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Packages that use Point3D | |
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jgromacs.analysis | jgromacs.analysis is a collection of classes providing static methods for various analysis tasks |
jgromacs.data | jgromacs.data is a collection of classes representing multiple levels of structural data |
Uses of Point3D in jgromacs.analysis |
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Methods in jgromacs.analysis that return types with arguments of type Point3D | |
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static java.util.ArrayList<Point3D> |
Dynamics.getTrajectoryOfAtom(Trajectory t,
int atomindex)
Returns the trajectory of a single atom in the course of the simulation |
Methods in jgromacs.analysis with parameters of type Point3D | |
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static Angle |
Angles.getAngleBetweenPlanes(Point3D A,
Point3D B,
Point3D C,
Point3D D)
Calculates the angle between two planes defined by points A, B, C and points B, C, D |
static Angle |
Angles.getAngleBetweenVectors(Point3D v1,
Point3D v2)
Calculates the angle between two vectors |
static IndexSet |
Distances.getAtomIndicesInRadius(Structure s,
Point3D point,
double radius)
Returns the index set of atoms in a structure that are closer to a reference point than a given radius |
static FrameIndexSet |
Distances.getFramesWhereAtomIsCloseToPoint(Trajectory t,
int atomindex,
Point3D point,
double cutoff)
Returns the list of frames in the trajectory where an atoms is closer to a reference point than a given cutoff |
static FrameIndexSet |
Distances.getFramesWhereAtomIsDistantFromPoint(Trajectory t,
int atomindex,
Point3D point,
double cutoff)
Returns the list of frames in the trajectory where an atoms is more distant from a reference point than a given cutoff |
Uses of Point3D in jgromacs.data |
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Methods in jgromacs.data that return Point3D | |
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Point3D |
Point3D.crossProduct(Point3D other)
Returns the cross product of this vector and another vector |
Point3D |
Residue.getAlphaCarbonCoordinates()
Returns the position of alpha-carbon atom |
Point3D |
PointList.getCentroid()
Returns the centroid of points |
Point3D |
Atom.getCoordinates()
Returns the coordinates of atom |
Point3D |
PointList.getPoint(int i)
Returns the point of index i |
Point3D |
Point3D.minus(Point3D other)
Subtracts another vector from this vector |
Point3D |
Point3D.multiplyByScalar(double scalar)
Returns this vector multiplied by a scalar |
Point3D |
Point3D.plus(Point3D other)
Adds another vector to this vector |
Point3D |
Point3D.transformByMatrix(jama.Matrix matrix)
Returns the resulting vector of a matrix transformation |
Methods in jgromacs.data that return types with arguments of type Point3D | |
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java.util.ArrayList<Point3D> |
PointList.getPointsAsArrayList()
Returns points in an ArrayList |
Methods in jgromacs.data with parameters of type Point3D | |
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void |
PointList.addPoint(Point3D point)
Adds a new point to the point list |
Point3D |
Point3D.crossProduct(Point3D other)
Returns the cross product of this vector and another vector |
double |
Point3D.distance(Point3D other)
Returns the Euclidean distance between this point and another point |
double |
Point3D.innerProduct(Point3D other)
Returns the inner product of this vector and another vector |
Point3D |
Point3D.minus(Point3D other)
Subtracts another vector from this vector |
Point3D |
Point3D.plus(Point3D other)
Adds another vector to this vector |
void |
PointList.removePoint(Point3D point)
Removes the given point from the point list |
void |
Structure.setAtomCoordinates(int i,
Point3D coordinates)
Sets the coordinates of atom #i |
void |
Residue.setAtomCoordinates(int i,
Point3D coordinates)
Sets the coordinates of atom #i |
void |
Structure.setAtomOfIndexCoordinates(int index,
Point3D coordinates)
Sets the coordinates of atom of given index |
void |
Residue.setAtomOfIndexCoordinates(int index,
Point3D coordinates)
Sets the coordinates of atom of given index |
void |
Atom.setCoordinates(Point3D coordinates)
Sets the coordinates of atom |
void |
PointList.setPoint(int i,
Point3D point)
Replaces the point of index i with a given point |
void |
PointList.translate(Point3D vector)
Translates the points by a given vector |
Method parameters in jgromacs.data with type arguments of type Point3D | |
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void |
PointList.setPointFromArrayList(java.util.ArrayList<Point3D> points)
Loads points from an ArrayList |
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