Uses of Interface
org.biojava.bio.structure.Atom

Packages that use Atom
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.helper Helper classes for structural alignment. 
org.biojava.bio.structure.align.pairwise Classes for the pairwise alignment of structures. 
 

Uses of Atom in org.biojava.bio.structure
 

Classes in org.biojava.bio.structure that implement Atom
 class AtomImpl
          Implementation of an Atom of a PDB file.
 

Methods in org.biojava.bio.structure that return Atom
static Atom Calc.add(Atom a, Atom b)
          add two atoms ( a + b).
static Atom[] Calc.centerAtoms(Atom[] atomSet)
          Center the atoms at the Centroid.
static Atom Calc.createVirtualCBAtom(AminoAcid amino)
          creates a virtual C-beta atom.
 Atom Group.getAtom(int position)
          Get at atom by position.
 Atom HetatomImpl.getAtom(int position)
          return an atom by its position in the internal List.
 Atom Group.getAtom(java.lang.String name)
          Get an atom.
 Atom HetatomImpl.getAtom(java.lang.String name)
          get an atom throws StructureException if atom not found.
static Atom[] StructureTools.getAtomArray(Structure s, java.lang.String[] atomNames)
          Returns an array of the requested Atoms from the Structure object.
static Atom[] StructureTools.getAtomCAArray(Structure s)
          Returns an Atom array of the CA atoms.
static Atom[] StructureTools.getBackboneAtomArray(Structure s)
          Returns an Atom array of the MainChain atoms.
 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.
static Atom Calc.getCenterVector(Atom[] atomSet)
          Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
static Atom Calc.getCentroid(Atom[] atomSet)
          Returns the center of mass of the set of atoms.
 Atom AminoAcidImpl.getN()
          get N atom.
 Atom AminoAcid.getN()
          get N atom.
 Atom AminoAcidImpl.getO()
          get O atom.
 Atom AminoAcid.getO()
          get O atom.
 Atom SVDSuperimposer.getTranslation()
          Get the shift vector.
 Atom AtomIterator.next()
          Return next atom.
static Atom Calc.substract(Atom a, Atom b)
          substract two atoms ( a - b).
static Atom Calc.unitVector(Atom a)
          return the unit vector of vector a .
static Atom Calc.vectorProduct(Atom a, Atom b)
          Vector product .
 

Methods in org.biojava.bio.structure that return types with arguments of type Atom
 java.util.List<Atom> Group.getAtoms()
          Get list of atoms.
 java.util.List<Atom> HetatomImpl.getAtoms()
          get all atoms of this group .
 java.util.Iterator<Atom> Group.iterator()
          get an Atom Iterator.
 java.util.Iterator<Atom> HetatomImpl.iterator()
          return an AtomIterator.
 

Methods in org.biojava.bio.structure with parameters of type Atom
static Atom Calc.add(Atom a, Atom b)
          add two atoms ( a + b).
 void Group.addAtom(Atom atom)
          add an atom to this group.
 void HetatomImpl.addAtom(Atom atom)
          add an atom to this group.
static double Calc.amount(Atom a)
          amount.
static double Calc.angle(Atom a, Atom b)
          angle.
static Atom[] Calc.centerAtoms(Atom[] atomSet)
          Center the atoms at the Centroid.
static Atom Calc.getCenterVector(Atom[] atomSet)
          Returns the Vector that needs to be applied to shift a set of atoms to the Centroid.
static Atom Calc.getCentroid(Atom[] atomSet)
          Returns the center of mass of the set of atoms.
static double Calc.getDistance(Atom a, Atom b)
          calculate distance between two atoms.
static double SVDSuperimposer.getRMS(Atom[] atomSet1, Atom[] atomSet2)
          Calculate the RMS (root mean square) deviation of two sets of atoms.
static double SVDSuperimposer.getRMS(Atom[] atomSet1, Atom[] atomSet2)
          Calculate the RMS (root mean square) deviation of two sets of atoms.
static void Calc.rotate(Atom atom, double[][] m)
          rotate a single atom aroud a rotation matrix.
static void Calc.rotate(Atom atom, Matrix m)
          Rotate an atom around a Matrix object.
static void Calc.shift(Atom a, Atom b)
          Shift a vector.
static void Calc.shift(Group group, Atom a)
          Shift a Group with a vector.
static void Calc.shift(Structure structure, Atom a)
          shift a structure with a vector.
static double Calc.skalarProduct(Atom a, Atom b)
          skalar product.
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 Atom Calc.unitVector(Atom a)
          return the unit vector of vector a .
static Atom Calc.vectorProduct(Atom a, Atom b)
          Vector product .
 

Method parameters in org.biojava.bio.structure with type arguments of type Atom
 void Group.setAtoms(java.util.List<Atom> atoms)
          Set the atoms of this group.
 void HetatomImpl.setAtoms(java.util.List<Atom> atoms)
          set the atoms of this group
 

Constructors in org.biojava.bio.structure with parameters of type Atom
SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2)
          Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
SVDSuperimposer(Atom[] atomSet1, Atom[] atomSet2)
          Create a SVDSuperimposer object and calculate a SVD superimposition of two sets of atoms.
 

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

Methods in org.biojava.bio.structure.align that return Atom
 Atom[] StructurePairAligner.getAlignmentAtoms(Structure s)
           
 

Methods in org.biojava.bio.structure.align with parameters of type Atom
 void StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
          calculate the protein structure superimposition, between two sets of atoms.
 void StructurePairAligner.align(Atom[] ca1, Atom[] ca2, StrucAligParameters params)
          calculate the protein structure superimposition, between two sets of atoms.
 

Uses of Atom in org.biojava.bio.structure.align.helper
 

Methods in org.biojava.bio.structure.align.helper that return Atom
static Atom AlignTools.getCenter(Atom[] ca, int pos, int fragmentLength)
          get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
static Atom[] AlignTools.getFragment(Atom[] caall, int pos, int fragmentLength)
          get a continue subset of Atoms based by the starting position and the length
static Atom[] AlignTools.getFragmentFromIdxList(Atom[] caall, int[] idx)
          get a subset of Atoms based by their positions
static Atom[] AlignTools.getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)
          get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
 

Methods in org.biojava.bio.structure.align.helper with parameters of type Atom
static Atom AlignTools.getCenter(Atom[] ca, int pos, int fragmentLength)
          get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
static double[] AlignTools.getDiagonalAtK(Atom[] atoms, int k)
           
static Matrix AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2)
          matrix of all distances between two sets of 3d coords"
static Matrix AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2)
          matrix of all distances between two sets of 3d coords"
static Atom[] AlignTools.getFragment(Atom[] caall, int pos, int fragmentLength)
          get a continue subset of Atoms based by the starting position and the length
static Atom[] AlignTools.getFragmentFromIdxList(Atom[] caall, int[] idx)
          get a subset of Atoms based by their positions
static Atom[] AlignTools.getFragmentNoClone(Atom[] caall, int pos, int fragmentLength)
          get a continue subset of Atoms based by the starting position and the length does not clone the original atoms.
 

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

Methods in org.biojava.bio.structure.align.pairwise that return Atom
 Atom FragmentPair.getCenter1()
           
 Atom FragmentPair.getCenter2()
           
 Atom AlternativeAlignment.getShift()
          returns the shift vector that has to be applied on structure to to shift on structure one
 Atom FragmentPair.getTrans()
           
 Atom FragmentPair.getUnitv()
           
 

Methods in org.biojava.bio.structure.align.pairwise with parameters of type Atom
 JointFragments[] FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
           
 JointFragments[] FragmentJoiner.approach_ap3(Atom[] ca1, Atom[] ca2, FragmentPair[] fraglst, StrucAligParameters params)
           
 void AlternativeAlignment.calcScores(Atom[] ca1, Atom[] ca2)
          calculates scores for this alignment ( %id )
 void AlternativeAlignment.calcScores(Atom[] ca1, Atom[] ca2)
          calculates scores for this alignment ( %id )
 void AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
           
 void AlternativeAlignment.calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
           
 void AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
           
 void AlternativeAlignment.finish(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
           
static Matrix AlternativeAlignment.getDistanceMatrix(Atom[] ca1, Atom[] ca2)
           
static Matrix AlternativeAlignment.getDistanceMatrix(Atom[] ca1, Atom[] ca2)
           
static double FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)
          get the RMS of the JointFragments pair frag
static double FragmentJoiner.getRMS(Atom[] ca1, Atom[] ca2, JointFragments frag)
          get the RMS of the JointFragments pair frag
 void AlternativeAlignment.refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
          Refinement procedure based on superposition and dynamic programming.
 void AlternativeAlignment.refine(StrucAligParameters params, Atom[] ca1, Atom[] ca2)
          Refinement procedure based on superposition and dynamic programming.
 void FragmentPair.setCenter1(Atom center1)
           
 void FragmentPair.setCenter2(Atom center2)
           
 void FragmentPair.setTrans(Atom trans)
           
 void FragmentPair.setUnitv(Atom unitv)