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

Packages that use Atom

org.biojava.bio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align
org.biojava.bio.structure.align.helper
org.biojava.bio.structure.align.pairwise

Uses of Atom in org.biojava.bio.structure

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

class

AtomImpl Implementation of an Atom of a PDB file.

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

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	HetatomImpl.getAtom(int position) return an atom by its position in the internal List.
Atom	Group.getAtom(int position) get at atom by position.
Atom	HetatomImpl.getAtom(String name) get an atom throws StructureException if atom not found.
Atom	Group.getAtom(String name) get an atom throws StructureException if atom not found.
static Atom[]	StructureTools.getAtomArray(Structure s, 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	AminoAcidImpl.getC() get C atom.
Atom	AminoAcid.getC() get C atom.
Atom	AminoAcidImpl.getCA() get CA atom.
Atom	AminoAcid.getCA() get CA atom.
Atom	AminoAcidImpl.getCB() get CB atom.
Atom	AminoAcid.getCB() get CB atom.
static Atom	Calc.getCenterVector(Atom[] atomSet)
static Atom	Calc.getCentroid(Atom[] atomSet) returns the center of mass of the set of atoms
Atom	AminoAcidImpl.getN() get N atom.
Atom	AminoAcid.getN() get N atom.
Atom	AminoAcidImpl.getO() get O atom.
Atom	AminoAcid.getO() get O atom.
Atom	SVDSuperimposer.getTranslation()
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 with parameters of type Atom

static Atom	Calc.add(Atom a, Atom b) add two atoms ( a + b).
void	HetatomImpl.addAtom(Atom atom) add an atom to this group.
void	Group.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)
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) of two sets of atoms
static double	SVDSuperimposer.getRMS(Atom[] atomSet1, Atom[] atomSet2) calculate the RMS (root mean square) 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 .

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

SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2)

SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2)

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

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

void	StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) calculate the actual protein structure superimposition.
void	StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params) calculate the actual protein structure superimposition.

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

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

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

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

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 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

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

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

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

JointFragments[]	FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
JointFragments[]	FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
void	AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
void	AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
void	AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
void	AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
static double	FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)
static double	FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)
void	AlternativeAlignment.refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2) Refinement procedure based on superposition and dynamic programming.
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)