Uses of Class
org.biojava.bio.structure.StructureException

Packages that use StructureException

org.biojava.bio.structure

Interfaces and classes for molecular structure.

Uses of StructureException in org.biojava.bio.structure

Methods in org.biojava.bio.structure that throw StructureException

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 double	Calc.getDistance(Atom a, Atom b) calculate distance between two atoms
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 double	Calc.getPhi(AminoAcid a, AminoAcid b) phi angle
static double	Calc.getPsi(AminoAcid a, AminoAcid b) psi angle
static boolean	Calc.isConnected(AminoAcid a, AminoAcid b) test if two amino acids are connected, i.e.
static void	Calc.rotate(Structure structure, double[][] m) rotate a structure
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