Uses of Interface
org.biojava.bio.structure.Atom

Packages that use Atom

Package	Description
org.biojava.bio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align	Classes for the super-imposition of structures.
org.biojava.bio.structure.align.helper	Helper classes for structural alignment.
org.biojava.bio.structure.align.pairwise	Classes for the pairwise alignment of structures.

Uses of Atom in org.biojava.bio.structure

Classes in org.biojava.bio.structure that implement Atom

Modifier and Type	Class	Description
class	AtomImpl	Implementation of an Atom of a PDB file.

Methods in org.biojava.bio.structure that return Atom

Modifier and Type	Method	Description
static Atom	Calc.add(Atom a, Atom b)	add two atoms ( a + b).
static Atom[]	Calc.centerAtoms(Atom[] atomSet)	Center the atoms at the Centroid.
static Atom	Calc.createVirtualCBAtom(AminoAcid amino)	creates a virtual C-beta atom.
Atom	Group.getAtom(int position)	Get at atom by position.
Atom	Group.getAtom(java.lang.String name)	Get an atom.
Atom	HetatomImpl.getAtom(int position)	return an atom by its position in the internal List.
Atom	HetatomImpl.getAtom(java.lang.String name)	get an atom throws StructureException if atom not found.
static Atom[]	StructureTools.getAtomArray(Structure s, java.lang.String[] atomNames)	Returns an array of the requested Atoms from the Structure object.
static Atom[]	StructureTools.getAtomCAArray(Structure s)	Returns an Atom array of the CA atoms.
static Atom[]	StructureTools.getBackboneAtomArray(Structure s)	Returns an Atom array of the MainChain atoms.
Atom	AminoAcid.getC()	get C atom.
Atom	AminoAcidImpl.getC()	get C atom.
Atom	AminoAcid.getCA()	get CA atom.
Atom	AminoAcidImpl.getCA()	get CA atom.
Atom	AminoAcid.getCB()	get CB atom.
Atom	AminoAcidImpl.getCB()	get CB atom.
static Atom	Calc.getCenterVector(Atom[] atomSet)	Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
static Atom	Calc.getCentroid(Atom[] atomSet)	Returns the center of mass of the set of atoms.
Atom	AminoAcid.getN()	get N atom.
Atom	AminoAcidImpl.getN()	get N atom.
Atom	AminoAcid.getO()	get O atom.
Atom	AminoAcidImpl.getO()	get O atom.
Atom	SVDSuperimposer.getTranslation()	Get the shift vector.
Atom	AtomIterator.next()	Return next atom.
static Atom	Calc.substract(Atom a, Atom b)	substract two atoms ( a - b).
static Atom	Calc.unitVector(Atom a)	return the unit vector of vector a .
static Atom	Calc.vectorProduct(Atom a, Atom b)	Vector product .

Methods in org.biojava.bio.structure that return types with arguments of type Atom

Modifier and Type	Method	Description
java.util.List<Atom>	Group.getAtoms()	Get list of atoms.
java.util.List<Atom>	HetatomImpl.getAtoms()	get all atoms of this group .
java.util.Iterator<Atom>	Group.iterator()	get an Atom Iterator.
java.util.Iterator<Atom>	HetatomImpl.iterator()	return an AtomIterator.

Methods in org.biojava.bio.structure with parameters of type Atom

Modifier and Type	Method	Description
static Atom	Calc.add(Atom a, Atom b)	add two atoms ( a + b).
void	Group.addAtom(Atom atom)	add an atom to this group.
void	HetatomImpl.addAtom(Atom atom)	add an atom to this group.
static double	Calc.amount(Atom a)	amount.
static double	Calc.angle(Atom a, Atom b)	angle.
static Atom[]	Calc.centerAtoms(Atom[] atomSet)	Center the atoms at the Centroid.
static Atom	Calc.getCenterVector(Atom[] atomSet)	Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
static Atom	Calc.getCentroid(Atom[] atomSet)	Returns the center of mass of the set of atoms.
static double	Calc.getDistance(Atom a, Atom b)	calculate distance between two atoms.
static double	SVDSuperimposer.getRMS(Atom[] atomSet1, Atom[] atomSet2)	Calculate the RMS (root mean square) deviation of two sets of atoms.
static void	Calc.rotate(Atom atom, double[][] m)	rotate a single atom aroud a rotation matrix.
static void	Calc.rotate(Atom atom, Matrix m)	Rotate an atom around a Matrix object.
static void	Calc.shift(Atom a, Atom b)	Shift a vector.
static void	Calc.shift(Group group, Atom a)	Shift a Group with a vector.
static void	Calc.shift(Structure structure, Atom a)	shift a structure with a vector.
static double	Calc.skalarProduct(Atom a, Atom b)	skalar product.
static Atom	Calc.substract(Atom a, Atom b)	substract two atoms ( a - b).
static double	Calc.torsionAngle(Atom a, Atom b, Atom c, Atom d)	torsion angle = angle between the normal vectors of the two plains a-b-c and b-c-d.
static Atom	Calc.unitVector(Atom a)	return the unit vector of vector a .
static Atom	Calc.vectorProduct(Atom a, Atom b)	Vector product .

Method parameters in org.biojava.bio.structure with type arguments of type Atom

Modifier and Type	Method	Description
void	Group.setAtoms(java.util.List<Atom> atoms)	Set the atoms of this group.
void	HetatomImpl.setAtoms(java.util.List<Atom> atoms)	set the atoms of this group

Constructors in org.biojava.bio.structure with parameters of type Atom

Constructor	Description
SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2)	Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.

Uses of Atom in org.biojava.bio.structure.align

Methods in org.biojava.bio.structure.align that return Atom

Modifier and Type	Method	Description
Atom[]	StructurePairAligner.getAlignmentAtoms(Structure s)

Methods in org.biojava.bio.structure.align with parameters of type Atom

Modifier and Type	Method	Description
void	StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)	calculate the protein structure superimposition, between two sets of atoms.

Uses of Atom in org.biojava.bio.structure.align.helper

Methods in org.biojava.bio.structure.align.helper that return Atom

Modifier and Type	Method	Description
static Atom	AlignTools.getCenter(Atom[] ca, int pos, int fragmentLength)	get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
static Atom[]	AlignTools.getFragment(Atom[] caall, int pos, int fragmentLength)	get a continue subset of Atoms based by the starting position and the length
static Atom[]	AlignTools.getFragmentFromIdxList(Atom[] caall, int[] idx)	get a subset of Atoms based by their positions
static Atom[]	AlignTools.getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)	get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.

Methods in org.biojava.bio.structure.align.helper with parameters of type Atom

Modifier and Type	Method	Description
static Atom	AlignTools.getCenter(Atom[] ca, int pos, int fragmentLength)	get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
static double[]	AlignTools.getDiagonalAtK(Atom[] atoms, int k)
static Matrix	AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2)	matrix of all distances between two sets of 3d coords"
static Atom[]	AlignTools.getFragment(Atom[] caall, int pos, int fragmentLength)	get a continue subset of Atoms based by the starting position and the length
static Atom[]	AlignTools.getFragmentFromIdxList(Atom[] caall, int[] idx)	get a subset of Atoms based by their positions
static Atom[]	AlignTools.getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)	get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.

Uses of Atom in org.biojava.bio.structure.align.pairwise

Methods in org.biojava.bio.structure.align.pairwise that return Atom

Modifier and Type	Method	Description
Atom	FragmentPair.getCenter1()
Atom	FragmentPair.getCenter2()
Atom	AlternativeAlignment.getShift()	returns the shift vector that has to be applied on structure to to shift on structure one
Atom	FragmentPair.getTrans()
Atom	FragmentPair.getUnitv()

Methods in org.biojava.bio.structure.align.pairwise with parameters of type Atom

Modifier and Type	Method	Description
JointFragments[]	FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
void	AlternativeAlignment.calcScores(Atom[] ca1, Atom[] ca2)	calculates scores for this alignment ( %id )
void	AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
void	AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
static Matrix	AlternativeAlignment.getDistanceMatrix(Atom[] ca1, Atom[] ca2)
static double	FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)	get the RMS of the JointFragments pair frag
void	AlternativeAlignment.refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2)	Refinement procedure based on superposition and dynamic programming.
void	FragmentPair.setCenter1(Atom center1)
void	FragmentPair.setCenter2(Atom center2)
void	FragmentPair.setTrans(Atom trans)
void	FragmentPair.setUnitv(Atom unitv)