RDKit
Open-source cheminformatics and machine learning.
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Functions | |
RDKIT_FORCEFIELD_EXPORT 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. | |
RDKIT_FORCEFIELD_EXPORT void | calcAngleBendGrad (RDGeom::Point3D *r, double *dist, double **g, double &dE_dTheta, double &cosTheta, double &sinTheta) |
RDKIT_FORCEFIELD_EXPORT double | calcBondRestLength (double bondOrder, const AtomicParams *end1Params, const AtomicParams *end2Params) |
calculates and returns the UFF rest length for a bond | |
RDKIT_FORCEFIELD_EXPORT double | calcBondForceConstant (double restLength, const AtomicParams *end1Params, const AtomicParams *end2Params) |
calculates and returns the UFF force constant for a bond | |
RDKIT_FORCEFIELD_EXPORT double | calculateCosY (const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint) |
RDKIT_FORCEFIELD_EXPORT std::tuple< double, double, double, double > | calcInversionCoefficientsAndForceConstant (int at2AtomicNum, bool isCBoundToO) |
calculates and returns the UFF force constant for an improper torsion | |
RDKIT_FORCEFIELD_EXPORT double | calcNonbondedMinimum (const AtomicParams *at1Params, const AtomicParams *at2Params) |
calculates and returns the UFF minimum position for a vdW contact | |
RDKIT_FORCEFIELD_EXPORT double | calcNonbondedDepth (const AtomicParams *at1Params, const AtomicParams *at2Params) |
calculates and returns the UFF well depth for a vdW contact | |
RDKIT_FORCEFIELD_EXPORT 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 | |
RDKIT_FORCEFIELD_EXPORT void | calcTorsionGrad (RDGeom::Point3D *r, RDGeom::Point3D *t, double *d, double **g, double &sinTerm, double &cosPhi) |
RDKIT_FORCEFIELD_EXPORT double | equation17 (double bondOrder23, const AtomicParams *at2Params, const AtomicParams *at3Params) |
RDKIT_FORCEFIELD_EXPORT bool | isInGroup6 (int num) |
RDKIT_FORCEFIELD_EXPORT void ForceFields::UFF::Utils::calcAngleBendGrad | ( | RDGeom::Point3D * | r, |
double * | dist, | ||
double ** | g, | ||
double & | dE_dTheta, | ||
double & | cosTheta, | ||
double & | sinTheta ) |
RDKIT_FORCEFIELD_EXPORT 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
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 |
RDKIT_FORCEFIELD_EXPORT double ForceFields::UFF::Utils::calcBondForceConstant | ( | double | restLength, |
const AtomicParams * | end1Params, | ||
const AtomicParams * | end2Params ) |
calculates and returns the UFF force constant for a bond
restLength | the rest length of the bond |
end1Params | pointer to the parameters for end1 |
end2Params | pointer to the parameters for end2 |
RDKIT_FORCEFIELD_EXPORT double ForceFields::UFF::Utils::calcBondRestLength | ( | double | bondOrder, |
const AtomicParams * | end1Params, | ||
const AtomicParams * | end2Params ) |
calculates and returns the UFF rest length for a bond
bondOrder | the order of the bond (as a double) |
end1Params | pointer to the parameters for end1 |
end2Params | pointer to the parameters for end2 |
RDKIT_FORCEFIELD_EXPORT std::tuple< double, double, double, double > ForceFields::UFF::Utils::calcInversionCoefficientsAndForceConstant | ( | int | at2AtomicNum, |
bool | isCBoundToO ) |
calculates and returns the UFF force constant for an improper torsion
at2AtomicNum | atomic number for atom 2 |
isCBoundToO | boolean flag; true if atom 2 is sp2 carbon bound to sp2 oxygen |
RDKIT_FORCEFIELD_EXPORT double ForceFields::UFF::Utils::calcNonbondedDepth | ( | const AtomicParams * | at1Params, |
const AtomicParams * | at2Params ) |
calculates and returns the UFF well depth for a vdW contact
at1Params | pointer to the parameters for end1 |
at2Params | pointer to the parameters for end2 |
RDKIT_FORCEFIELD_EXPORT double ForceFields::UFF::Utils::calcNonbondedMinimum | ( | const AtomicParams * | at1Params, |
const AtomicParams * | at2Params ) |
calculates and returns the UFF minimum position for a vdW contact
at1Params | pointer to the parameters for end1 |
at2Params | pointer to the parameters for end2 |
RDKIT_FORCEFIELD_EXPORT void ForceFields::UFF::Utils::calcTorsionGrad | ( | RDGeom::Point3D * | r, |
RDGeom::Point3D * | t, | ||
double * | d, | ||
double ** | g, | ||
double & | sinTerm, | ||
double & | cosPhi ) |
RDKIT_FORCEFIELD_EXPORT 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
RDKIT_FORCEFIELD_EXPORT 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)
RDKIT_FORCEFIELD_EXPORT double ForceFields::UFF::Utils::equation17 | ( | double | bondOrder23, |
const AtomicParams * | at2Params, | ||
const AtomicParams * | at3Params ) |
RDKIT_FORCEFIELD_EXPORT bool ForceFields::UFF::Utils::isInGroup6 | ( | int | num | ) |