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

I

IndexSet - Class in jgromacs.data

Objects of this class represent a single index set

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

Constructs a new IndexSet object

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

Constructs a new IndexSet object of a given name

IndexSet(ArrayList<Integer>) - Constructor for class jgromacs.data.IndexSet

Constructs a new IndexSet object and loads data from an ArrayList

IndexSet(ArrayList<Integer>, String) - Constructor for class jgromacs.data.IndexSet

Constructs a new IndexSet object of a given name and loads data from an ArrayList

IndexSet(TreeSet<Integer>) - Constructor for class jgromacs.data.IndexSet

Constructs a new IndexSet object and loads data from a TreeSet

IndexSet(TreeSet<Integer>, String) - Constructor for class jgromacs.data.IndexSet

Constructs a new IndexSet object of a given name and loads data from a TreeSet

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

Constructs a new IndexSet object identical to a given IndexSet

IndexSetList - Class in jgromacs.data

Objects of this class represent a list of index sets

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

Constructs a new IndexSetList object

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

Returns the inner product of this vector and another vector

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

Inserts a new gap to position #i

insertPosition(int, SequencePosition) - Method in class jgromacs.data.Sequence

Inserts the given sequence position to position #i Note that you may have to re-index sequence positions after using this method

insertPosition(int, ResidueType, String) - Method in class jgromacs.data.Sequence

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

insertPosition(int, int, ResidueType) - Method in class jgromacs.data.Sequence

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

insertPosition(int, int, ResidueType, String) - Method in class jgromacs.data.Sequence

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

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

Returns the intersection of this frame index set and another

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

Returns the intersection of this index set and another

IOData - Class in jgromacs.io

This class contains static methods for IO of data objects

IOData() - Constructor for class jgromacs.io.IOData

IOMath - Class in jgromacs.io

This class contains static methods for IO of ArrayList and Matrix objects

IOMath() - Constructor for class jgromacs.io.IOMath

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

Returns true if it is an alpha carbon atom

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

Returns true if it is an amino acid

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

Returns true if it is an amino acid (not water or else)

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

Returns true if the given atom is in the residue

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

Returns true if it is a backbone atom

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

Returns true if it is a beta carbon atom

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

Returns true if it is a carbonyl oxygen atom

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

Returns true if it is a C-terminal carbon atom

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

Returns true if it is a delta carbon atom

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

Returns true if it is an epsilon carbon atom

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

Returns true if the frame index set contains a given frame index

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

Returns true if it is a gamma carbon atom

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

Returns true if it is a heavy atom (not hydrogen)

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

Returns true if the atom is a Hydrogen

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

Returns true if the index set contains a given index

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

Returns true if it is a main chain atom

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

Returns true if it is a main chain hydrogen atom

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

Returns true if it is a main chain or beta carbon atom

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

Returns true if it is a main chain or hydrogen atom

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

Returns true if column #i is a match column (i.e.

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

Returns true if it is an N-terminal nitrogen atom

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

Returns true if it is not an amino acid neither a water molecule

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

Returns true if it is not an amino acid nor water

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

Returns true if sequence position #i is a gap

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

Returns true if it is a side chain atom

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

Returns true if it is a side chain atom but not hydrogen

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

Returns true if it is a terminal oxygen atom

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

Returns true if it is a water molecule

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

Returns true if it is water (not amino acid or else)

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

Returns true if it is a zeta carbon atom