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

Packages that use StructureException
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.pairwise: Classes for the pairwise alignment of structures.

Uses of StructureException in org.biojava.bio.structure

Methods in org.biojava.bio.structure that throw StructureException
`static Atom[]` `Calc.centerAtoms(Atom[] atomSet)` center the atoms at the Centroid
`static Atom` `Calc.createVirtualCBAtom(AminoAcid amino)` creates a virtual C-beta atom.
`Chain` `StructureImpl.findChain(java.lang.String chainId)`
`Chain` `Structure.findChain(java.lang.String chainId)` request a particular chain from a structure.
`Chain` `StructureImpl.findChain(java.lang.String chainId, int modelnr)`
`Chain` `Structure.findChain(java.lang.String chainId, int modelnr)` request a particular chain from a particular model
`Group` `StructureImpl.findGroup(java.lang.String chainName, java.lang.String pdbResnum)`
`Group` `Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum)` request a particular group from a structure.
`Group` `StructureImpl.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)`
`Group` `Structure.findGroup(java.lang.String chainId, java.lang.String pdbResnum, int modelnr)` request a particular group from a structure.
`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(java.lang.String name)` get an atom throws StructureException if atom not found.
`Atom` `Group.getAtom(java.lang.String name)` get an atom throws StructureException if atom not found.
`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.
`Chain` `StructureImpl.getChainByPDB(java.lang.String chainId)`
`Chain` `Structure.getChainByPDB(java.lang.String chainId)` request a chain by it's PDB code by default takes only the first model
`Chain` `StructureImpl.getChainByPDB(java.lang.String chainId, int modelnr)`
`Chain` `Structure.getChainByPDB(java.lang.String chainId, int modelnr)` request a chain by it's PDB code by default takes only the first model
`static double` `Calc.getDistance(Atom a, Atom b)` calculate distance between two atoms.
`Group` `Chain.getGroupByPDB(java.lang.String pdbresnum)` get a group by its PDB residue numbering.
`Group` `ChainImpl.getGroupByPDB(java.lang.String pdbresnum)`
`Group[]` `Chain.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd)` get all groups that are located between two PDB residue numbers
`Group[]` `ChainImpl.getGroupsByPDB(java.lang.String pdbresnumStart, java.lang.String pdbresnumEnd)`
`Atom` `AminoAcidImpl.getN()` get N atom.
`Atom` `AminoAcid.getN()` get N atom.
`Atom` `AminoAcidImpl.getO()` get O atom.
`Atom` `AminoAcid.getO()` get O atom.
`static double` `Calc.getPhi(AminoAcid a, AminoAcid b)` phi angle.
`static double` `Calc.getPsi(AminoAcid a, AminoAcid b)` psi angle.
`static double` `SVDSuperimposer.getRMS(Atom[] atomSet1, Atom[] atomSet2)` calculate the RMS (root mean square) of two sets of atoms
`static boolean` `Calc.isConnected(AminoAcid a, AminoAcid b)` test if two amino acids are connected, i.e.
`static void` `Calc.rotate(Group group, double[][] rotationmatrix)` rotate a structure .
`static void` `Calc.rotate(Structure structure, double[][] rotationmatrix)` rotate a structure .
`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.

Constructors in org.biojava.bio.structure that throw StructureException
`SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2)`

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

Methods in org.biojava.bio.structure.align that throw StructureException
`void` `StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)` calculate the actual protein structure superimposition.
`void` `StructurePairAligner.align(Structure s1, Structure s2)`
`void` `StructurePairAligner.align(Structure s1, Structure s2, StrucAligParameters params)`

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

Methods in org.biojava.bio.structure.align.pairwise that throw StructureException
`void` `AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)`
`void` `AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)`
`void` `AlternativeAlignment.refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2)` Refinement procedure based on superposition and dynamic programming.