ForceFields::UFF::Utils Namespace Reference

## Functions

double | calcAngleForceConstant (double theta0, double bondOrder12, double bondOrder23, const AtomicParams *at1Params, const AtomicParams *at2Params, const AtomicParams *at3Params)
| Calculate the force constant for an angle bend. More...
void | calcAngleBendGrad (RDGeom::Point3D *r, double *dist, double **g, double &dE_dTheta, double &cosTheta, double &sinTheta)
double | calcBondRestLength (double bondOrder, const AtomicParams *end1Params, const AtomicParams *end2Params)
| calculates and returns the UFF rest length for a bond More...
double | calcBondForceConstant (double restLength, const AtomicParams *end1Params, const AtomicParams *end2Params)
| calculates and returns the UFF force constant for a bond More...
double | calculateCosY (const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint)
boost::tuple< double, double, double, double > | calcInversionCoefficientsAndForceConstant (int at2AtomicNum, bool isCBoundToO)
| calculates and returns the UFF force constant for an improper torsion More...
double | calcNonbondedMinimum (const AtomicParams *at1Params, const AtomicParams *at2Params)
| calculates and returns the UFF minimum position for a vdW contact More...
double | calcNonbondedDepth (const AtomicParams *at1Params, const AtomicParams *at2Params)
| calculates and returns the UFF well depth for a vdW contact More...
double | calculateCosTorsion (const RDGeom::Point3D &p1, const RDGeom::Point3D &p2, const RDGeom::Point3D &p3, const RDGeom::Point3D &p4)
| calculates and returns the cosine of a torsion angle More...
void | calcTorsionGrad (RDGeom::Point3D *r, RDGeom::Point3D *t, double *d, double **g, double &sinTerm, double &cosPhi)
double | equation17 (double bondOrder23, const AtomicParams *at2Params, const AtomicParams *at3Params)
bool | isInGroup6 (int num)

## Function Documentation

void ForceFields::UFF::Utils::calcAngleBendGrad | ( | RDGeom::Point3D * | r,
|  | double * | dist,
|  | double ** | g,
|  | double & | dE_dTheta,
|  | double & | cosTheta,
|  | double & | sinTheta
| ) |  |

double ForceFields::UFF::Utils::calcAngleForceConstant | ( | double | theta0,
|  | double | bondOrder12,
|  | double | bondOrder23,
|  | const AtomicParams * | at1Params,
|  | const AtomicParams * | at2Params,
|  | const AtomicParams * | at3Params
| ) |  |

Calculate the force constant for an angle bend.

The angle is between atom1 - atom2 - atom3

Parameters

  theta0 | the preferred value of the angle (in radians)
  bondOrder12 | order of the bond between atoms 1 and 2 (as a double)
  bondOrder23 | order of the bond between atoms 2 and 3 (as a double)
  at1Params | pointer to the parameters for atom 1
  at2Params | pointer to the parameters for atom 2
  at3Params | pointer to the parameters for atom 3

double ForceFields::UFF::Utils::calcBondForceConstant | ( | double | restLength,
|  | const AtomicParams * | end1Params,
|  | const AtomicParams * | end2Params
| ) |  |

calculates and returns the UFF force constant for a bond

Parameters

  restLength | the rest length of the bond
  end1Params | pointer to the parameters for end1
  end2Params | pointer to the parameters for end2

Returns
  the force constant

double ForceFields::UFF::Utils::calcBondRestLength | ( | double | bondOrder,
|  | const AtomicParams * | end1Params,
|  | const AtomicParams * | end2Params
| ) |  |

calculates and returns the UFF rest length for a bond

Parameters

  bondOrder | the order of the bond (as a double)
  end1Params | pointer to the parameters for end1
  end2Params | pointer to the parameters for end2

Returns
  the rest length

boost::tuple<double, double, double, double> ForceFields::UFF::Utils::calcInversionCoefficientsAndForceConstant | ( | int | at2AtomicNum,
|  | bool | isCBoundToO
| ) |  |

calculates and returns the UFF force constant for an improper torsion

Parameters

  at2AtomicNum | atomic number for atom 2
  isCBoundToO | boolean flag; true if atom 2 is sp2 carbon bound to sp2 oxygen

Returns
  the force constant

double ForceFields::UFF::Utils::calcNonbondedDepth | ( | const AtomicParams * | at1Params,
|  | const AtomicParams * | at2Params
| ) |  |

calculates and returns the UFF well depth for a vdW contact

Parameters

  at1Params | pointer to the parameters for end1
  at2Params | pointer to the parameters for end2

Returns
  the depth of the well

double ForceFields::UFF::Utils::calcNonbondedMinimum | ( | const AtomicParams * | at1Params,
|  | const AtomicParams * | at2Params
| ) |  |

calculates and returns the UFF minimum position for a vdW contact

Parameters

  at1Params | pointer to the parameters for end1
  at2Params | pointer to the parameters for end2

Returns
  the position of the minimum

void ForceFields::UFF::Utils::calcTorsionGrad | ( | RDGeom::Point3D * | r,
|  | RDGeom::Point3D * | t,
|  | double * | d,
|  | double ** | g,
|  | double & | sinTerm,
|  | double & | cosPhi
| ) |  |

double ForceFields::UFF::Utils::calculateCosTorsion | ( | const RDGeom::Point3D & | p1,
|  | const RDGeom::Point3D & | p2,
|  | const RDGeom::Point3D & | p3,
|  | const RDGeom::Point3D & | p4
| ) |  |

calculates and returns the cosine of a torsion angle

double ForceFields::UFF::Utils::calculateCosY | ( | const RDGeom::Point3D & | iPoint,
|  | const RDGeom::Point3D & | jPoint,
|  | const RDGeom::Point3D & | kPoint,
|  | const RDGeom::Point3D & | lPoint
| ) |  |

calculates and returns the cosine of the Y angle in an improper torsion (see UFF paper, equation 19)

double ForceFields::UFF::Utils::equation17 | ( | double | bondOrder23,
|  | const AtomicParams * | at2Params,
|  | const AtomicParams * | at3Params
| ) |  |

bool ForceFields::UFF::Utils::isInGroup6 | ( | int | num | ) |