Package | Description |
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org.biojava.bio.structure |
Interfaces and classes for protein structure (PDB).
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org.biojava.bio.structure.align |
Classes for the super-imposition of structures.
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org.biojava.bio.structure.align.helper |
Helper classes for structural alignment.
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org.biojava.bio.structure.align.pairwise |
Classes for the pairwise alignment of structures.
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Modifier and Type | Class and Description |
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class |
AtomImpl
Implementation of an Atom of a PDB file.
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Modifier and Type | Method and Description |
---|---|
static Atom |
Calc.add(Atom a,
Atom b)
add two atoms ( a + b).
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static Atom[] |
Calc.centerAtoms(Atom[] atomSet)
Center the atoms at the Centroid.
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static Atom |
Calc.createVirtualCBAtom(AminoAcid amino)
creates a virtual C-beta atom.
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Atom |
Group.getAtom(int position)
Get at atom by position.
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Atom |
HetatomImpl.getAtom(int position)
return an atom by its position in the internal List.
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Atom |
Group.getAtom(java.lang.String name)
Get an atom.
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Atom |
HetatomImpl.getAtom(java.lang.String name)
get an atom throws StructureException if atom not found.
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static Atom[] |
StructureTools.getAtomArray(Structure s,
java.lang.String[] atomNames)
Returns an array of the requested Atoms from the Structure object.
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static Atom[] |
StructureTools.getAtomCAArray(Structure s)
Returns an Atom array of the CA atoms.
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static Atom[] |
StructureTools.getBackboneAtomArray(Structure s)
Returns an Atom array of the MainChain atoms.
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Atom |
AminoAcid.getC()
get C atom.
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Atom |
AminoAcidImpl.getC()
get C atom.
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Atom |
AminoAcid.getCA()
get CA atom.
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Atom |
AminoAcidImpl.getCA()
get CA atom.
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Atom |
AminoAcid.getCB()
get CB atom.
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Atom |
AminoAcidImpl.getCB()
get CB atom.
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static Atom |
Calc.getCenterVector(Atom[] atomSet)
Returns the Vector that needs to be applied to shift a set of atoms
to the Centroid.
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static Atom |
Calc.getCentroid(Atom[] atomSet)
Returns the center of mass of the set of atoms.
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Atom |
AminoAcid.getN()
get N atom.
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Atom |
AminoAcidImpl.getN()
get N atom.
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Atom |
AminoAcid.getO()
get O atom.
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Atom |
AminoAcidImpl.getO()
get O atom.
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Atom |
SVDSuperimposer.getTranslation()
Get the shift vector.
|
Atom |
AtomIterator.next()
Return next atom.
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static Atom |
Calc.substract(Atom a,
Atom b)
substract two atoms ( a - b).
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static Atom |
Calc.unitVector(Atom a)
return the unit vector of vector a .
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static Atom |
Calc.vectorProduct(Atom a,
Atom b)
Vector product .
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Modifier and Type | Method and Description |
---|---|
java.util.List<Atom> |
Group.getAtoms()
Get list of atoms.
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java.util.List<Atom> |
HetatomImpl.getAtoms()
get all atoms of this group .
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java.util.Iterator<Atom> |
Group.iterator()
get an Atom Iterator.
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java.util.Iterator<Atom> |
HetatomImpl.iterator()
return an AtomIterator.
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Modifier and Type | Method and 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.
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void |
HetatomImpl.addAtom(Atom atom)
add an atom to this group.
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static double |
Calc.amount(Atom a)
amount.
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static double |
Calc.angle(Atom a,
Atom b)
angle.
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static Atom[] |
Calc.centerAtoms(Atom[] atomSet)
Center the atoms at the Centroid.
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static Atom |
Calc.getCenterVector(Atom[] atomSet)
Returns the Vector that needs to be applied to shift a set of atoms
to the Centroid.
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static Atom |
Calc.getCentroid(Atom[] atomSet)
Returns the center of mass of the set of atoms.
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static double |
Calc.getDistance(Atom a,
Atom b)
calculate distance between two atoms.
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static double |
SVDSuperimposer.getRMS(Atom[] atomSet1,
Atom[] atomSet2)
Calculate the RMS (root mean square) deviation of two sets of atoms.
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static double |
SVDSuperimposer.getRMS(Atom[] atomSet1,
Atom[] atomSet2)
Calculate the RMS (root mean square) deviation of two sets of atoms.
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static void |
Calc.rotate(Atom atom,
double[][] m)
rotate a single atom aroud a rotation matrix.
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static void |
Calc.rotate(Atom atom,
Matrix m)
Rotate an atom around a Matrix object.
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static void |
Calc.shift(Atom a,
Atom b)
Shift a vector.
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static void |
Calc.shift(Group group,
Atom a)
Shift a Group with a vector.
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static void |
Calc.shift(Structure structure,
Atom a)
shift a structure with a vector.
|
static double |
Calc.skalarProduct(Atom a,
Atom b)
skalar product.
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static Atom |
Calc.substract(Atom a,
Atom b)
substract two atoms ( a - b).
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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.
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static Atom |
Calc.unitVector(Atom a)
return the unit vector of vector a .
|
static Atom |
Calc.vectorProduct(Atom a,
Atom b)
Vector product .
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Modifier and Type | Method and Description |
---|---|
void |
Group.setAtoms(java.util.List<Atom> atoms)
Set the atoms of this group.
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void |
HetatomImpl.setAtoms(java.util.List<Atom> atoms)
set the atoms of this group
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Constructor and Description |
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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.
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Modifier and Type | Method and Description |
---|---|
Atom[] |
StructurePairAligner.getAlignmentAtoms(Structure s) |
Modifier and Type | Method and Description |
---|---|
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.
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Modifier and Type | Method and Description |
---|---|
static Atom |
AlignTools.getCenter(Atom[] ca,
int pos,
int fragmentLength)
get the centroid for the set of atoms starting fromposition pos, length fragmentLenght
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static Atom[] |
AlignTools.getFragment(Atom[] caall,
int pos,
int fragmentLength)
get a continue subset of Atoms based by the starting position and the length
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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.
|
Modifier and Type | Method and Description |
---|---|
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
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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.
|
Modifier and Type | Method and 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 one
|
Atom |
FragmentPair.getTrans() |
Atom |
FragmentPair.getUnitv() |
Modifier and Type | Method and Description |
---|---|
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) |