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).