note that you may have to re-index sequence positions after using this method
void	Sequence.insertPosition(int i, ResidueType type, java.lang.String annotation) Inserts sequence position of given residue type and annotation to position #i Note that you may have to re-index sequence positions after using this method
void	Sequence.setPosition(int i, int index, ResidueType type) Replaces position #i with the a sequence position of given index and residue type
void	Sequence.setPosition(int i, int index, ResidueType type, java.lang.String annotation) Replaces position #i with the a sequence position of given index, residue type and annotation
void	Sequence.setPosition(int i, ResidueType type, java.lang.String annotation) Replaces position #i with the a sequence position of given residue type and annotation
void	Sequence.setPositionByIndex(int index, ResidueType type) Replaces the position of given index with the a sequence position of given residue type
void	Sequence.setPositionByIndex(int index, ResidueType type, java.lang.String annotation) Replaces the position of given index with the a sequence position of given residue type and annotation
void	SequencePosition.setResidueType(ResidueType residueType) Sets the residue type of sequence position
void	Residue.setResidueType(ResidueType residueType) Sets the type of residue

Constructors in jgromacs.data with parameters of type ResidueType

Residue(int index, java.lang.String name, ResidueType residueType)
Constructs a new Residue object of given index, name and residue type

Residue(int index, java.lang.String name, java.lang.String chainID, ResidueType residueType)
Constructs a new Residue object of given index, name, chainID and residue type

SequencePosition(int index, ResidueType residueType)
Constructs a new SequencePosition object of given index and residue type

SequencePosition(int index, ResidueType residueType, java.lang.String annotation)
Constructs a new SequencePosition object of given index, residue type and annotation

SequencePosition(ResidueType residueType, java.lang.String annotation)
Constructs a new SequencePosition object of residue type and annotation