Uses of Class
com.actelion.research.chem.Coordinates

Packages that use Coordinates

Package	Description
com.actelion.research.chem
com.actelion.research.chem.alignment3d
com.actelion.research.chem.conf
com.actelion.research.chem.conf.torsionstrain
com.actelion.research.chem.descriptor.flexophore
com.actelion.research.chem.descriptor.flexophore.calculator
com.actelion.research.chem.descriptor.flexophore.generator
com.actelion.research.chem.docking
com.actelion.research.chem.docking.scoring.chemscore
com.actelion.research.chem.io.pdb.converter
com.actelion.research.chem.phesa
com.actelion.research.chem.phesa.pharmacophore
com.actelion.research.chem.phesaflex
org.openmolecules.chem.conf.gen
org.openmolecules.chem.conf.so

Uses of Coordinates in com.actelion.research.chem

Fields in com.actelion.research.chem declared as Coordinates

Modifier and Type	Field	Description
protected Coordinates[]	Molecule.mCoordinates

Methods in com.actelion.research.chem that return Coordinates

Modifier and Type	Method	Description
Coordinates	Coordinates.add(Coordinates c)
Coordinates	Coordinates.addC(Coordinates c)
Coordinates	Coordinates.between(Coordinates c1, Coordinates c2, double f)	Updates this to contain a point on the straight line through c1 and c2.
Coordinates	Coordinates.center(Coordinates c)	Calculates the center point between this and c and sets this to the center point.
static Coordinates	Coordinates.createBarycenter(Coordinates... coords)
Coordinates	Coordinates.cross(Coordinates c)
Coordinates[]	Molecule.getAtomCoordinates()
static Coordinates	ExtendedMolecule.getCenterGravity(ExtendedMolecule mol)
static Coordinates	ExtendedMolecule.getCenterGravity(ExtendedMolecule mol, int[] indices)
Coordinates	Molecule.getCoordinates(int atom)
Coordinates[]	Molecule3D.getCoordinates()
static Coordinates	Coordinates.getMirror(Coordinates p, Coordinates c1, Coordinates c2, Coordinates c3)	Get the mirror image of p through the plane defined by c1, c2, c3
Coordinates	Coordinates.max(Coordinates c)
static Coordinates	Coordinates.max(Coordinates[] c)
Coordinates	Coordinates.min(Coordinates c)
static Coordinates	Coordinates.min(Coordinates[] c)
static Coordinates	Coordinates.random()
Coordinates	Coordinates.rotate(double[][] m)
Coordinates	Coordinates.rotate(Coordinates normal, double theta)
Coordinates	Coordinates.rotateC(double[][] m)
Coordinates	Coordinates.scale(double scale)
Coordinates	Coordinates.scaleC(double scale)
Coordinates	Coordinates.set(Coordinates c)	Copies x,y,z from c to this
Coordinates	Coordinates.sub(Coordinates c)
Coordinates	Coordinates.subC(Coordinates c)
Coordinates	Coordinates.unit()
Coordinates	Coordinates.unitC()

Methods in com.actelion.research.chem with parameters of type Coordinates

Modifier and Type	Method	Description
Coordinates	Coordinates.add(Coordinates c)
Coordinates	Coordinates.addC(Coordinates c)
Coordinates	Coordinates.between(Coordinates c1, Coordinates c2, double f)	Updates this to contain a point on the straight line through c1 and c2.
Coordinates	Coordinates.center(Coordinates c)	Calculates the center point between this and c and sets this to the center point.
void	Coordinates.center(Coordinates c1, Coordinates c2)	Updates this to contains the center between c1 and c2.
int	Coordinates.compareTo(Coordinates o)
double	Coordinates.cosAngle(Coordinates c)
static Coordinates	Coordinates.createBarycenter(Coordinates... coords)
Coordinates	Coordinates.cross(Coordinates c)
double	Coordinates.distance(Coordinates c)
double	Coordinates.distanceSquared(Coordinates c)
double	Coordinates.distSquareTo(Coordinates c)
double	Coordinates.dot(Coordinates c)
double	Coordinates.getAngle(Coordinates c)	Gets the angle formed between the 2 vectors ([0,PI])
double	Coordinates.getAngleXY(Coordinates c)	Calculates the angle of the line from this location to c projected into the x/y plane.
double	Molecule.getAverageBondLength(int atoms, int bonds, double defaultBondLength, Coordinates[] coords)	Calculates and returns the mean bond length of all bonds 0...bonds.
double	Coordinates.getDihedral(Coordinates c2, Coordinates c3, Coordinates c4)
static double	Coordinates.getDihedral(Coordinates c1, Coordinates c2, Coordinates c3, Coordinates c4)	Calculates a signed torsion as an exterior spherical angle from a valid sequence of 4 points in space.
java.lang.String	Canonizer.getEncodedCoordinates(boolean keepPositionAndScale, Coordinates[] atomCoordinates)	Encodes the molecule's atom coordinates into a compact String.
static Coordinates	Coordinates.getMirror(Coordinates p, Coordinates c1, Coordinates c2, Coordinates c3)	Get the mirror image of p through the plane defined by c1, c2, c3
static double	Coordinates.getRmsd(Coordinates[] c1, Coordinates[] c2)
static double	Coordinates.getRmsd(Coordinates[] c1, Coordinates[] c2, int l)
boolean	Coordinates.insideBounds(Coordinates[] bounds)
Coordinates	Coordinates.max(Coordinates c)
static Coordinates	Coordinates.max(Coordinates[] c)
Coordinates	Coordinates.min(Coordinates c)
static Coordinates	Coordinates.min(Coordinates[] c)
void	IDCodeParserWithoutCoordinateInvention.parseCoordinates(byte[] encodedCoords, int coordsStart, StereoMolecule mol, Coordinates[] coords)	This method parses an id-coordinate string (new format only) and writes the coordinates into a Coordinates array.
Coordinates	Coordinates.rotate(Coordinates normal, double theta)
Coordinates	Coordinates.set(Coordinates c)	Copies x,y,z from c to this
void	Molecule3D.setCoordinates(int atom, Coordinates c)
Coordinates	Coordinates.sub(Coordinates c)
Coordinates	Coordinates.subC(Coordinates c)

Constructors in com.actelion.research.chem with parameters of type Coordinates

Constructor	Description
Coordinates(Coordinates c)

Uses of Coordinates in com.actelion.research.chem.alignment3d

Methods in com.actelion.research.chem.alignment3d with parameters of type Coordinates

Modifier and Type	Method	Description
void	KabschAlignment.align(Coordinates trans1, Matrix rot, Coordinates trans2)

Constructors in com.actelion.research.chem.alignment3d with parameters of type Coordinates

Constructor	Description
KabschAlignment(Coordinates[] coords1, Coordinates[] coords2, int[][] mapping)

Uses of Coordinates in com.actelion.research.chem.conf

Methods in com.actelion.research.chem.conf that return Coordinates

Modifier and Type	Method	Description
Coordinates[]	Conformer.getCoordinates()
Coordinates	Conformer.getCoordinates(int atom)

Methods in com.actelion.research.chem.conf with parameters of type Coordinates

Modifier and Type	Method	Description
void	Conformer.setCoordinates(int atom, Coordinates coords)	Copies x,y,z from coords into this atom's coordinates
void	Conformer.setCoordinatesReplace(int atom, Coordinates coords)	Replaces the atom's Coordinates object by the given one

Uses of Coordinates in com.actelion.research.chem.conf.torsionstrain

Methods in com.actelion.research.chem.conf.torsionstrain with parameters of type Coordinates

Modifier and Type	Method	Description
static void	StatisticalTorsionTerm.getCartesianTorsionGradient(int[] atoms, Conformer conf, double[] gradient, double dEdPhi, Coordinates[] coords, int[][] rearAtoms)

Uses of Coordinates in com.actelion.research.chem.descriptor.flexophore

Methods in com.actelion.research.chem.descriptor.flexophore that return Coordinates

Modifier and Type	Method	Description
Coordinates	IndexCoordinates.getCoord()
Coordinates	PPNodeViz.getCoordinates()
Coordinates	PPNodeVizTriangle.getCoordinatesA()
Coordinates	PPNodeVizTriangle.getCoordinatesB()
Coordinates	PPNodeVizTriangle.getCoordinatesC()

Methods in com.actelion.research.chem.descriptor.flexophore with parameters of type Coordinates

Modifier and Type	Method	Description
void	IndexCoordinates.setCoord(Coordinates coord)
void	PPNodeViz.setCoordinates(Coordinates c)

Constructors in com.actelion.research.chem.descriptor.flexophore with parameters of type Coordinates

Constructor	Description
IndexCoordinates(int index, int indexOriginalAtom, Coordinates coord)

Uses of Coordinates in com.actelion.research.chem.descriptor.flexophore.calculator

Methods in com.actelion.research.chem.descriptor.flexophore.calculator that return Coordinates

Modifier and Type	Method	Description
static Coordinates[]	GeometryCalculator.getBounds(Molecule3D molecule)	Gets the Bounds of a molecule
static Coordinates[]	StructureCalculator.getBounds(Molecule3D mol)
static Coordinates	StructureCalculator.getCenter(Molecule3D mol)
static Coordinates	GeometryCalculator.getCenterGravity(Molecule3D mol)	Gets the center of Gravity of a molecule
static Coordinates	GeometryCalculator.getCoordinates(Molecule mol, int atm)
static Coordinates[]	StructureCalculator.getLigandBounds(Molecule3D mol)
static Coordinates	StructureCalculator.getLigandCenter(Molecule3D mol)

Methods in com.actelion.research.chem.descriptor.flexophore.calculator with parameters of type Coordinates

Modifier and Type	Method	Description
static Molecule3D	StructureCalculator.crop(Molecule3D mol, Coordinates center, double radius)
static double	GeometryCalculator.getAngle(Coordinates c1, Coordinates c2, Coordinates c3)
static void	StructureCalculator.insertLigand(Molecule3D mol, Molecule3D lig, Coordinates center)
static int	StructureCalculator.makeProteinFlexible(Molecule3D mol, Coordinates center, double radius, boolean keepBackboneRigid)
static void	StructureCalculator.replaceLigand(Molecule3D mol, Molecule3D lig, Coordinates center)	Replaces the preoptimized ligand in mol
static void	StructureCalculator.rotateLigand(Molecule3D mol, double angle, Coordinates normal, Coordinates center)
static void	GeometryCalculator.translate(Molecule3D molecule, Coordinates c)	Translate a Molecule
static void	StructureCalculator.translateLigand(Molecule3D mol, Coordinates v)

Uses of Coordinates in com.actelion.research.chem.descriptor.flexophore.generator

Methods in com.actelion.research.chem.descriptor.flexophore.generator that return types with arguments of type Coordinates

Modifier and Type	Method	Description
java.util.List<Coordinates>	MultCoordFragIndex.getCoordinates()

Methods in com.actelion.research.chem.descriptor.flexophore.generator with parameters of type Coordinates

Modifier and Type	Method	Description
void	MultCoordFragIndex.addCoord(Coordinates coordinates)

Uses of Coordinates in com.actelion.research.chem.docking

Methods in com.actelion.research.chem.docking that return Coordinates

Modifier and Type	Method	Description
static Coordinates	DockingUtils.getCOM(Conformer conf)
static Coordinates	DockingUtils.getCOM(StereoMolecule conf)
static Coordinates	DockingUtils.randomVectorInSphere(java.util.Random r)

Uses of Coordinates in com.actelion.research.chem.docking.scoring.chemscore

Methods in com.actelion.research.chem.docking.scoring.chemscore with parameters of type Coordinates

Modifier and Type	Method	Description
static MetalTerm	MetalTerm.create(Conformer ligand, int acceptor, int[] acceptorNeighbours, Coordinates fitPoint, double scale)

Uses of Coordinates in com.actelion.research.chem.io.pdb.converter

Fields in com.actelion.research.chem.io.pdb.converter declared as Coordinates

Modifier and Type	Field	Description
protected Coordinates	MoleculeGrid.max
protected Coordinates	MoleculeGrid.min

Methods in com.actelion.research.chem.io.pdb.converter that return Coordinates

Modifier and Type	Method	Description
static Coordinates[]	GeometryCalculator.getBounds(StereoMolecule molecule)	Gets the Bounds of a molecule
Coordinates	MoleculeGrid.getCartCoordinates(int[] gridCoords)
static Coordinates	GeometryCalculator.getCenterGravity(StereoMolecule mol)	Gets the center of Gravity of a molecule
static Coordinates	GeometryCalculator.getCoordinates(StereoMolecule mol, int atm)

Methods in com.actelion.research.chem.io.pdb.converter with parameters of type Coordinates

Modifier and Type	Method	Description
static double	GeometryCalculator.getAngle(Coordinates c1, Coordinates c2, Coordinates c3)
int	MoleculeGrid.getClosestNeighbour(Coordinates c, double maxDist)	Returns the closest neighbour.
int[]	MoleculeGrid.getGridCoordinates(Coordinates c)
java.util.Set<java.lang.Integer>	MoleculeGrid.getNeighbours(Coordinates[] bounds, double maxDist)	Gets a Set of all neigbouring atoms.
java.util.Set<java.lang.Integer>	MoleculeGrid.getNeighbours(Coordinates c, double maxDist)	Gets a Set of all neigbouring atoms.
java.util.Set<java.lang.Integer>	MoleculeGrid.getNeighbours(Coordinates c, double maxDist, boolean enforceDist)
java.util.Set<java.lang.Integer>	MoleculeGrid.getNeighbours(Coordinates c, double maxDist, boolean enforceDist, int requiredFlags)	Gets a Set of all neigbouring atoms.
boolean	MoleculeGrid.hasNeighbours(Coordinates c, double maxDist)
static void	GeometryCalculator.translate(StereoMolecule molecule, Coordinates c)	Translate a Molecule

Constructors in com.actelion.research.chem.io.pdb.converter with parameters of type Coordinates

Constructor	Description
MoleculeGrid(StereoMolecule mol, double gridWidth, Coordinates extension)	Creates the Grid: Complexity O(nAtoms)

Uses of Coordinates in com.actelion.research.chem.phesa

Fields in com.actelion.research.chem.phesa declared as Coordinates

Modifier and Type	Field	Description
protected Coordinates	Gaussian3D.center

Methods in com.actelion.research.chem.phesa that return Coordinates

Modifier and Type	Method	Description
Coordinates	Gaussian3D.getCenter()
Coordinates	MolecularVolume.getCOM()
Coordinates	VolumeGaussian.getReferenceVector()
Coordinates	Gaussian3D.getRotatedCenter(double[][] rotMatrix, double scaleFactor, double[] translation)
Coordinates	VolumeGaussian.getShiftVector()

Methods in com.actelion.research.chem.phesa that return types with arguments of type Coordinates

Modifier and Type	Method	Description
java.util.ArrayList<Coordinates>	MolecularVolume.getHydrogens()

Methods in com.actelion.research.chem.phesa with parameters of type Coordinates

Modifier and Type	Method	Description
void	VolumeGaussian.addShift(Coordinates shift)
static void	PheSAAlignment.getRotationMatrix(double theta, Coordinates axis, double[][] r)
double	Gaussian3D.getVolumeOverlap(Gaussian3D g2, Coordinates c2, double distCutoff)
void	Gaussian3D.setCenter(Coordinates center)
void	VolumeGaussian.setReferenceVector(Coordinates referenceVector)
void	VolumeGaussian.setShiftVector(Coordinates shift)
void	VolumeGaussian.translateRef(Coordinates trans)
void	MolecularVolume.translateToCOM(Coordinates com)

Constructors in com.actelion.research.chem.phesa with parameters of type Coordinates

Constructor	Description
AtomicGaussian(int atomId, int atomicNo, Coordinates center)
Gaussian3D(int atomId, int atomicNo, Coordinates center, double weight)
Quaternion(Coordinates axis, double angle)
VolumeGaussian(int atomId, int atomicNo, Coordinates center, Coordinates shiftVector, int role)

Uses of Coordinates in com.actelion.research.chem.phesa.pharmacophore

Methods in com.actelion.research.chem.phesa.pharmacophore that return Coordinates

Modifier and Type	Method	Description
Coordinates	AcceptorPoint.getCenter()
Coordinates	AromRingPoint.getCenter()
Coordinates	ChargePoint.getCenter()
Coordinates	DonorPoint.getCenter()
Coordinates	ExitVectorPoint.getCenter()
Coordinates	IPharmacophorePoint.getCenter()
Coordinates	AcceptorPoint.getDirectionality()
Coordinates	AromRingPoint.getDirectionality()
Coordinates	ChargePoint.getDirectionality()
Coordinates	DonorPoint.getDirectionality()
Coordinates	ExitVectorPoint.getDirectionality()
Coordinates	IPharmacophorePoint.getDirectionality()
Coordinates	PPGaussian.getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)

Methods in com.actelion.research.chem.phesa.pharmacophore with parameters of type Coordinates

Modifier and Type	Method	Description
static java.util.Map<java.lang.Integer,java.util.ArrayList<PPTriangle>>	PPTriangleCreator.create(java.util.List<PPGaussian> ppGaussians, Coordinates com)
void	AcceptorPoint.getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
void	AromRingPoint.getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
void	ChargePoint.getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
void	DonorPoint.getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
void	ExitVectorPoint.getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
void	IPharmacophorePoint.getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
double	PPGaussian.getSimilarity(PPGaussian ppGauss2, Coordinates directionality)
double	AromRingPoint.getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
double	ChargePoint.getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
default double	IPharmacophorePoint.getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
double	PPGaussian.getVectorSimilarity(PPGaussian ppGauss2, Coordinates directionalityMod)
void	PPGaussian.setCenter(Coordinates center)
void	AcceptorPoint.setDirectionality(Coordinates directionality)
void	AromRingPoint.setDirectionality(Coordinates directionality)
void	ChargePoint.setDirectionality(Coordinates directionality)
void	DonorPoint.setDirectionality(Coordinates directionality)
void	ExitVectorPoint.setDirectionality(Coordinates directionality)
void	IPharmacophorePoint.setDirectionality(Coordinates directionality)

Constructors in com.actelion.research.chem.phesa.pharmacophore with parameters of type Coordinates

Constructor	Description
PPTriangle(IPharmacophorePoint pp1, IPharmacophorePoint pp2, IPharmacophorePoint pp3, double d12, double d13, double d23, Coordinates molCom)
SimplePPGaussian(Coordinates center, IPharmacophorePoint.Functionality functionality)

Uses of Coordinates in com.actelion.research.chem.phesaflex

Methods in com.actelion.research.chem.phesaflex with parameters of type Coordinates

Modifier and Type	Method	Description
static void	MathHelper.getRotMatrix(Coordinates u, double theta, double[][] R)
static void	MathHelper.getRotMatrixDerivative(Coordinates u, double theta, Coordinates[][] dR)

Uses of Coordinates in org.openmolecules.chem.conf.gen

Methods in org.openmolecules.chem.conf.gen that return Coordinates

Modifier and Type	Method	Description
Coordinates	RigidFragment.getCoreCoordinates(int conformer, int atom)
Coordinates	RigidFragment.getExtendedCoordinates(int conformer, int atom)

Constructors in org.openmolecules.chem.conf.gen with parameters of type Coordinates

Constructor	Description
CacheEntry(Coordinates[][] coordinates, double[] likelihoods)

Uses of Coordinates in org.openmolecules.chem.conf.so

Methods in org.openmolecules.chem.conf.so with parameters of type Coordinates

Modifier and Type	Method	Description
protected void	ConformationRule.rotateAtom(Conformer conformer, int atom, int refAtom, Coordinates unit, double theta)