Uses of Interface org.biojava.bio.structure.Atom (BioJava-1.5-beta API)

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## 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)`

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