Uses of Class
com.actelion.research.chem.Coordinates
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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, c3Coordinates
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 thisCoordinates
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, c3static 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 thisvoid
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)
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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)
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Uses of Coordinates in com.actelion.research.chem.alignment3d.transformation
Methods in com.actelion.research.chem.alignment3d.transformation that return Coordinates Modifier and Type Method Description Coordinates
ExponentialMap. getP()
Methods in com.actelion.research.chem.alignment3d.transformation with parameters of type Coordinates Modifier and Type Method Description void
Rotation. apply(Coordinates coords)
void
Scaling. apply(Coordinates coords)
void
Transformation. apply(Coordinates coords)
void
TransformationSequence. apply(Coordinates coords)
void
Translation. apply(Coordinates coords)
Constructors in com.actelion.research.chem.alignment3d.transformation with parameters of type Coordinates Constructor Description ExponentialMap(Coordinates p)
Quaternion(Coordinates axis, double angle)
Translation(Coordinates translation)
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Uses of Coordinates in com.actelion.research.chem.chemicalspaces.synthon
Methods in com.actelion.research.chem.chemicalspaces.synthon that return Coordinates Modifier and Type Method Description static Coordinates
SynthonReactor. eulerRodrigues(Coordinates v, Coordinates k, double theta)
Methods in com.actelion.research.chem.chemicalspaces.synthon with parameters of type Coordinates Modifier and Type Method Description static Coordinates
SynthonReactor. eulerRodrigues(Coordinates v, Coordinates k, double theta)
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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 coordinatesvoid
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)
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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)
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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 moleculestatic Coordinates[]
StructureCalculator. getBounds(Molecule3D mol)
static Coordinates
StructureCalculator. getCenter(Molecule3D mol)
static Coordinates
GeometryCalculator. getCenterGravity(Molecule3D mol)
Gets the center of Gravity of a moleculestatic 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 molstatic void
StructureCalculator. rotateLigand(Molecule3D mol, double angle, Coordinates normal, Coordinates center)
static void
GeometryCalculator. translate(Molecule3D molecule, Coordinates c)
Translate a Moleculestatic void
StructureCalculator. translateLigand(Molecule3D mol, Coordinates v)
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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)
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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)
Methods in com.actelion.research.chem.docking with parameters of type Coordinates Modifier and Type Method Description static double
ScoringTask. calcScore(StereoMolecule receptor, int probeAtomType, Coordinates c, int[] receptorAtomTypes)
calculate interaction of probe atom with receptor -
Uses of Coordinates in com.actelion.research.chem.docking.receptorpharmacophore
Constructors in com.actelion.research.chem.docking.receptorpharmacophore with parameters of type Coordinates Constructor Description NegativeReceptorImage(StereoMolecule ligand, StereoMolecule receptor, double gridWidth, Coordinates extension)
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Uses of Coordinates in com.actelion.research.chem.docking.scoring
Methods in com.actelion.research.chem.docking.scoring with parameters of type Coordinates Modifier and Type Method Description void
ProbeScanning.Probe. updateCoordinates(Coordinates c)
Constructors in com.actelion.research.chem.docking.scoring with parameters of type Coordinates Constructor Description Probe(Coordinates c, IPharmacophorePoint.Functionality type)
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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)
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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 moleculeCoordinates
MoleculeGrid. getCartCoordinates(int[] gridCoords)
static Coordinates
GeometryCalculator. getCenterGravity(StereoMolecule mol)
Gets the center of Gravity of a moleculestatic 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 MoleculeConstructors in com.actelion.research.chem.io.pdb.converter with parameters of type Coordinates Constructor Description MoleculeGrid(StereoMolecule mol, double gridWidth, Coordinates extension)
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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
protected Coordinates
ShapeVolume. com
Methods in com.actelion.research.chem.phesa that return Coordinates Modifier and Type Method Description Coordinates
Gaussian3D. getCenter()
Coordinates
ShapeVolume. getCOM()
Coordinates
VolumeGaussian. getReferenceVector()
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)
static void
PheSAAlignment. rotateCoordsAroundAxis180(Coordinates coords, PheSAAlignment.axis a)
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)
void
ShapeVolume. translateToCOM(Coordinates com)
void
Gaussian3D. updateCoordinates(Coordinates[] coords)
protected void
ShapeVolume. updateCoordinates(java.util.List<? extends Gaussian3D> gaussians, Coordinates[] coords)
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)
VolumeGaussian(int atomId, int atomicNo, Coordinates center, Coordinates shiftVector, int role)
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Uses of Coordinates in com.actelion.research.chem.phesa.pharmacophore
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)
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)
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Uses of Coordinates in com.actelion.research.chem.phesa.pharmacophore.pp
Methods in com.actelion.research.chem.phesa.pharmacophore.pp that return Coordinates Modifier and Type Method Description Coordinates
AcceptorPoint. getCenter()
Coordinates
AliphaticPoint. getCenter()
Coordinates
AromRingPoint. getCenter()
Coordinates
ChargePoint. getCenter()
Coordinates
DonorPoint. getCenter()
Coordinates
ExitVectorPoint. getCenter()
Coordinates
IPharmacophorePoint. getCenter()
Coordinates
SimplePharmacophorePoint. getCenter()
Coordinates
AcceptorPoint. getDirectionality()
Coordinates
AliphaticPoint. getDirectionality()
Coordinates
AromRingPoint. getDirectionality()
Coordinates
ChargePoint. getDirectionality()
Coordinates
DonorPoint. getDirectionality()
Coordinates
ExitVectorPoint. getDirectionality()
Coordinates
IPharmacophorePoint. getDirectionality()
Coordinates
SimplePharmacophorePoint. getDirectionality()
Coordinates
AcceptorPoint. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Coordinates
AliphaticPoint. getRotatedDirectionality(double[][] m, double scaleFactor)
Coordinates
AromRingPoint. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Coordinates
ChargePoint. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Coordinates
DonorPoint. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Coordinates
ExitVectorPoint. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Coordinates
IPharmacophorePoint. getRotatedDirectionality(double[][] m, double scaleFactor)
Coordinates
PPGaussian. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Coordinates
SimplePharmacophorePoint. getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
Methods in com.actelion.research.chem.phesa.pharmacophore.pp with parameters of type Coordinates Modifier and Type Method Description void
AcceptorPoint. getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
void
AliphaticPoint. 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)
void
SimplePharmacophorePoint. getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
double
PPGaussian. getSimilarity(PPGaussian ppGauss2, Coordinates directionality)
double
AliphaticPoint. getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
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)
double
SimplePharmacophorePoint. getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
void
PPGaussian. setCenter(Coordinates center)
void
AcceptorPoint. setDirectionality(Coordinates directionality)
void
AliphaticPoint. 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)
void
SimplePharmacophorePoint. setDirectionality(Coordinates directionality)
void
AcceptorPoint. updateCoordinates(Coordinates[] coords)
void
AliphaticPoint. updateCoordinates(Coordinates[] coords)
void
AromRingPoint. updateCoordinates(Coordinates[] coords)
void
ChargePoint. updateCoordinates(Coordinates[] coords)
void
DonorPoint. updateCoordinates(Coordinates[] coords)
void
ExitVectorPoint. updateCoordinates(Coordinates[] coords)
void
IPharmacophorePoint. updateCoordinates(Coordinates[] coords)
void
PPGaussian. updateCoordinates(Coordinates[] coords)
void
SimplePharmacophorePoint. updateCoordinates(Coordinates[] coords)
Constructors in com.actelion.research.chem.phesa.pharmacophore.pp with parameters of type Coordinates Constructor Description SimplePharmacophorePoint(int atomID, Coordinates center, IPharmacophorePoint.Functionality functionality)
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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)
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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)
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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)
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