## 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.
org.biojava.bio.structure.gui.util: Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.io: Input and Output 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(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.
`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` `ChainImpl.getGroupByPDB(String pdbresnum)`
`Group` `Chain.getGroupByPDB(String pdbresnum)` get a group by its PDB residue numbering.
`Group[]` `ChainImpl.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd)` Get all groups that are located between two PDB residue numbers.
`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, boolean ignoreMissing)` Get all groups that are located between two PDB residue numbers.
`Group[]` `Chain.getGroupsByPDB(String pdbresnumStart, String pdbresnumEnd, boolean ignoreMissing)` Get all groups that are located between two PDB residue numbers.
`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) deviation 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)` Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.

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 protein structure superimposition, between two sets of atoms.
`void` `StructurePairAligner.align(Structure s1, Structure s2)` calculate the alignment between the two full structures with default parameters
`void` `StructurePairAligner.align(Structure s1, Structure s2, StrucAligParameters params)` calculate the alignment between the two full structures with user provided parameters

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.

Uses of StructureException in org.biojava.bio.structure.gui.util

Methods in org.biojava.bio.structure.gui.util that throw StructureException
`Structure` `StructurePairSelector.getStructure1()`
`Structure` `PDBUploadPanel.getStructure1()`
`Structure` `PDBServerPanel.getStructure1()`
`Structure` `PDBDirPanel.getStructure1()`
`Structure` `StructurePairSelector.getStructure2()`
`Structure` `PDBUploadPanel.getStructure2()`
`Structure` `PDBServerPanel.getStructure2()`
`Structure` `PDBDirPanel.getStructure2()`

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

Methods in org.biojava.bio.structure.io that throw StructureException
`boolean` `SeqRes2AtomAligner.align(List<Group> seqRes, List<Group> atomRes)` aligns two chains of groups, where the first chain is representing the list of amino acids as obtained from the SEQRES records, and the second chain represents the groups obtained from the ATOM records (and containing the actual ATOM information).