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()
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.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.descriptor.flexophore
Methods in com.actelion.research.chem.descriptor.flexophore that return Coordinates Modifier and Type Method Description static Coordinates
Molecule3DFunctions. getCenterGravity(Molecule3D mol)
static Coordinates
Molecule3DFunctions. getCenterGravity(Molecule3D mol, int[] indices)
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.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)
static void
PheSAAlignment. rotateCoords(Coordinates coords, double[][] m)
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)
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 that return Coordinates Modifier and Type Method Description Coordinates
AcceptorPoint. getCenter()
Coordinates
AromRingPoint. getCenter()
Coordinates
ChargePoint. getCenter()
Coordinates
DonorPoint. getCenter()
Coordinates
IPharmacophorePoint. getCenter()
Coordinates
AcceptorPoint. getDirectionality()
Coordinates
AromRingPoint. getDirectionality()
Coordinates
ChargePoint. getDirectionality()
Coordinates
DonorPoint. 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
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
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)
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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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