Uses of Class org.biojava.bio.structure.StructureException (BioJava-1.5-beta API)

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## 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 |
org.biojava.bio.structure.align.pairwise |

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(String chainId)`
`Chain` | `Structure.findChain(String chainId)` request a particular chain from a structure.
`Chain` | `StructureImpl.findChain(String chainId, int modelnr)`
`Chain` | `Structure.findChain(String chainId, int modelnr)` request a particular chain from a particular model
`Group` | `StructureImpl.findGroup(String chainName, String pdbResnum)`
`Group` | `Structure.findGroup(String chainId, String pdbResnum)` request a particular group from a structure.
`Group` | `StructureImpl.findGroup(String chainId, String pdbResnum, int modelnr)`
`Group` | `Structure.findGroup(String chainId, 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(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.
`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(String chainId)`
`Chain` | `Structure.getChainByPDB(String chainId)` request a chain by it's PDB code by default takes only the first model
`Chain` | `StructureImpl.getChainByPDB(String chainId, int modelnr)`
`Chain` | `Structure.getChainByPDB(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(String pdbresnum)` get a group by its PDB residue numbering.
`Group` | `ChainImpl.getGroupByPDB(String pdbresnum)`
`Group[]` | `Chain.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)` get all groups that are located between two PDB residue numbers
`Group[]` | `ChainImpl.getGroupsByPDB(String pdbresnumStart, 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.

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