Uses of Interface
org.biojava.nbio.structure.Atom
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Uses of Atom in org.biojava.nbio.protmod.structure
Methods in org.biojava.nbio.protmod.structure that return Atom Modifier and Type Method Description static Atom[]
StructureUtil. findLinkage(Group group1, Group group2, String nameOfAtomOnGroup1, String nameOfAtomOnGroup2, double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length.static Atom[]
StructureUtil. findNearestAtomLinkage(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length, from potential atoms.Methods in org.biojava.nbio.protmod.structure with parameters of type Atom Modifier and Type Method Description static double
StructureUtil. getAtomDistance(Atom atom1, Atom atom2)
static StructureAtom
StructureUtil. getStructureAtom(Atom atom, boolean isParentAminoAcid)
static StructureAtomLinkage
StructureUtil. getStructureAtomLinkage(Atom atom1, boolean isParentAminoAcid1, Atom atom2, boolean isParentAminoAcid2)
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Uses of Atom in org.biojava.nbio.structure
Classes in org.biojava.nbio.structure that implement Atom Modifier and Type Class 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 Description protected List<Atom>
HetatomImpl. atoms
Methods in org.biojava.nbio.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. centerAtoms(Atom[] atomSet, Atom centroid)
Center the atoms at the Centroid, if the centroid is already know.static Atom
Calc. centerOfMass(Atom[] points)
Returns the center of mass of the set of atoms.static Atom[]
StructureTools. cloneAtomArray(Atom[] ca)
Provides an equivalent copy of Atoms in a new array.static Atom
Calc. createVirtualCBAtom(AminoAcid amino)
creates a virtual C-beta atom. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.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, including Hydrogens (if present) and all HETATOMs.static Atom[]
StructureTools. getAllAtomArray(Structure s)
Convert all atoms of the structure (all models) into an Atom arraystatic Atom[]
StructureTools. getAllAtomArray(Structure s, int model)
Convert all atoms of the structure (specified model) into an Atom arraystatic 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.static Atom[]
StructureTools. getAllNonHAtomArray(Structure s, boolean hetAtoms, int modelNr)
Returns and array of all non-Hydrogen atoms in the given Structure, optionally including HET atoms or not.Atom
Group. getAtom(int position)
Get at atom by position.Atom
Group. getAtom(String name)
Get an atom given its PDB name.Atom
HetatomImpl. getAtom(int position)
Get at atom by position.Atom
HetatomImpl. getAtom(String name)
Get an atom given its PDB name.Atom
Bond. getAtomA()
Gets atom 'A' of this bond.Atom
BondImpl. 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
Bond. getAtomB()
Gets atom 'B' of this bond.Atom
BondImpl. 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 notAtom
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. 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 knownstatic Atom
Calc. getCentroid(Atom[] atomSet)
Returns the centroid 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
NucleotideImpl. getO3Prime()
Returns the O3' atom if present, otherwise nullAtom
NucleotideImpl. getO5Prime()
Returns the O5' atom if present, otherwise nullAtom
Bond. getOther(Atom exclude)
A utility method to get the other atom in a bond, given one of its atoms.Atom
BondImpl. 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 nullstatic 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.static Atom
Calc. getTranslationVector(javax.vecmath.Matrix4d transform)
Extract the translational vector as an Atom of a transformation matrix.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 sstatic Atom
Calc. scaleAdd(double s, Atom x, Atom b)
Perform linear transformation s*X+B, and store the result in bstatic 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 Description List<Atom>
Group. getAtoms()
Get list of atoms.List<Atom>
HetatomImpl. getAtoms()
Get list of atoms.Iterator<Atom>
Group. iterator()
Get an Atom Iterator.Iterator<Atom>
HetatomImpl. iterator()
return an AtomIterator.Methods in org.biojava.nbio.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)
Gets the length of the vector (2-norm)static double
Calc. angle(Atom a, Atom b)
Gets the angle between two vectorsstatic javax.vecmath.Point3d[]
Calc. atomsToPoints(Atom[] atoms)
Convert an array of atoms into an array of vecmath pointsstatic 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. centerOfMass(Atom[] points)
Returns the center of mass of the set of atoms.static Atom[]
StructureTools. cloneAtomArray(Atom[] ca)
Provides an equivalent copy of Atoms in a new array.static Group[]
StructureTools. cloneGroups(Atom[] ca)
Clone a set of representative Atoms, but returns the parent groupsstatic String
StructureTools. convertAtomsToSeq(Atom[] atoms)
static Atom[]
StructureTools. duplicateCA2(Atom[] ca2)
Utility method for working with circular permutations.static Set<Group>
StructureTools. getAllGroupsFromSubset(Atom[] atoms)
Expand a set of atoms into all groups from the same structure.static Set<Group>
StructureTools. getAllGroupsFromSubset(Atom[] atoms, GroupType types)
Expand a set of atoms into all groups from the same structure.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 knownstatic Atom
Calc. getCentroid(Atom[] atomSet)
Returns the centroid 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 instructure
that contain at least one Atom that is withinradius
Angstroms ofcentroid
.static Set<Group>
StructureTools. getGroupsWithinShell(Structure structure, Atom atom, Set<ResidueNumber> excludeResidues, double distance, boolean includeWater)
static List<Group>
StructureTools. getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff)
Finds all ligand groups from the target which fall within the cutoff distance of some atom from the query set.Atom
Bond. getOther(Atom exclude)
A utility method to get the other atom in a bond, given one of its atoms.Atom
BondImpl. getOther(Atom exclude)
A utility method to get the other atom in a bond, given one of its atoms.static double
Calc. getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2)
Calculate the TM-Score for the superposition.static double
Calc. getTMScore(Atom[] atomSet1, Atom[] atomSet2, int len1, int len2, boolean normalizeMin)
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. ligands).boolean
Atom. hasBond(Atom other)
Test if another atom has a bond to this atomboolean
AtomImpl. hasBond(Atom other)
Test if another atom has a bond to this atomstatic boolean
StructureTools. hasDeuteratedEquiv(Atom atom, Group currentGroup)
Check to see if a Hydrogen has a Deuterated brother in the group.static boolean
StructureTools. hasNonDeuteratedEquiv(Atom atom, Group currentGroup)
Check to see if an Deuterated atom has a non deuterated brother in the group.static Atom
Calc. invert(Atom a)
static double
Calc. rmsd(Atom[] x, Atom[] y)
Calculate the RMSD of two Atom arrays, already superposed.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 sstatic Atom
Calc. scaleAdd(double s, Atom x, Atom b)
Perform linear transformation s*X+B, and store the result in bstatic 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 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. the angle between the normal vectors of the two plains a-b-c and b-c-d.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. the vecmath library double-precision 4x4 rotation+translation matrix).static void
Calc. translate(Atom atom, javax.vecmath.Vector3d v)
Translates an atom object, given a Vector3d (i.e. the vecmath library double-precision 3-d vector)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 Description static List<javax.vecmath.Point3d>
Calc. atomsToPoints(Collection<Atom> atoms)
Convert an array of atoms into an array of vecmath pointsvoid
Group. setAtoms(List<Atom> atoms)
Set the atoms of this group.void
HetatomImpl. setAtoms(List<Atom> atoms)
Set the atoms of this group.Constructors in org.biojava.nbio.structure with parameters of type Atom Constructor Description AtomPositionMap(Atom[] atoms)
Creates a new AtomPositionMap containing peptide alpha-carbon atomsAtomPositionMap(Atom[] atoms, AtomPositionMap.GroupMatcher matcher)
Creates a new AtomPositionMap containing only atoms matched bymatcher
.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. -
Uses of Atom in org.biojava.nbio.structure.align
Methods in org.biojava.nbio.structure.align that return Atom Modifier and Type Method 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 Description abstract AFPChain
AbstractStructureAlignment. align(Atom[] ca1, Atom[] ca2)
abstract AFPChain
AbstractStructureAlignment. align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain
BioJavaStructureAlignment. align(Atom[] ca1, Atom[] ca2)
AFPChain
BioJavaStructureAlignment. align(Atom[] ca1, Atom[] ca2, Object params)
AFPChain
StructureAlignment. align(Atom[] ca1, Atom[] ca2)
Run an alignment while specifying the atoms to be aligned.AFPChain
StructureAlignment. align(Atom[] ca1, Atom[] ca2, Object params)
run an alignment and also send a bean containing the parameters.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 alignmentstatic 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 BConstructors in org.biojava.nbio.structure.align with parameters of type Atom Constructor Description 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 Description static Atom[]
GuiWrapper. getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)
Atom
CECalculator. getShift()
Gets the shift from the last call tocalc_rmsd
.Atom
CeCalculatorEnhanced. getShift()
Gets the shift from the last call tocalc_rmsd
.Methods in org.biojava.nbio.structure.align.ce with parameters of type Atom Modifier and Type Method Description 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)
AFPChain
CeMain. align(Atom[] ca1, Atom[] ca2, Object param)
Align ca2 onto ca1.AFPChain
OptimalCECPMain. align(Atom[] ca1, Atom[] ca2, Object param)
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.double
CECalculator. calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform)
superimpose and get rmsddouble
CeCalculatorEnhanced. calc_rmsd(Atom[] pro1, Atom[] pro2, int strLen, boolean storeTransform, boolean show)
superimpose and get rmsdvoid
CECalculator. 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.static Object
GuiWrapper. display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain
CECalculator. extractFragments(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
AFPChain
CeCalculatorEnhanced. 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, CECPParameters params)
static Structure
GuiWrapper. getAlignedStructure(Atom[] ca1, Atom[] ca2)
static Atom[]
GuiWrapper. getAtomArray(Atom[] ca, List<Group> hetatoms, List<Group> nucs)
double[][]
CECalculator. 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)
void
CECalculator. nextStep(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void
CeCalculatorEnhanced. 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 alignmentstatic AFPChain
CeCPMain. postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m, CECalculator calculator, CECPParameters param)
Circular permutation specific code to be run after the standard CE alignmentstatic void
GuiWrapper. showAlignmentImage(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Object jmol)
void
CECalculator. traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
void
CeCalculatorEnhanced. traceFragmentMatrix(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
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[][]
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. -
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 Description 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 name1, String name2, Atom[] ca1, Atom[] ca2)
static void
JFatCatClient. sendAFPChainToServer(String serverLocation, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
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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 Description protected AFPChain
FatCat. align(Atom[] ca1, Atom[] ca2, FatCatParameters params, boolean doRigid)
AFPChain
FatCatFlexible. align(Atom[] ca1, Atom[] ca2)
AFPChain
FatCatFlexible. align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain
FatCatRigid. align(Atom[] ca1, Atom[] ca2)
AFPChain
FatCatRigid. align(Atom[] ca1, Atom[] ca2, Object param)
AFPChain
FatCat. alignFlexible(Atom[] ca1, Atom[] ca2, FatCatParameters params)
AFPChain
FatCat. alignRigid(Atom[] ca1, Atom[] ca2)
AFPChain
FatCat. alignRigid(Atom[] ca1, Atom[] ca2, FatCatParameters params)
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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 Description 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 AFPsstatic 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
AFPOptimizer. optimizeAln(FatCatParameters params, AFPChain afpChain, Atom[] ca1, Atom[] ca2)
optimize the alignment by dynamic programmingstatic void
AFPPostProcessor. postProcess(FatCatParameters params, 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 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 -
Uses of Atom in org.biojava.nbio.structure.align.gui
Methods in org.biojava.nbio.structure.align.gui that return Atom Modifier and Type Method Description static Atom[]
DisplayAFP. getAtomArray(Atom[] ca, List<Group> hetatms)
Returns the first atom for each groupstatic Atom
DisplayAFP. getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious)
Return the atom at alignment position aligPos. at the present only works with block 0Methods in org.biojava.nbio.structure.align.gui with parameters of type Atom Modifier and Type Method Description static Structure
DisplayAFP. createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Create a "fake" Structure objects that contains the two sets of atoms aligned on top of each other.static StructureAlignmentJmol
DisplayAFP. display(AFPChain afpChain, Group[] twistedGroups, Atom[] ca1, Atom[] ca2, List<Group> hetatms1, List<Group> hetatms2)
Note: ca2, hetatoms2 and nucleotides2 should not be rotated.static StructureAlignmentJmol
StructureAlignmentDisplay. display(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Display an AFPChain alignmentstatic Atom[]
DisplayAFP. getAtomArray(Atom[] ca, List<Group> hetatms)
Returns the first atom for each groupstatic Atom
DisplayAFP. getAtomForAligPos(AFPChain afpChain, int chainNr, int aligPos, Atom[] ca, boolean getPrevious)
Return the atom at alignment position aligPos. at the present only works with block 0static List<String>
DisplayAFP. getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca)
Return a list of pdb Strings corresponding to the aligned positions of the molecule.static List<String>
MultipleAlignmentJmolDisplay. getPDBresnum(int structNum, MultipleAlignment multAln, Atom[] ca)
Utility method used in theMultipleAlignmentJmol
Frame, when the aligned residues of a structure in the alignment have to be selected for formatting them (coloring and style).static void
DisplayAFP. showAlignmentPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)
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Uses of Atom in org.biojava.nbio.structure.align.gui.aligpanel
Methods in org.biojava.nbio.structure.align.gui.aligpanel that return Atom Modifier and Type Method Description Atom[]
AligPanel. getCa1()
Atom[]
StatusDisplay. getCa1()
Atom[]
AligPanel. getCa2()
Atom[]
StatusDisplay. getCa2()
Methods in org.biojava.nbio.structure.align.gui.aligpanel with parameters of type Atom Modifier and Type Method Description void
AligPanel. setCa1(Atom[] ca1)
void
StatusDisplay. setCa1(Atom[] ca1)
void
AligPanel. setCa2(Atom[] ca2)
void
StatusDisplay. setCa2(Atom[] ca2)
Constructors in org.biojava.nbio.structure.align.gui.aligpanel with parameters of type Atom Constructor Description MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol)
Constructor using an afpChain and the atom arrays for pairwise alignments. -
Uses of Atom in org.biojava.nbio.structure.align.gui.jmol
Methods in org.biojava.nbio.structure.align.gui.jmol with parameters of type Atom Modifier and Type Method Description static String
StructureAlignmentJmol. getJmolScript4Block(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int blockNr)
static String
StructureAlignmentJmol. getJmolString(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static String
JmolTools. getPdbInfo(Atom a)
get jmol style info: jmol style: [MET]508:A.CA/1 #3918 insertion code: [ASP]1^A:A.CA/1 #2static String
JmolTools. getPdbInfo(Atom a, boolean printResName)
void
AbstractAlignmentJmol. setAtoms(Atom[] atoms)
Create and set a new structure from a given atom array.Constructors in org.biojava.nbio.structure.align.gui.jmol with parameters of type Atom Constructor Description StructureAlignmentJmol(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
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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 Description static Atom
AlignUtils. getCenter(Atom[] ca, int pos, int fragmentLength)
Get the centroid for the set of atoms starting from position pos, length fragmentLenghtstatic Atom[]
AlignUtils. getFragment(Atom[] caall, int pos, int fragmentLength)
Get a continue subset of Atoms based by the starting position and the lengthstatic Atom[]
AlignUtils. getFragmentFromIdxList(Atom[] caall, int[] idx)
Get a subset of Atoms based by their positionsstatic Atom[]
AlignUtils. 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 Description static Atom
AlignUtils. getCenter(Atom[] ca, int pos, int fragmentLength)
Get the centroid for the set of atoms starting from position pos, length fragmentLenghtstatic double[]
AlignUtils. getDiagonalAtK(Atom[] atoms, int k)
Get distances along diagonal k from coordinate array coords.static Matrix
AlignUtils. getDistanceMatrix(Atom[] ca1, Atom[] ca2)
Matrix of all distances between two sets of Atoms.static Atom[]
AlignUtils. getFragment(Atom[] caall, int pos, int fragmentLength)
Get a continue subset of Atoms based by the starting position and the lengthstatic Atom[]
AlignUtils. getFragmentFromIdxList(Atom[] caall, int[] idx)
Get a subset of Atoms based by their positionsstatic Atom[]
AlignUtils. 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 Description Atom[]
AFPChain. getBlockShiftVector()
Methods in org.biojava.nbio.structure.align.model with parameters of type Atom Modifier and Type Method 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.String
AFPChain. toCE(Atom[] ca1, Atom[] ca2)
static String
AfpChainWriter. toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
String
AFPChain. toFatcat(Atom[] ca1, Atom[] ca2)
static String
AfpChainWriter. toFatCat(AFPChain afpChain, 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 formatstatic String
AfpChainWriter. toPrettyAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showHTML, boolean showAlignmentBlock)
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. -
Uses of Atom in org.biojava.nbio.structure.align.multiple
Constructors in org.biojava.nbio.structure.align.multiple with parameters of type Atom Constructor Description 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 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 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.nbio.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
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)
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)
void
AlignmentProgressListener. startingAlignment(String name1, Atom[] ca1, String name2, Atom[] ca2)
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Uses of Atom in org.biojava.nbio.structure.align.quaternary
Methods in org.biojava.nbio.structure.align.quaternary that return Atom Modifier and Type Method Description Atom[]
QsAlignResult. getAlignedAtomsForSubunits1(int index)
Atom[]
QsAlignResult. getAlignedAtomsForSubunits2(int index)
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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 Description AFPChain
SmithWaterman3Daligner. align(Atom[] ca1, Atom[] ca2)
AFPChain
SmithWaterman3Daligner. align(Atom[] ca1, Atom[] ca2, Object parameters)
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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 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. getProjectedPoint(Atom point)
Projects a given point onto the axis of rotationAtom[]
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 axisAtom
RotationAxis. getRotationPos()
Get a position on the rotation axis.Atom
RotationAxis. getScrewTranslation()
Get the component of translation parallel to the axis of rotationstatic Atom
AFPAlignmentDisplay. getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Methods in org.biojava.nbio.structure.align.util that return types with arguments of type Atom Modifier and Type Method Description Pair<Atom>
RotationAxis. getAxisEnds(Atom[] atoms)
Find a segment of the axis that covers the specified set of atoms.Methods in org.biojava.nbio.structure.align.util with parameters of type Atom Modifier and Type Method 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 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 AFPChain
AlignmentTools. deleteColumn(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int block, int pos)
Delete an alignment position from the original alignment object.static AFPChain
AlignmentTools. deleteHighestDistanceColumn(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Find the alignment position with the highest atomic distance between the equivalent atomic positions of the arrays and remove it from the alignment.static void
AlignmentTools. fillAlignedAtomArrays(AFPChain afpChain, Atom[] ca1, Atom[] ca2, Atom[] ca1aligned, Atom[] ca2aligned)
Fill the aligned Atom arrays with the equivalent residues in the afpChain.static void
AFPAlignmentDisplay. getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Extract the alignment outputstatic void
AFPAlignmentDisplay. getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq)
static Atom[]
AFPAlignmentDisplay. getAlignedAtoms1(AFPChain afpChain, Atom[] ca1)
static Atom[]
AFPAlignmentDisplay. getAlignedAtoms2(AFPChain afpChain, Atom[] ca2)
static List<Chain>
AlignmentTools. getAlignedModel(Atom[] ca)
get an artificial List of chains containing the Atoms and groups.static Structure
AlignmentTools. getAlignedStructure(Atom[] ca1, Atom[] ca2)
Get an artifical Structure containing both chains.Pair<Atom>
RotationAxis. getAxisEnds(Atom[] atoms)
Find a segment of the axis that covers the specified set of atoms.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 rotationAtom
RotationAxis. getProjectedPoint(Atom point)
Projects a given point onto the axis of rotationstatic 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, boolean normalizeMin)
static Atom
AFPAlignmentDisplay. getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Group[]
AlignmentTools. prepareGroupsForDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Rotate the Atoms/Groups so they are aligned for the 3D visualisationstatic 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(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 mapvoid
RotationAxis. rotate(Atom[] atoms, double theta)
static void
AlignmentTools. shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups)
only shift CA positions.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.Constructors in org.biojava.nbio.structure.align.util with parameters of type Atom Constructor 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 Description 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 neededstatic AFPChain
AFPChainXMLParser. fromXML(String xml, 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
AFPChainXMLConverter. toXML(AFPChain afpChain, StringWriter swriter, Atom[] ca1, Atom[] ca2)
Write the XML representation to a StringWriterstatic String
AFPChainXMLConverter. toXML(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Convert an afpChain to a simple XML representation -
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 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 Description AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads)
Constructs a new AsaCalculator. -
Uses of Atom in org.biojava.nbio.structure.cluster
Methods in org.biojava.nbio.structure.cluster that return Atom Modifier and Type Method Description Atom[]
SubunitCluster. getAlignedAtomsSubunit(int index)
Atom[]
Subunit. getRepresentativeAtoms()
Get all the representative Atoms of the Subunit.Constructors in org.biojava.nbio.structure.cluster with parameters of type Atom Constructor Description Subunit(Atom[] reprAtoms, String name, StructureIdentifier identifier, Structure structure)
A Subunit is solely defined by the coordinates of the representative Atoms of its residues. -
Uses of Atom in org.biojava.nbio.structure.contact
Methods in org.biojava.nbio.structure.contact that return Atom Modifier and Type Method 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 Description Pair<Atom>
AtomContact. getPair()
Methods in org.biojava.nbio.structure.contact with parameters of type Atom Modifier and Type Method Description void
Grid. addAtoms(Atom[] atoms)
Adds a set of atoms, subsequent call toGrid.getIndicesContacts()
orGrid.getAtomContacts()
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[] atoms, BoundingBox bounds)
Adds a set of atoms, subsequent call toGrid.getIndicesContacts()
orGrid.getAtomContacts()
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.AtomContact
AtomContactSet. getContact(Atom atom1, Atom atom2)
Returns the corresponding AtomContact or null if no contact exists between the 2 given atomsboolean
AtomContactSet. hasContact(Atom atom1, Atom atom2)
Method parameters in org.biojava.nbio.structure.contact with type arguments of type Atom Modifier and Type Method Description void
AtomContact. setPair(Pair<Atom> pair)
Constructors in org.biojava.nbio.structure.contact with parameters of type Atom Constructor Description StructureInterface(Atom[] firstMolecule, Atom[] secondMolecule, String firstMoleculeId, String secondMoleculeId, AtomContactSet contacts, CrystalTransform firstTransf, CrystalTransform secondTransf)
Constructs a StructureInterfaceConstructor parameters in org.biojava.nbio.structure.contact with type arguments of type Atom Constructor Description AtomContact(Pair<Atom> pair, double distance)
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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 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 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 proteinConstructors in org.biojava.nbio.structure.domain.pdp with parameters of type Atom Constructor Description CutDomain(Atom[] ca, PDPDistanceMatrix pdpMatrix)
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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 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 Description static AtomSite
MMCIFFileTools. convertAtomToAtomSite(Atom a, int model, String chainName, String chainId)
Converts an Atom object to anAtomSite
object.static AtomSite
MMCIFFileTools. convertAtomToAtomSite(Atom a, int model, String chainName, String chainId, int atomId)
Converts an Atom object to anAtomSite
object. -
Uses of Atom in org.biojava.nbio.structure.io.mmtf
Methods in org.biojava.nbio.structure.io.mmtf that return types with arguments of type Atom Modifier and Type Method Description List<Atom>
MmtfSummaryDataBean. getAllAtoms()
static List<Atom>
MmtfUtils. getAtomsForGroup(Group inputGroup)
Get a list of atoms for a group.Method parameters in org.biojava.nbio.structure.io.mmtf with type arguments of type Atom Modifier and Type Method Description static int
MmtfUtils. getNumBondsInGroup(List<Atom> atomsInGroup)
Find the number of bonds in a groupvoid
MmtfSummaryDataBean. setAllAtoms(List<Atom> allAtoms)
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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 Description Atom[]
CeSymmResult. getAtoms()
Methods in org.biojava.nbio.structure.symmetry.internal with parameters of type Atom Modifier and Type Method 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
GraphComponentRefiner. refine(AFPChain selfAlignment, Atom[] atoms, int order)
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.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)
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Uses of Atom in org.biojava.nbio.structure.symmetry.utils
Methods in org.biojava.nbio.structure.symmetry.utils that return Atom Modifier and Type Method Description static Atom[]
SymmetryTools. getRepresentativeAtoms(Structure structure)
Returns the representative Atom Array of the first model, if the structure is NMR, or the Array for each model, if it is a biological assembly with multiple models.Methods in org.biojava.nbio.structure.symmetry.utils with parameters of type Atom Modifier and Type Method 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 ofafpChain
, measured in degrees.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 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)
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