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

Packages that use Atom

org.biojava.bio.structure

Interfaces and classes for molecular structure.

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

Atom	Hetatom.getAtom(String name) get an Atom or null, if Atom not in this group
Atom	Hetatom.getAtom(int position) return an atom by its position in the internal ArrayList
Atom	Group.getAtom(String name) get an atom throws StructureException if atom not found
Atom	Group.getAtom(int position) get at atom by position
static Atom	Calc.add(Atom a, Atom b) add two atoms ( a + b)
static Atom	Calc.substract(Atom a, Atom b) substract two atoms ( a - b)
static Atom	Calc.vectorProduct(Atom a, Atom b) Vector product
static Atom	Calc.unitVector(Atom a) return the unit vector of vector a
Atom	AminoAcid.getN() get N atom
Atom	AminoAcid.getCA() get CA atom
Atom	AminoAcid.getC() get C atom
Atom	AminoAcid.getO() get O atom
Atom	AminoAcid.getCB() get CB atom

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

void	Hetatom.addAtom(Atom atom) add an atom to this group
void	Group.addAtom(Atom atom) add an atom to this group
static double	Calc.getDistance(Atom a, Atom b) calculate distance between two atoms
static Atom	Calc.add(Atom a, Atom b) add two atoms ( a + b)
static Atom	Calc.substract(Atom a, Atom b) substract two atoms ( a - b)
static Atom	Calc.vectorProduct(Atom a, Atom b) Vector product
static double	Calc.skalarProduct(Atom a, Atom b) skalar product
static double	Calc.amount(Atom a) amount
static double	Calc.angle(Atom a, Atom b) angle
static Atom	Calc.unitVector(Atom a) return the unit vector of vector a
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 void	Calc.shift(Structure structure, Atom a) shift a structure with a vector