Open Babel: vector3 Class Reference

Public Member Functions

# vector3 Class Reference

Represents a vector in 3-dimensional real space. More...

`#include <openbabel/math/vector3.h>`

Inheritance diagram for vector3:

List of all members.

## Public Member Functions
| vector3 (const double inX=0.0, const double inY=0.0, const double inZ=0.0)
| vector3 (double inV[3])
| vector3 (const vector3 &v)
| ~vector3 ()
void | Set (const double inX, const double inY, const double inZ)
void | Set (const double *c)
void | SetX (const double inX)
void | SetY (const double inY)
void | SetZ (const double inZ)
double | GetX () const
double | GetY () const
double | GetZ () const
void | Get (double *c)
double | operator[] (unsigned int i) const
vector3 & | operator= (const vector3 &v)
const double * | AsArray () const
vector3 & | operator+= (const vector3 &v)
vector3 & | operator-= (const vector3 &v)
vector3 & | operator+= (const double *f)
vector3 & | operator-= (const double *f)
vector3 & | operator*= (const double &c)
vector3 & | operator/= (const double &c)
vector3 & | operator*= (const matrix3x3 &)
void | randomUnitVector (OBRandom *oeRand=NULL)
vector3 & | normalize ()
bool | CanBeNormalized () const
double | length_2 () const
double | length () const
const double & | x () const
const double & | y () const
const double & | z () const
double & | x ()
double & | y ()
double & | z ()
int | operator== (const vector3 &) const
int | operator!= (const vector3 &other) const
bool | IsApprox (const vector3 &other, const double &precision) const
double | distSq (const vector3 &vv) const
bool | createOrthoVector (vector3 &v) const

## Detailed Description

Represents a vector in 3-dimensional real space.

The vector3 class was designed to simplify operations with floating point coordinates. To this end many of the common operations have been overloaded for simplicity. Vector addition, subtraction, scalar multiplication, dot product, cross product, magnitude and a number of other utility functions are built in to the vector class. For a full description of the class member functions please consult the documentation. The following code demonstrates several of the functions of the vector class:

        vector3 v1,v2,v3;
        v1 = VX;
        v2 = VY;
        v3 = cross(v1,v2);
        v3 *= 2.5;
        v3.normalize();

## Constructor & Destructor Documentation

vector3 | ( | const double | inX = `0.0`,
|  | const double | inY = `0.0`,
|  | const double | inZ = `0.0`
| ) |  | `[inline]`

Constructor.

vector3 | ( | double | inV[3] ) | `[inline]`

vector3 | ( | const vector3 & | v ) | `[inline]`

Copy Constructor.

~vector3 | ( | ) | `[inline]`

Destructor.

## Member Function Documentation

void Set | ( | const double | inX,
|  | const double | inY,
|  | const double | inZ
| ) |  | `[inline]`

Set x,y and z-component of a vector.

Referenced by OBRotamerList::AddRotamer(), OBRing::findCenterAndNormal(), OBFloatGrid::GetMidpointVector(), OBBuilder::GetNewBondVector(), OBAtom::GetVector(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OBForceField::ValidateConjugateGradients(), and OBForceField::ValidateSteepestDescent().

void Set | ( | const double * | c ) | `[inline]`

Set x,y and z-component of a vector from c[0]..c[2].

void SetX | ( | const double | inX ) | `[inline]`

Access function to set the x-coordinate of the vector.

Referenced by OBForceField::GetGrid(), OBForceField::MolecularDynamicsTakeNSteps(), vector3::operator*=(), and OpenBabel::transformedFractionalCoordinate().

void SetY | ( | const double | inY ) | `[inline]`

Access function to set the y-coordinate of the vector.

Referenced by OBForceField::GetGrid(), OBForceField::MolecularDynamicsTakeNSteps(), vector3::operator*=(), and OpenBabel::transformedFractionalCoordinate().

void SetZ | ( | const double | inZ ) | `[inline]`

Access function to set the z-coordinate of the vector.

Referenced by OpenBabel::CalcSignedVolume(), OBForceField::GetGrid(), OBForceField::MolecularDynamicsTakeNSteps(), vector3::operator*=(), and OpenBabel::transformedFractionalCoordinate().

double GetX | ( | ) | const`[inline]`

Access function to get the x-coordinate of the vector.

double GetY | ( | ) | const`[inline]`

Access function to get the y-coordinate of the vector.

double GetZ | ( | ) | const`[inline]`

Access function to get the z-coordinate of the vector.

void Get | ( | double * | c ) | `[inline]`

Set c[0]..c[2] to the components of the vector.

Warning:
  No error checking is performed

Referenced by OBForceField::VectorBondDerivative().

double operator[] | ( | unsigned int | i ) | const

Access function to x: [0], y: [1], and z[2].

This (slow) method allows to access the elements of the vector as if it were an array of doubles. If the index is > 2, then a warning is printed and 0.0 is returned. Otherwise, if i is 0, 1 or 2, then a reference to x, y or z is returned, respectively.

Warning:
  This method is primarily designed to facilitate the integration ('Open Babelization') of code that uses arrays of doubles rather than the vector class. Due to the error checks the method is of course very slow and should therefore be avoided in production code.

vector3& operator= | ( | const vector3 & | v ) | `[inline]`

Assignment.

const double* AsArray | ( | ) | const`[inline]`

Returns:
  the vector as a const double *

vector3& operator+= | ( | const vector3 & | v ) | `[inline]`

Vector addition (add `v` to *this)

Returns:
  *this + v

vector3& operator-= | ( | const vector3 & | v ) | `[inline]`

Vector subtraction (subtract `v` from *this)

Returns:
  *this - v

vector3& operator+= | ( | const double * | f ) | `[inline]`

Scalar addition (add `f` to *this)

Returns:
  *this + f

vector3& operator-= | ( | const double * | f ) | `[inline]`

Scalar subtraction (subtract `f` from *this)

Returns:
  *this - f

vector3& operator*= | ( | const double & | c ) | `[inline]`

Scalar multiplication (multiply *this by `c`)

Returns:
  *this * c

vector3& operator/= | ( | const double & | c ) | `[inline]`

Scalar division (divide *this by `c`)

Returns:
  *this divided by c

vector3 & operator*= | ( | const matrix3x3 & | m ) |

Multiplication of matrix and vector

Returns:
  the result (i.e., the updated vector)

Todo:
  Currently unimplemented

calculates the product m*(*this) of the matrix m and the column vector represented by *this

void randomUnitVector | ( | OBRandom * | obRandP = `NULL` ) |

Create a random unit vector.

Replaces *this with a random unit vector, which is (supposed to be) uniformly distributed over the unit sphere. Uses the random number generator obRand, or uses the system number generator with a time seed if obRand == NULL.

Parameters:

  obRandP | random number generator to use, or NULL, if the system random number generator (with time seed) should be used

Referenced by OBBuilder::GetNewBondVector(), matrix3x3::randomRotation(), OBBond::SetLength(), OBForceField::VectorBondDerivative(), and OBForceField::VectorLengthDerivative().

vector3 & normalize | ( | ) |

Scales a vector to give it length one.

Returns:
  the result (i.e., the normalized vector)

This method normalizes *this. In other words, it divides the x,y,z coords of *this by this->length(). If *this can't be safely normalized, it remains unchanged. See CanBeNormalized().

Returns:
  a reference to *this

Referenced by OBRing::findCenterAndNormal(), OBBuilder::GetNewBondVector(), OpenBabel::InternalToCartesian(), OBForceField::LineSearch(), matrix3x3::PlaneReflection(), matrix3x3::RotAboutAxisByAngle(), OBAtom::SetHybAndGeom(), OBBond::SetLength(), OBForceField::ValidateLineSearch(), and OBForceField::VectorAngleDerivative().

bool CanBeNormalized | ( | ) | const

Returns:
  Whether a vector can be normalized

This method returns true if *this can be safely normalized. Vectors that can't be safely normalized are:

- the zero vector (0,0,0)
- vectors having coords that can't be squared without triggering an overflow or underflow. This means doubles having absolute value greater than 1e150 or smaller than 1e-150.

double length_2 | ( | ) | const`[inline]`

Returns:
  The length of the vector squared

Referenced by OpenBabel::CartesianToInternal(), vector3::IsApprox(), and OBBond::SetLength().

double length | ( | ) | const`[inline]`

Returns:
  The vector length

Referenced by OpenBabel::CalcTorsionAngle(), OpenBabel::CartesianToInternal(), OBUnitCell::GetA(), OBAtom::GetAngle(), OBUnitCell::GetB(), OBUnitCell::GetC(), OBForceField::LineSearch(), OpenBabel::Point2Line(), OpenBabel::Point2PlaneSigned(), OBUnitCell::SetData(), OBBuilder::Swap(), OpenBabel::vectorAngle(), OBForceField::VectorAngleDerivative(), OBForceField::VectorLengthDerivative(), OBForceField::VectorOOPDerivative(), and OBForceField::VectorTorsionDerivative().

const double& x | ( | ) | const`[inline]`

Access function to get the x-coordinate of the vector.

Referenced by OBMol::AddHydrogens(), SpaceGroup::AddTransform(), OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBBuilder::Connect(), OpenBabel::cross(), transform3d::DescribeAsValues(), vector3::distSq(), OpenBabel::dot(), OBGridData::GetAxes(), OBForceField::GetGrid(), OpenBabel::GetLabelAlignment(), OBBuilder::GetNewBondVector(), OBGridData::GetValue(), matrix3x3::matrix3x3(), OBForceField::MolecularDynamicsTakeNSteps(), transform3d::Normalize(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OpenBabel::operator*(), vector3::operator*=(), OpenBabel::operator+(), OpenBabel::operator-(), OpenBabel::operator/(), OpenBabel::operator<<(), vector3::operator==(), matrix3x3::PlaneReflection(), OBGrid::PointIsInBox(), matrix3x3::RotAboutAxisByAngle(), matrix3x3::SetColumn(), OBFloatGrid::SetLimits(), matrix3x3::SetRow(), OBAtom::SetVector(), OBForceField::SteepestDescentTakeNSteps(), SpaceGroup::Transform(), OpenBabel::transformedFractionalCoordinate(), OBMol::Translate(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateGradientError(), OBForceField::ValidateSteepestDescent(), and OBUnitCell::WrapFractionalCoordinate().

const double& y | ( | ) | const`[inline]`

Access function to get the y-coordinate of the vector.

Referenced by OBMol::AddHydrogens(), SpaceGroup::AddTransform(), OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBBuilder::Connect(), OpenBabel::cross(), vector3::distSq(), OpenBabel::dot(), OBGridData::GetAxes(), OBForceField::GetGrid(), OpenBabel::GetLabelAlignment(), OBBuilder::GetNewBondVector(), OBGridData::GetValue(), matrix3x3::matrix3x3(), OBForceField::MolecularDynamicsTakeNSteps(), transform3d::Normalize(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OpenBabel::operator*(), vector3::operator*=(), OpenBabel::operator+(), OpenBabel::operator-(), OpenBabel::operator/(), OpenBabel::operator<<(), vector3::operator==(), matrix3x3::PlaneReflection(), OBGrid::PointIsInBox(), matrix3x3::RotAboutAxisByAngle(), matrix3x3::SetColumn(), OBFloatGrid::SetLimits(), matrix3x3::SetRow(), OBAtom::SetVector(), OBForceField::SteepestDescentTakeNSteps(), SpaceGroup::Transform(), OpenBabel::transformedFractionalCoordinate(), OBMol::Translate(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateGradientError(), OBForceField::ValidateSteepestDescent(), and OBUnitCell::WrapFractionalCoordinate().

const double& z | ( | ) | const`[inline]`

Access function to get the z-coordinate of the vector.

Referenced by OBMol::AddHydrogens(), SpaceGroup::AddTransform(), OBForceField::ConjugateGradientsInitialize(), OBForceField::ConjugateGradientsTakeNSteps(), OBBuilder::Connect(), OBMol::ConnectTheDots(), OpenBabel::cross(), vector3::distSq(), OpenBabel::dot(), OBGridData::GetAxes(), OBForceField::GetGrid(), OBBuilder::GetNewBondVector(), OBGridData::GetValue(), matrix3x3::matrix3x3(), OBForceField::MolecularDynamicsTakeNSteps(), transform3d::Normalize(), OBForceField::NumericalDerivative(), OBForceField::NumericalSecondDerivative(), OpenBabel::operator*(), vector3::operator*=(), OpenBabel::operator+(), OpenBabel::operator-(), OpenBabel::operator/(), OpenBabel::operator<<(), vector3::operator==(), matrix3x3::PlaneReflection(), OBGrid::PointIsInBox(), matrix3x3::RotAboutAxisByAngle(), matrix3x3::SetColumn(), OBFloatGrid::SetLimits(), matrix3x3::SetRow(), OBAtom::SetVector(), OBForceField::SteepestDescentTakeNSteps(), SpaceGroup::Transform(), OpenBabel::transformedFractionalCoordinate(), OBMol::Translate(), OBForceField::ValidateConjugateGradients(), OBForceField::ValidateGradientError(), and OBUnitCell::WrapFractionalCoordinate().

double& x | ( | ) | `[inline]`

Access function to set the x-coordinate of the vector.

double& y | ( | ) | `[inline]`

Access function to set the y-coordinate of the vector.

double& z | ( | ) | `[inline]`

Access function to set the z-coordinate of the vector.

int operator== | ( | const vector3 & | other ) | const

Comparison Methods.

Equivalence of vectors

Deprecated:
  This method uses unreliable floating point == comparisons Use vector3::IsApprox() instead.

Returns:
  true if every component is equal

int operator!= | ( | const vector3 & | other ) | const`[inline]`

Deprecated:
  This method uses unreliable floating point == comparisons Use vector3::IsApprox() instead.

Returns:
  true if at least one component of the two vectors is !=

bool IsApprox | ( | const vector3 & | other,
|  | const double & | precision
| ) |  | const

Safe comparison for floating-point vector3.

Returns:
  true if the vector *this is approximately equal to the vector `other`, to the precision `precision`. More specifically, this method works exactly like the OpenBabel::IsApprox() function, replacing the absolute value for doubles by the norm for vectors.

Parameters:

  other | The vector for comparison
  precision | This parameter plays the same role as in OpenBabel::IsApprox().

double distSq | ( | const vector3 & | vv ) | const`[inline]`

}@

Returns:
  square of the distance between *this and vv

equivalent to length_2(*this-vv)

Referenced by OBForceField::GetGrid().

bool createOrthoVector | ( | vector3 & | res ) | const

Construct a unit vector orthogonal to *this.

Creates a vector of length one, orthogonal to *this.

Returns:
  Whether the method was successful

It requires that *this is normalizable; otherwise it just returns false. See CanBeNormalized()

Parameters:

  res | reference by which to pass the result.

Returns:
  always true. (Return value kept for compatibility, as old versions of OpenBabel used to check for normalizability).

The documentation for this class was generated from the following files:

- vector3.h
- matrix3x3.cpp
- vector3.cpp

All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines