Uses of Interface
org.biojava.bio.structure.Atom
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Packages that use Atom Package Description 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. -
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Uses of Atom in org.biojava.bio.structure
Classes in org.biojava.bio.structure that implement Atom Modifier and Type Class Description class
AtomImpl
Implementation of an Atom of a PDB file.Methods in org.biojava.bio.structure that return Atom Modifier and Type Method Description 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
Group. getAtom(java.lang.String name)
Get an atom.Atom
HetatomImpl. getAtom(int position)
return an atom by its position in the internal List.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
AminoAcid. getC()
get C atom.Atom
AminoAcidImpl. getC()
get C atom.Atom
AminoAcid. getCA()
get CA atom.Atom
AminoAcidImpl. getCA()
get CA atom.Atom
AminoAcid. getCB()
get CB atom.Atom
AminoAcidImpl. 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
AminoAcid. getN()
get N atom.Atom
AminoAcidImpl. getN()
get N atom.Atom
AminoAcid. getO()
get O atom.Atom
AminoAcidImpl. 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 Modifier and Type Method Description 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 Modifier and Type Method Description 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 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 Modifier and Type Method Description 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 groupConstructors in org.biojava.bio.structure with parameters of type Atom Constructor Description 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 Modifier and Type Method Description Atom[]
StructurePairAligner. getAlignmentAtoms(Structure s)
Methods in org.biojava.bio.structure.align with parameters of type Atom Modifier and Type Method Description 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 Modifier and Type Method Description static Atom
AlignTools. getCenter(Atom[] ca, int pos, int fragmentLength)
get the centroid for the set of atoms starting fromposition pos, length fragmentLenghtstatic Atom[]
AlignTools. getFragment(Atom[] caall, int pos, int fragmentLength)
get a continue subset of Atoms based by the starting position and the lengthstatic Atom[]
AlignTools. getFragmentFromIdxList(Atom[] caall, int[] idx)
get a subset of Atoms based by their positionsstatic 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 Modifier and Type Method Description static Atom
AlignTools. getCenter(Atom[] ca, int pos, int fragmentLength)
get the centroid for the set of atoms starting fromposition pos, length fragmentLenghtstatic 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 Atom[]
AlignTools. getFragment(Atom[] caall, int pos, int fragmentLength)
get a continue subset of Atoms based by the starting position and the lengthstatic Atom[]
AlignTools. getFragmentFromIdxList(Atom[] caall, int[] idx)
get a subset of Atoms based by their positionsstatic 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 Modifier and Type Method Description 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 oneAtom
FragmentPair. getTrans()
Atom
FragmentPair. getUnitv()
Methods in org.biojava.bio.structure.align.pairwise with parameters of type Atom Modifier and Type Method Description 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. calculateSuperpositionByIdx(Atom[] ca1, Atom[] ca2)
void
AlternativeAlignment. finish(StrucAligParameters params, 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 fragvoid
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)
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