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Packages that use Atom | |
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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 |
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Classes in org.biojava.bio.structure that implement Atom | |
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class |
AtomImpl
Implementation of an Atom of a PDB file. |
Methods in org.biojava.bio.structure that return Atom | |
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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 |
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. |
static Atom[] |
StructureTools.getAtomArray(Structure s,
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 | |
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List<Atom> |
HetatomImpl.getAtoms()
get all atoms of this group . |
List<Atom> |
Group.getAtoms()
Get list of atoms. |
Iterator<Atom> |
HetatomImpl.iterator()
return an AtomIterator. |
Iterator<Atom> |
Group.iterator()
get an Atom Iterator. |
Methods in org.biojava.bio.structure with parameters of type Atom | |
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static Atom |
Calc.add(Atom a,
Atom b)
add two atoms ( a + b). |
void |
HetatomImpl.addAtom(Atom atom)
add an atom to this group. |
void |
Group.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 | |
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void |
HetatomImpl.setAtoms(List<Atom> atoms)
set the atoms of this group |
void |
Group.setAtoms(List<Atom> atoms)
Set the atoms of this group. |
Constructors in org.biojava.bio.structure with parameters of type Atom | |
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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 |
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Methods in org.biojava.bio.structure.align that return Atom | |
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Atom[] |
StructurePairAligner.getAlignmentAtoms(Structure s)
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Methods in org.biojava.bio.structure.align with parameters of type Atom | |
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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 |
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Methods in org.biojava.bio.structure.align.helper that return Atom | |
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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 | |
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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 |
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Methods in org.biojava.bio.structure.align.pairwise that return Atom | |
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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 | |
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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)
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