Package com.actelion.research.chem.descriptor.flexophore.calculator

Class GeometryCalculator

java.lang.Object

com.actelion.research.chem.descriptor.flexophore.calculator.GeometryCalculator

public class GeometryCalculator
extends java.lang.Object

Utility class to perform 3D geometry calculations on molecules

Constructor Summary

Constructors

Constructor	Description
GeometryCalculator()

Method Summary

Modifier and Type	Method	Description
static double	getAngle(Coordinates c1, Coordinates c2, Coordinates c3)
static double	getAngle(Molecule3D mol, int a1, int a2, int a3)	Gets the Angle between 3 atoms
static double	getAngle(Molecule mol, int a1, int a2, int a3)
static Coordinates[]	getBounds(Molecule3D molecule)	Gets the Bounds of a molecule
static Coordinates	getCenterGravity(Molecule3D mol)	Gets the center of Gravity of a molecule
static Coordinates	getCoordinates(Molecule mol, int atm)
static double	getDihedral(Molecule3D mol, int a1, int a2, int a3, int a4)	Gets the Dihedral Angle between 4 atoms
static void	translate(Molecule3D molecule, Coordinates c)	Translate a Molecule

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeometryCalculator

public GeometryCalculator()

Method Detail

getCoordinates

public static final Coordinates getCoordinates(Molecule mol,
                                               int atm)

getAngle

public static final double getAngle(Molecule3D mol,
                                    int a1,
                                    int a2,
                                    int a3)

Gets the Angle between 3 atoms

Parameters:

mol -

Returns:

the angle

getAngle

public static final double getAngle(Coordinates c1,
                                    Coordinates c2,
                                    Coordinates c3)

getAngle

public static final double getAngle(Molecule mol,
                                    int a1,
                                    int a2,
                                    int a3)

getDihedral

public static final double getDihedral(Molecule3D mol,
                                       int a1,
                                       int a2,
                                       int a3,
                                       int a4)

Gets the Dihedral Angle between 4 atoms

Parameters:

mol -

Returns:

the angle

getCenterGravity

public static final Coordinates getCenterGravity(Molecule3D mol)

Gets the center of Gravity of a molecule

Parameters:

mol -

Returns:

getBounds

public static final Coordinates[] getBounds(Molecule3D molecule)

Gets the Bounds of a molecule

Parameters:

molecule -

Returns:

an Array of Coordinares [lowerBounds, upperbounds]

translate

public static final void translate(Molecule3D molecule,
                                   Coordinates c)

Translate a Molecule

Parameters:

molecule -

c -