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

Packages that use Atom

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client	This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.fatcat	Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc
org.biojava.nbio.structure.align.helper	Helper classes for structural alignment.
org.biojava.nbio.structure.align.model
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.pairwise	Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.seq
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.align.xml	Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.asa
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.domain
org.biojava.nbio.structure.domain.pdp
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.
org.biojava.nbio.structure.symmetry.core
org.biojava.nbio.structure.symmetry.internal
org.biojava.nbio.structure.symmetry.utils

Uses of Atom in org.biojava.nbio.structure

Classes in org.biojava.nbio.structure that implement Atom

Modifier and Type	Class and Description
class	AtomImpl Implementation of an Atom of a PDB file.

Fields in org.biojava.nbio.structure with type parameters of type Atom

Modifier and Type	Field and Description
protected List<Atom>	HetatomImpl.atoms

Methods in org.biojava.nbio.structure that return Atom

Modifier and Type	Method and 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.centerAtoms(Atom[] atomSet, Atom centroid) Center the atoms at the Centroid, if the centroid is already know.
static Atom	Calc.centerOfMass(Atom[] points)
static Atom[]	StructureTools.cloneAtomArray(Atom[] ca) Provides an equivalent copy of Atoms in a new array.
static Atom[]	StructureTools.cloneCAArray(Atom[] ca) Deprecated. Use the better-named StructureTools.cloneAtomArray(Atom[]) instead
static Atom	Calc.createVirtualCBAtom(AminoAcid amino) creates a virtual C-beta atom.
static Atom[]	StructureTools.duplicateCA2(Atom[] ca2) Utility method for working with circular permutations.
static Atom[]	StructureTools.getAllAtomArray(Chain c) Returns and array of all atoms of the chain (first model), including Hydrogens (if present) and all HETATOMs.
static Atom[]	StructureTools.getAllAtomArray(Structure s) Convert all atoms of the structure (first model) into an Atom array
static Atom[]	StructureTools.getAllNonHAtomArray(Chain c, boolean hetAtoms) Returns and array of all non-Hydrogen atoms in the given Chain, optionally including HET atoms or not Waters are not included.
static Atom[]	StructureTools.getAllNonHAtomArray(Structure s, boolean hetAtoms) Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.
Atom	HetatomImpl.getAtom(int position) Get at atom by position.
Atom	Group.getAtom(int position) Get at atom by position.
Atom	HetatomImpl.getAtom(String name) Get an atom given its PDB name.
Atom	Group.getAtom(String name) Get an atom given its PDB name.
Atom	BondImpl.getAtomA() Gets atom 'A' of this bond.
Atom	Bond.getAtomA() Gets atom 'A' of this bond.
static Atom[]	StructureTools.getAtomArray(Chain c, String[] atomNames) Returns an array of the requested Atoms from the Chain object.
static Atom[]	StructureTools.getAtomArray(Structure s, String[] atomNames) Returns an array of the requested Atoms from the Structure object.
static Atom[]	StructureTools.getAtomArrayAllModels(Structure s, String[] atomNames) Returns an array of the requested Atoms from the Structure object.
Atom	BondImpl.getAtomB() Gets atom 'B' of this bond.
Atom	Bond.getAtomB() Gets atom 'B' of this bond.
static Atom[]	StructureTools.getAtomCAArray(Chain c) Returns an Atom array of the C-alpha atoms.
static Atom[]	StructureTools.getAtomCAArray(Structure s) Return an Atom array of the C-alpha atoms.
static Atom[]	StructureTools.getBackboneAtomArray(Structure s) Return an Atom array of the main chain atoms: CA, C, N, O Any group that contains those atoms will be included, be it a standard aminoacid or not
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.getCenterVector(Atom[] atomSet, Atom centroid) Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
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	NucleotideImpl.getO3Prime() Returns the O3' atom if present, otherwise null
Atom	NucleotideImpl.getO5Prime() Returns the O5' atom if present, otherwise null
Atom	BondImpl.getOther(Atom exclude) A utility method to get the other atom in a bond, given one of its atoms.
Atom	Bond.getOther(Atom exclude) A utility method to get the other atom in a bond, given one of its atoms.
Atom	NucleotideImpl.getP() Returns the P atom if present, otherwise null
static Atom[]	StructureTools.getRepresentativeAtomArray(Chain c) Gets a representative atom for each group that is part of the chain backbone.
static Atom[]	StructureTools.getRepresentativeAtomArray(Structure s) Gets a representative atom for each group that is part of the chain backbone.
Atom	SVDSuperimposer.getTranslation() Get the shift vector.
static Atom	Calc.getTranslationVector(javax.vecmath.Matrix4d transform) Extract the translational vector of a Vecmath transformation.
static Atom	Calc.invert(Atom a)
Atom	AtomIterator.next() Return next atom.
static Atom	Calc.scale(Atom a, double s) Multiply elements of a by s
static Atom	Calc.scaleAdd(double s, Atom x, Atom b) Perform linear transformation s*X+B, and store the result in b
static Atom	Calc.scaleEquals(Atom a, double s) Multiply elements of a by s (in place)
static Atom	Calc.subtract(Atom a, Atom b) subtract two atoms ( a - b).
static Atom	Calc.unitVector(Atom a) Returns the unit vector of vector a .
static Atom	Calc.vectorProduct(Atom a, Atom b) Vector product (cross product).

Methods in org.biojava.nbio.structure that return types with arguments of type Atom

Modifier and Type	Method and Description
List<Atom>	HetatomImpl.getAtoms() Get list of atoms.
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.nbio.structure with parameters of type Atom

Modifier and Type	Method and Description
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) Gets the length of the vector (2-norm)
static double	Calc.angle(Atom a, Atom b) Gets the angle between two vectors
static javax.vecmath.Point3d[]	Calc.atomsToPoints(Atom[] atoms) Convert an array of atoms into an array of vecmath points
static double	Calc.calcRotationAngleInDegrees(Atom centerPt, Atom targetPt) Calculates the angle from centerPt to targetPt in degrees.
static Atom[]	Calc.centerAtoms(Atom[] atomSet) Center the atoms at the Centroid.
static Atom[]	Calc.centerAtoms(Atom[] atomSet, Atom centroid) Center the atoms at the Centroid, if the centroid is already know.
static Atom[]	Calc.centerAtoms(Atom[] atomSet, Atom centroid) Center the atoms at the Centroid, if the centroid is already know.
static Atom	Calc.centerOfMass(Atom[] points)
static Atom[]	StructureTools.cloneAtomArray(Atom[] ca) Provides an equivalent copy of Atoms in a new array.
static Atom[]	StructureTools.cloneCAArray(Atom[] ca) Deprecated. Use the better-named StructureTools.cloneAtomArray(Atom[]) instead
static Group[]	StructureTools.cloneGroups(Atom[] ca) Clone a set of representative Atoms, but returns the parent groups
static String	StructureTools.convertAtomsToSeq(Atom[] atoms)
static Atom[]	StructureTools.duplicateCA2(Atom[] ca2) Utility method for working with circular permutations.
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.getCenterVector(Atom[] atomSet, Atom centroid) Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
static Atom	Calc.getCenterVector(Atom[] atomSet, Atom centroid) Returns the Vector that needs to be applied to shift a set of atoms to the Centroid, if the centroid is already known
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	Calc.getDistanceFast(Atom a, Atom b) Will calculate the square of distances between two atoms.
static Map<Group,Double>	StructureTools.getGroupDistancesWithinShell(Structure structure, Atom centroid, Set<ResidueNumber> excludeResidues, double radius, boolean includeWater, boolean useAverageDistance) Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Atom atom, Set<ResidueNumber> excludeResidues, double distance, boolean includeWater)
Atom	BondImpl.getOther(Atom exclude) A utility method to get the other atom in a bond, given one of its atoms.
Atom	Bond.getOther(Atom exclude) A utility method to get the other atom in a bond, given one of its 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 double	SVDSuperimposer.getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) Calculate the TM-Score for the superposition.
static double	SVDSuperimposer.getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) Calculate the TM-Score for the superposition.
static double	SVDSuperimposer.getTMScoreAlternate(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) Calculate the TM-Score for the superposition.
static double	SVDSuperimposer.getTMScoreAlternate(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2) Calculate the TM-Score for the superposition.
static javax.vecmath.Matrix4d	Calc.getTransformation(Matrix rot, Atom trans) Convert JAMA rotation and translation to a Vecmath transformation matrix.
static List<Group>	StructureTools.getUnalignedGroups(Atom[] ca) List of groups from the structure not included in ca (e.g.
static Atom	Calc.invert(Atom a)
static void	Calc.rotate(Atom[] ca, Matrix matrix)
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 double	Calc.scalarProduct(Atom a, Atom b) Scalar product (dot product).
static Atom	Calc.scale(Atom a, double s) Multiply elements of a by s
static Atom	Calc.scaleAdd(double s, Atom x, Atom b) Perform linear transformation s*X+B, and store the result in b
static Atom	Calc.scaleEquals(Atom a, double s) Multiply elements of a by s (in place)
static void	Calc.shift(Atom[] ca, Atom b) Shift an array of atoms at once.
static void	Calc.shift(Atom[] ca, Atom b) Shift an array of atoms at once.
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 Atom	Calc.subtract(Atom a, Atom b) subtract two atoms ( a - b).
static double	Calc.torsionAngle(Atom a, Atom b, Atom c, Atom d) Calculate the torsion angle, i.e.
static void	Calc.transform(Atom[] ca, javax.vecmath.Matrix4d t) Transform an array of atoms at once.
static void	Calc.transform(Atom atom, javax.vecmath.Matrix4d m) Transforms an atom object, given a Matrix4d (i.e.
static void	Calc.translate(Atom atom, javax.vecmath.Vector3d v) Translates an atom object, given a Vector3d (i.e.
static Atom	Calc.unitVector(Atom a) Returns the unit vector of vector a .
static Atom	Calc.vectorProduct(Atom a, Atom b) Vector product (cross product).

Method parameters in org.biojava.nbio.structure with type arguments of type Atom

Modifier and Type	Method and Description
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.nbio.structure with parameters of type Atom

Constructor and Description
AtomPositionMap(Atom[] atoms) Creates a new AtomPositionMap containing peptide alpha-carbon atoms
AtomPositionMap(Atom[] atoms, AtomPositionMap.GroupMatcher matcher) Creates a new AtomPositionMap containing only atoms matched by matcher.
BondImpl(Atom atomA, Atom atomB, int bondOrder) Constructs a new bond from a pair of atoms and the bond order of the bond between them.
BondImpl(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) Constructs a new bond from a pair of atoms and the bond order of the bond between them.
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.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return Atom

Modifier and Type	Method and Description
Atom[]	StructurePairAligner.getAlignmentAtoms(Structure s) Returns the atoms that are being used for the alignment.
Atom[]	CallableStructureAlignment.getCa1()

Methods in org.biojava.nbio.structure.align with parameters of type Atom

Modifier and Type	Method and Description
AFPChain	BioJavaStructureAlignment.align(Atom[] ca1, Atom[] ca2)
AFPChain	BioJavaStructureAlignment.align(Atom[] ca1, Atom[] ca2)
AFPChain	StructureAlignment.align(Atom[] ca1, Atom[] ca2) Run an alignment while specifying the atoms to be aligned.
AFPChain	StructureAlignment.align(Atom[] ca1, Atom[] ca2) Run an alignment while specifying the atoms to be aligned.
abstract AFPChain	AbstractStructureAlignment.align(Atom[] ca1, Atom[] ca2)
abstract AFPChain	AbstractStructureAlignment.align(Atom[] ca1, Atom[] ca2)
AFPChain	BioJavaStructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain	BioJavaStructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain	StructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params) run an alignment and also send a bean containing the parameters.
AFPChain	StructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params) run an alignment and also send a bean containing the parameters.
abstract AFPChain	AbstractStructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params)
abstract AFPChain	AbstractStructureAlignment.align(Atom[] ca1, Atom[] ca2, Object params)
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.
void	CallableStructureAlignment.setCa1(Atom[] ca1)
static Group[]	AFPTwister.twistOptimized(AFPChain afpChain, Atom[] ca1, Atom[] ca2) superimposing according to the optimized alignment
static Group[]	AFPTwister.twistOptimized(AFPChain afpChain, Atom[] ca1, Atom[] ca2) superimposing according to the optimized alignment
static Group[]	AFPTwister.twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2) calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B
static Group[]	AFPTwister.twistPDB(AFPChain afpChain, Atom[] ca1, Atom[] ca2) calculate the total rmsd of the blocks output a merged pdb file for both proteins protein 1, in chain A protein 2 is twisted according to the twists detected, in chain B

Constructors in org.biojava.nbio.structure.align with parameters of type Atom

Constructor and Description
CallableStructureAlignment(Atom[] ca1, Atom[] ca2, String algorithmName, ConfigStrucAligParams params) Constructor for all-to-all alignment calculation.
CallableStructureAlignment(Atom[] ca1, Atom[] ca2, String algorithmName, ConfigStrucAligParams params) Constructor for all-to-all alignment calculation.

Uses of Atom in org.biojava.nbio.structure.align.ce

Methods in org.biojava.nbio.structure.align.ce that return Atom

Modifier and Type	Method and Description
static Atom[]	GuiWrapper.getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)
Atom	CeCalculatorEnhanced.getShift() Gets the shift from the last call to calc_rmsd.
Atom	CECalculator.getShift() Gets the shift from the last call to calc_rmsd.

Methods in org.biojava.nbio.structure.align.ce with parameters of type Atom

Modifier and Type	Method and Description
AFPChain	CeMain.align(Atom[] ca1, Atom[] ca2)
AFPChain	CeMain.align(Atom[] ca1, Atom[] ca2)
AFPChain	OptimalCECPMain.align(Atom[] ca1, Atom[] ca2, Object param) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	OptimalCECPMain.align(Atom[] ca1, Atom[] ca2, Object param) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	CeCPMain.align(Atom[] ca1, Atom[] ca2, Object param) Aligns ca1 and ca2 using a heuristic to check for CPs.
AFPChain	CeCPMain.align(Atom[] ca1, Atom[] ca2, Object param) Aligns ca1 and ca2 using a heuristic to check for CPs.
AFPChain	CeMain.align(Atom[] ca1, Atom[] ca2, Object param) Align ca2 onto ca1.
AFPChain	CeMain.align(Atom[] ca1, Atom[] ca2, Object param) Align ca2 onto ca1.
AFPChain	OptimalCECPMain.alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	OptimalCECPMain.alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] alignments) Finds the optimal alignment between two proteins allowing for a circular permutation (CP).
AFPChain	OptimalCECPMain.alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) Aligns ca1 with ca2 permuted by cp residues.
AFPChain	OptimalCECPMain.alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) Aligns ca1 with ca2 permuted by cp residues.
double	CECalculator.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform) superimpose and get rmsd
double	CECalculator.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform) superimpose and get rmsd
double	CeCalculatorEnhanced.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) superimpose and get rmsd
double	CeCalculatorEnhanced.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) superimpose and get rmsd
double	CECalculator.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) Deprecated. Use CECalculator.calc_rmsd(Atom[],Atom[],int,boolean) instead
double	CECalculator.calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show) Deprecated. Use CECalculator.calc_rmsd(Atom[],Atom[],int,boolean) instead
void	CeCalculatorEnhanced.convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) copy data from this class into AFPChain container object.
void	CeCalculatorEnhanced.convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) copy data from this class into AFPChain container object.
void	CECalculator.convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) copy data from this class into AFPChain container object.
void	CECalculator.convertAfpChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) copy data from this class into AFPChain container object.
static Object	GuiWrapper.display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Object	GuiWrapper.display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CeCalculatorEnhanced.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CeCalculatorEnhanced.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CECalculator.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain	CECalculator.extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) Takes as input an AFPChain where ca2 has been artificially duplicated.
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated) Takes as input an AFPChain where ca2 has been artificially duplicated.
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, CECPParameters params)
static AFPChain	CeCPMain.filterDuplicateAFPs(AFPChain afpChain, CECalculator ceCalc, Atom[] ca1, Atom[] ca2duplicated, CECPParameters params)
static Structure	GuiWrapper.getAlignedStructure(Atom[] ca1, Atom[] ca2)
static Structure	GuiWrapper.getAlignedStructure(Atom[] ca1, Atom[] ca2)
static Atom[]	GuiWrapper.getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)
double[][]	CeCalculatorEnhanced.initSumOfDistances(int nse1, int nse2, int winSize, int winSizeComb1, Atom[] ca1, Atom[] ca2)
double[][]	CeCalculatorEnhanced.initSumOfDistances(int nse1, int nse2, int winSize, int winSizeComb1, Atom[] ca1, Atom[] ca2)
double[][]	CECalculator.initSumOfDistances(int nse1, int nse2, int winSize, int winSizeComb1, Atom[] ca1, Atom[] ca2)
double[][]	CECalculator.initSumOfDistances(int nse1, int nse2, int winSize, int winSizeComb1, Atom[] ca1, Atom[] ca2)
void	CeCalculatorEnhanced.nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CeCalculatorEnhanced.nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CECalculator.nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CECalculator.nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator) Circular permutation specific code to be run after the standard CE alignment
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator) Circular permutation specific code to be run after the standard CE alignment
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param) Circular permutation specific code to be run after the standard CE alignment
static AFPChain	CeCPMain.postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param) Circular permutation specific code to be run after the standard CE alignment
static Group[]	GuiWrapper.prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Group[]	GuiWrapper.prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	GuiWrapper.showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Object jmol)
static void	GuiWrapper.showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Object jmol)
void	CeCalculatorEnhanced.traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CeCalculatorEnhanced.traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CECalculator.traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void	CECalculator.traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static double[][]	CeCalculatorEnhanced.updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params) Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
static double[][]	CeCalculatorEnhanced.updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params) Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
static double[][]	CECalculator.updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params) Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.
static double[][]	CECalculator.updateMatrixWithSequenceConservation(double[][] max, Atom[] ca1, Atom[] ca2, CeParameters params) Modifies an alignment matrix by favoring the alignment of similar and identical amino acids and penalizing the alignment of unrelated ones.

Uses of Atom in org.biojava.nbio.structure.align.client

Methods in org.biojava.nbio.structure.align.client with parameters of type Atom

Modifier and Type	Method and Description
static AFPChain	JFatCatClient.getAFPChainFromServer(String serverLocation, String name1, String name2, Atom[] ca1, Atom[] ca2)
static AFPChain	JFatCatClient.getAFPChainFromServer(String serverLocation, String name1, String name2, Atom[] ca1, Atom[] ca2)
static AFPChain	JFatCatClient.getAFPChainFromServer(String serverLocation, String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)
static AFPChain	JFatCatClient.getAFPChainFromServer(String serverLocation, String method, String name1, String name2, Atom[] ca1, Atom[] ca2, int timeout)
static void	JFatCatClient.sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	JFatCatClient.sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Uses of Atom in org.biojava.nbio.structure.align.fatcat

Methods in org.biojava.nbio.structure.align.fatcat with parameters of type Atom

Modifier and Type	Method and Description
AFPChain	FatCatRigid.align(Atom[] ca1, Atom[] ca2)
AFPChain	FatCatRigid.align(Atom[] ca1, Atom[] ca2)
AFPChain	FatCatFlexible.align(Atom[] ca1, Atom[] ca2)
AFPChain	FatCatFlexible.align(Atom[] ca1, Atom[] ca2)
protected AFPChain	FatCat.align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
protected AFPChain	FatCat.align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
AFPChain	FatCatRigid.align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain	FatCatRigid.align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain	FatCatFlexible.align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain	FatCatFlexible.align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain	FatCat.alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain	FatCat.alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain	FatCat.alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)

Uses of Atom in org.biojava.nbio.structure.align.fatcat.calc

Methods in org.biojava.nbio.structure.align.fatcat.calc with parameters of type Atom

Modifier and Type	Method and Description
void	FatCatAligner.align(Atom[] ca1, Atom[] ca2, boolean doRigid, FatCatParameters params)
void	FatCatAligner.align(Atom[] ca1, Atom[] ca2, boolean doRigid, FatCatParameters params)
protected static double	AFPChainer.calAfpRmsd(int afpn, int[] afpPositions, int listStart, AFPChain afpChain, Atom[] ca1, Atom[] ca2) //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
protected static double	AFPChainer.calAfpRmsd(int afpn, int[] afpPositions, int listStart, AFPChain afpChain, Atom[] ca1, Atom[] ca2) //return the rmsd of the residues from the segments that form the given AFP list //this value can be a measurement (1) for the connectivity of the AFPs
static void	AFPChainer.doChainAfp(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
static void	AFPChainer.doChainAfp(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) // Key function: chain (assembly) the AFPs // a AFP (k) is defined as (i, j, k), with i and j are staring points // AFP extension (eg.
static void	AFPCalculator.extractAFPChains(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPCalculator.extractAFPChains(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPOptimizer.optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) optimize the alignment by dynamic programming
static void	AFPOptimizer.optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2) optimize the alignment by dynamic programming
static void	AFPPostProcessor.postProcess(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPPostProcessor.postProcess(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPCalculator.sortAfps(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPCalculator.sortAfps(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Constructors in org.biojava.nbio.structure.align.fatcat.calc with parameters of type Atom

Constructor and Description
StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2, Atom[] c2, int iniLen, int[][] iniSet) optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues
StructureAlignmentOptimizer(int b1, int end1, Atom[] c1, int b2, int end2, Atom[] c2, int iniLen, int[][] iniSet) optimize the structural alignment by update the equivalent residues and then run dynamic programming input: len1 the length of structure 1; c1: the structure information of 1 len2 the length of structure 2; c2: the structure information of 2 iniLen and iniSet is the length and list of initial equivalent residues

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

Methods in org.biojava.nbio.structure.align.helper that return Atom

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 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.nbio.structure.align.helper with parameters of type Atom

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 Atoms.
static Matrix	AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2) Matrix of all distances between two sets of Atoms.
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.nbio.structure.align.model

Methods in org.biojava.nbio.structure.align.model that return Atom

Modifier and Type	Method and Description
Atom[]	AFPChain.getBlockShiftVector()

Methods in org.biojava.nbio.structure.align.model with parameters of type Atom

Modifier and Type	Method and Description
void	AFPChain.setBlockShiftVector(Atom[] blockShiftVector)
static String	AfpChainWriter.toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Prints the alignment in the simplest form: a list of aligned residues.
static String	AfpChainWriter.toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Prints the alignment in the simplest form: a list of aligned residues.
static String	AfpChainWriter.toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static String	AfpChainWriter.toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
String	AFPChain.toCE(Atom[] ca1, Atom[] ca2)
String	AFPChain.toCE(Atom[] ca1, Atom[] ca2)
static String	AfpChainWriter.toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static String	AfpChainWriter.toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
String	AFPChain.toFatcat(Atom[] ca1, Atom[] ca2)
String	AFPChain.toFatcat(Atom[] ca1, Atom[] ca2)
static String	AfpChainWriter.toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock) Output in FatCatCore format
static String	AfpChainWriter.toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock) Output in FatCatCore format
static String	AfpChainWriter.toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
static String	AfpChainWriter.toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
static String	AfpChainWriter.toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showAlignmentBlock) Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
static String	AfpChainWriter.toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showAlignmentBlock) Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.

Uses of Atom in org.biojava.nbio.structure.align.multiple

Constructors in org.biojava.nbio.structure.align.multiple with parameters of type Atom

Constructor and Description
MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2, boolean flexible) Constructor from an AFPChain instance.
MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2, boolean flexible) Constructor from an AFPChain instance.

Uses of Atom in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that return Atom

Modifier and Type	Method and Description
static Atom	MultipleAlignmentTools.getAtomForSequencePosition(MultipleAlignment msa, List<Integer> mapSeqToStruct, int str, int sequencePos) Returns the Atom of the specified structure that is aligned in the sequence alignment position specified.

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

Methods in org.biojava.nbio.structure.align.pairwise that return Atom

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()

Methods in org.biojava.nbio.structure.align.pairwise with parameters of type Atom

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	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params)
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments[] fragments, StrucAligParameters params)
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params)
void	FragmentJoiner.extendFragments(Atom[] ca1, Atom[] ca2, JointFragments fragments, StrucAligParameters params)
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)
void	AlignmentProgressListener.startingAlignment(String name1, Atom[] ca1, String name2, Atom[] ca2)
void	AlignmentProgressListener.startingAlignment(String name1, Atom[] ca1, String name2, Atom[] ca2)

Uses of Atom in org.biojava.nbio.structure.align.seq

Methods in org.biojava.nbio.structure.align.seq with parameters of type Atom

Modifier and Type	Method and Description
AFPChain	SmithWaterman3Daligner.align(Atom[] ca1, Atom[] ca2)
AFPChain	SmithWaterman3Daligner.align(Atom[] ca1, Atom[] ca2)
AFPChain	SmithWaterman3Daligner.align(Atom[] ca1, Atom[] ca2, Object parameters)
AFPChain	SmithWaterman3Daligner.align(Atom[] ca1, Atom[] ca2, Object parameters)

Uses of Atom in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util that return Atom

Modifier and Type	Method and Description
static Atom[]	AFPAlignmentDisplay.getAlignedAtoms1(AFPChain afpChain, Atom[] ca1)
static Atom[]	AFPAlignmentDisplay.getAlignedAtoms2(AFPChain afpChain, Atom[] ca2)
Atom[]	AtomCache.getAtoms(String name) Returns the CA atoms for the provided name.
Atom[]	AtomCache.getAtoms(StructureIdentifier name)
Atom	RotationAxis.getOtherTranslation() Deprecated.
Atom	RotationAxis.getProjectedPoint(Atom point) Projects a given point onto the axis of rotation
Atom[]	AtomCache.getRepresentativeAtoms(String name) Returns the representative atoms for the provided name.
Atom[]	AtomCache.getRepresentativeAtoms(StructureIdentifier name)
Atom	RotationAxis.getRotationAxis() Get a unit vector along the rotation axis
Atom	RotationAxis.getRotationPos() Get a position on the rotation axis.
Atom	RotationAxis.getScrewTranslation() Get the component of translation parallel to the axis of rotation
static Atom	AFPAlignmentDisplay.getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Methods in org.biojava.nbio.structure.align.util with parameters of type Atom

Modifier and Type	Method and Description
static void	AlignmentTools.alignmentToSIF(Writer out, AFPChain afpChain, Atom[] ca1, Atom[] ca2, String backboneInteraction, String alignmentInteraction) Creates a simple interaction format (SIF) file for an alignment.
static void	AlignmentTools.alignmentToSIF(Writer out, AFPChain afpChain, Atom[] ca1, Atom[] ca2, String backboneInteraction, String alignmentInteraction) Creates a simple interaction format (SIF) file for an alignment.
static AFPChain	AlignmentTools.createAFPChain(Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2) Fundamentally, an alignment is just a list of aligned residues in each protein.
static AFPChain	AlignmentTools.createAFPChain(Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2) Fundamentally, an alignment is just a list of aligned residues in each protein.
static Structure	AFPAlignmentDisplay.createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Structure	AFPAlignmentDisplay.createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	AFPAlignmentDisplay.getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Extract the alignment output
static void	AFPAlignmentDisplay.getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Extract the alignment output
static void	AFPAlignmentDisplay.getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq) Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen
static void	AFPAlignmentDisplay.getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq) Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen
static Atom[]	AFPAlignmentDisplay.getAlignedAtoms1(AFPChain afpChain, Atom[] ca1)
static Atom[]	AFPAlignmentDisplay.getAlignedAtoms2(AFPChain afpChain, Atom[] ca2)
String	RotationAxis.getJmolScript(Atom[] atoms) Returns a Jmol script which will display the axis of rotation.
String	RotationAxis.getJmolScript(Atom[] atoms, int axisID) Returns a Jmol script which will display the axis of rotation.
double	RotationAxis.getProjectedDistance(Atom point) Get the distance from a point to the axis of rotation
Atom	RotationAxis.getProjectedPoint(Atom point) Projects a given point onto the axis of rotation
static Matrix	AFPAlignmentDisplay.getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Matrix	AFPAlignmentDisplay.getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static double	AFPChainScorer.getTMScore(AFPChain align, Atom[] ca1, Atom[] ca2)
static double	AFPChainScorer.getTMScore(AFPChain align, Atom[] ca1, Atom[] ca2)
static Atom	AFPAlignmentDisplay.getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Atom	AFPAlignmentDisplay.getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNum, int[] optLens, int[][][] optAln)
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNum, int[] optLens, int[][][] optAln)
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Map<Integer,Integer> alignment) Takes an AFPChain and replaces the optimal alignment based on an alignment map
static AFPChain	AlignmentTools.replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Map<Integer,Integer> alignment) Takes an AFPChain and replaces the optimal alignment based on an alignment map
static AFPChain	AlignmentTools.replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2) It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.
static AFPChain	AlignmentTools.replaceOptAln(int[][][] newAlgn, AFPChain afpChain, Atom[] ca1, Atom[] ca2) It replaces an optimal alignment of an AFPChain and calculates all the new alignment scores and variables.
void	RotationAxis.rotate(Atom[] atoms, double theta)
static AFPChain	AlignmentTools.splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)
static AFPChain	AlignmentTools.splitBlocksByTopology(AFPChain a, Atom[] ca1, Atom[] ca2)
static void	AlignmentTools.updateSuperposition(AFPChain afpChain, Atom[] ca1, Atom[] ca2) After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.
static void	AlignmentTools.updateSuperposition(AFPChain afpChain, Atom[] ca1, Atom[] ca2) After the alignment changes (optAln, optLen, blockNum, at a minimum), many other properties which depend on the superposition will be invalid.

Constructors in org.biojava.nbio.structure.align.util with parameters of type Atom

Constructor and Description
RotationAxis(Atom axis, Atom pos, double theta) Create a rotation axis from a vector, a point, and an angle.
RotationAxis(Matrix rotation, Atom translation) Determine the location of the rotation axis based on a rotation matrix and a translation vector

Uses of Atom in org.biojava.nbio.structure.align.xml

Methods in org.biojava.nbio.structure.align.xml with parameters of type Atom

Modifier and Type	Method and Description
static AFPChain	AFPChainXMLParser.fromXML(String xml, Atom[] ca1, Atom[] ca2)
static AFPChain	AFPChainXMLParser.fromXML(String xml, Atom[] ca1, Atom[] ca2)
static AFPChain	AFPChainXMLParser.fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
static AFPChain	AFPChainXMLParser.fromXML(String xml, String name1, String name2, Atom[] ca1, Atom[] ca2) new utility method that checks that the order of the pair in the XML alignment is correct and flips the direction if needed
static void	AFPChainXMLConverter.printXMLEQRInferPositions(PrettyXMLWriter xml, AFPChain afpChain, int bk, Atom[] ca1, Atom[] ca2)
static void	AFPChainXMLConverter.printXMLEQRInferPositions(PrettyXMLWriter xml, AFPChain afpChain, int bk, Atom[] ca1, Atom[] ca2)
static void	AFPChainXMLParser.rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) replace the PDB res nums with atom positions:
static void	AFPChainXMLParser.rebuildAFPChain(AFPChain afpChain, Atom[] ca1, Atom[] ca2) replace the PDB res nums with atom positions:
static String	AFPChainXMLConverter.toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Convert an afpChain to a simple XML representation
static String	AFPChainXMLConverter.toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Convert an afpChain to a simple XML representation
static void	AFPChainXMLConverter.toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2) Write the XML representation to a StringWriter
static void	AFPChainXMLConverter.toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2) Write the XML representation to a StringWriter

Uses of Atom in org.biojava.nbio.structure.asa

Methods in org.biojava.nbio.structure.asa with parameters of type Atom

Modifier and Type	Method and Description
static double	AsaCalculator.getRadius(Atom atom) Gets the van der Waals radius of the given atom following the values defined by Chothia (1976) J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly the heavy atoms to account for Hydrogens.

Constructors in org.biojava.nbio.structure.asa with parameters of type Atom

Constructor and Description
AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads) Constructs a new AsaCalculator.

Uses of Atom in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact that return Atom

Modifier and Type	Method and Description
protected Atom[]	StructureInterface.getAtomsForAsa(int cofactorSizeToUse)
protected Atom[]	StructureInterface.getFirstAtomsForAsa(int cofactorSizeToUse)
protected Atom[]	StructureInterface.getSecondAtomsForAsa(int cofactorSizeToUse)

Methods in org.biojava.nbio.structure.contact that return types with arguments of type Atom

Modifier and Type	Method and Description
Pair<Atom>	AtomContact.getPair()

Methods in org.biojava.nbio.structure.contact with parameters of type Atom

Modifier and Type	Method and Description
void	Grid.addAtoms(Atom[] atoms) Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
void	Grid.addAtoms(Atom[] iAtoms, Atom[] jAtoms) Adds the i and j atoms and fills the grid.
void	Grid.addAtoms(Atom[] iAtoms, Atom[] jAtoms) Adds the i and j atoms and fills the grid.
void	Grid.addAtoms(Atom[] atoms, BoundingBox bounds) Adds a set of atoms, subsequent call to getContacts will produce the interatomic contacts.
void	Grid.addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds) Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
void	Grid.addAtoms(Atom[] iAtoms, BoundingBox icoordbounds, Atom[] jAtoms, BoundingBox jcoordbounds) Adds the i and j atoms and fills the grid, passing their bounds (array of size 6 with x,y,z minima and x,y,z maxima) This way the bounds don't need to be recomputed.
AtomContact	AtomContactSet.getContact(Atom atom1, Atom atom2) Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
List<AtomContact>	GridCell.getContactsToOtherCell(GridCell otherCell, Atom[] iAtoms, Atom[] jAtoms, double cutoff) Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts
List<AtomContact>	GridCell.getContactsToOtherCell(GridCell otherCell, Atom[] iAtoms, Atom[] jAtoms, double cutoff) Calculates all distances of atoms between this cell and the given cell returning those that are within the given cutoff as a list of AtomContacts
List<AtomContact>	GridCell.getContactsWithinCell(Atom[] iAtoms, Atom[] jAtoms, double cutoff) Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts
List<AtomContact>	GridCell.getContactsWithinCell(Atom[] iAtoms, Atom[] jAtoms, double cutoff) Calculates all distances of atoms within this cell returning those that are within the given cutoff as a list of AtomContacts
boolean	AtomContactSet.hasContact(Atom atom1, Atom atom2)

Method parameters in org.biojava.nbio.structure.contact with type arguments of type Atom

Modifier and Type	Method and Description
void	AtomContact.setPair(Pair<Atom> pair)

Constructors in org.biojava.nbio.structure.contact with parameters of type Atom

Constructor and Description
BoundingBox(Atom[] atoms) Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
StructureInterface(Atom[] firstMolecule, Atom[] secondMolecule, String firstMoleculeId, String secondMoleculeId, AtomContactSet contacts, CrystalTransform firstTransf, CrystalTransform secondTransf) Constructs a StructureInterface
StructureInterface(Atom[] firstMolecule, Atom[] secondMolecule, String firstMoleculeId, String secondMoleculeId, AtomContactSet contacts, CrystalTransform firstTransf, CrystalTransform secondTransf) Constructs a StructureInterface

Constructor parameters in org.biojava.nbio.structure.contact with type arguments of type Atom

Constructor and Description
AtomContact(Pair<Atom> pair, double distance)

Uses of Atom in org.biojava.nbio.structure.domain

Methods in org.biojava.nbio.structure.domain with parameters of type Atom

Modifier and Type	Method and Description
static List<Domain>	LocalProteinDomainParser.suggestDomains(Atom[] ca) Suggest domains for a set of Calpha atoms

Uses of Atom in org.biojava.nbio.structure.domain.pdp

Methods in org.biojava.nbio.structure.domain.pdp with parameters of type Atom

Modifier and Type	Method and Description
int	Cut.cut(Atom[] ca, Domain dom, CutValues val, int[][] dist, PDPDistanceMatrix pdpMatrix)
PDPDistanceMatrix	GetDistanceMatrix.getDistanceMatrix(Atom[] protein) A set of Calpha atoms that are representing the protein

Constructors in org.biojava.nbio.structure.domain.pdp with parameters of type Atom

Constructor and Description
CutDomain(Atom[] ca, PDPDistanceMatrix pdpMatrix)

Uses of Atom in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io with parameters of type Atom

Modifier and Type	Method and Description
static String	FileConvert.toPDB(Atom a) Prints the content of an Atom object as a PDB formatted line.
static String	FileConvert.toPDB(Atom a, String chainId)
static void	FileConvert.toPDB(Atom a, StringBuffer str)
static void	FileConvert.toPDB(Atom a, StringBuffer str, String chainID) Print ATOM record in the following syntax

Uses of Atom in org.biojava.nbio.structure.io.mmcif

Methods in org.biojava.nbio.structure.io.mmcif with parameters of type Atom

Modifier and Type	Method and Description
static AtomSite	MMCIFFileTools.convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId) Converts an Atom object to an AtomSite object.
static AtomSite	MMCIFFileTools.convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId, int atomId) Converts an Atom object to an AtomSite object.

Uses of Atom in org.biojava.nbio.structure.symmetry.core

Methods in org.biojava.nbio.structure.symmetry.core that return Atom

Modifier and Type	Method and Description
Atom[]	UniqueSequenceList.getCalphaAtoms()

Methods in org.biojava.nbio.structure.symmetry.core with parameters of type Atom

Modifier and Type	Method and Description
static String	UniqueSequenceList.getSequenceString(Atom[] caAlphaAtoms)
boolean	SequenceAlignmentCluster.identityMatch(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, String sequence) Match a sequence to this cluster at 100% identity.
boolean	UniqueSequenceList.isMatch(Atom[] caAlphaAtoms) Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list

Constructors in org.biojava.nbio.structure.symmetry.core with parameters of type Atom

Constructor and Description
UniqueSequenceList(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, String seqResSequence)

Uses of Atom in org.biojava.nbio.structure.symmetry.internal

Methods in org.biojava.nbio.structure.symmetry.internal that return Atom

Modifier and Type	Method and Description
Atom[]	CeSymmResult.getAtoms()

Methods in org.biojava.nbio.structure.symmetry.internal with parameters of type Atom

Modifier and Type	Method and Description
protected static CeSymmResult	CeSymm.align(Atom[] atoms, CESymmParameters params)
static CeSymmResult	CeSymm.analyze(Atom[] atoms) Analyze the symmetries of the input Atom array using the DEFAULT parameters.
static CeSymmResult	CeSymm.analyze(Atom[] atoms, CESymmParameters params) Analyze the symmetries of the input Atom array using the provided parameters.
static CeSymmResult	CeSymm.analyzeLevel(Atom[] atoms, CESymmParameters params) Analyze a single level of symmetry.
int	AngleOrderDetectorPlus.calculateOrder(AFPChain afpChain, Atom[] ca)
int	GraphComponentOrderDetector.calculateOrder(AFPChain selfAlignment, Atom[] ca)
int	OrderDetector.calculateOrder(AFPChain afpChain, Atom[] ca)
int	SequenceFunctionOrderDetector.calculateOrder(AFPChain afpChain, Atom[] ca)
CeSymmResult	CeSymmIterative.execute(Atom[] atoms) This method uses iteratively CeSymm to calculate all symmetries in the input array of atoms and organize them in a multiple alignment of the repeats.
MultipleAlignment	SequenceFunctionRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)
MultipleAlignment	SymmetryRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order) Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
MultipleAlignment	GraphComponentRefiner.refine(AFPChain selfAlignment, Atom[] atoms, int order)
static AFPChain	SequenceFunctionRefiner.refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) Refines a CE-Symm alignment so that it is perfectly symmetric.
static AFPChain	SequenceFunctionRefiner.refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k) Refines a CE-Symm alignment so that it is perfectly symmetric.
void	CeSymmResult.setAtoms(Atom[] atoms)

Uses of Atom in org.biojava.nbio.structure.symmetry.utils

Methods in org.biojava.nbio.structure.symmetry.utils with parameters of type Atom

Modifier and Type	Method and Description
static boolean[][]	SymmetryTools.blankOutBreakFlag(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, boolean[][] breakFlag, int blankWindowSize)
static Matrix	SymmetryTools.blankOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize)
static Matrix	SymmetryTools.blankOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize)
static List<List<Integer>>	SymmetryTools.buildSymmetryGraph(List<AFPChain> afps, Atom[] atoms, boolean undirected) Converts a set of AFP alignments into a Graph of aligned residues, where each vertex is a residue and each edge means the connection between the two residues in one of the alignments.
static MultipleAlignment	SymmetryTools.fromAFP(AFPChain symm, Atom[] atoms) Converts a refined symmetry AFPChain alignment into the standard representation of symmetry in a MultipleAlignment, that contains the entire Atom array of the strcuture and the symmetric repeats are orgaized in different rows in a single Block.
static double	SymmetryTools.getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees.
static double	SymmetryTools.getAngle(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Returns the magnitude of the angle between the first and second blocks of afpChain, measured in degrees.
Matrix	SymmetryTools.getDkMatrix(Atom[] ca1, Atom[] ca2, int fragmentLength, double[] dist1, double[] dist2, int rows, int cols)
Matrix	SymmetryTools.getDkMatrix(Atom[] ca1, Atom[] ca2, int fragmentLength, double[] dist1, double[] dist2, int rows, int cols)
static Matrix	SymmetryTools.getDkMatrix(Atom[] ca1, Atom[] ca2, int k, int fragmentLength)
static Matrix	SymmetryTools.getDkMatrix(Atom[] ca1, Atom[] ca2, int k, int fragmentLength)
static List<Group>	SymmetryTools.getGroups(Atom[] rAtoms) Returns the List of Groups of the corresponding representative Atom array.
static Matrix	SymmetryTools.grayOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff) Grays out the main diagonal of a duplicated distance matrix.
static Matrix	SymmetryTools.grayOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)
static void	SymmetryTools.updateSymmetryTransformation(SymmetryAxes axes, MultipleAlignment msa, Atom[] atoms) Calculates the set of symmetry operation Matrices (transformations) of the new alignment, based on the symmetry relations in the SymmetryAxes object.