RDKit
Open-source cheminformatics and machine learning.
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Functions | |
RDKIT_FORCEFIELD_EXPORT double | calcAngleRestValue (const MMFFAngle *mmffAngleParams) |
returns the MMFF rest value for an angle | |
RDKIT_FORCEFIELD_EXPORT double | calcAngleForceConstant (const MMFFAngle *mmffAngleParams) |
returns the MMFF force constant for an angle | |
RDKIT_FORCEFIELD_EXPORT double | calcCosTheta (RDGeom::Point3D p1, RDGeom::Point3D p2, RDGeom::Point3D p3, double dist1, double dist2) |
calculates and returns the cosine of the angle between points p1, p2, p3 | |
RDKIT_FORCEFIELD_EXPORT double | calcAngleBendEnergy (const double theta0, const double ka, bool isLinear, const double cosTheta) |
calculates and returns the angle bending MMFF energy | |
RDKIT_FORCEFIELD_EXPORT void | calcAngleBendGrad (RDGeom::Point3D *r, double *dist, double **g, double &dE_dTheta, double &cosTheta, double &sinTheta) |
RDKIT_FORCEFIELD_EXPORT double | calcBondRestLength (const MMFFBond *mmffBondParams) |
returns the MMFF rest length for a bond | |
RDKIT_FORCEFIELD_EXPORT double | calcBondForceConstant (const MMFFBond *mmffBondParams) |
returns the MMFF force constant for a bond | |
RDKIT_FORCEFIELD_EXPORT double | calcBondStretchEnergy (const double r0, const double kb, const double distance) |
calculates and returns the bond stretching MMFF energy | |
RDKIT_FORCEFIELD_EXPORT double | calcUnscaledVdWMinimum (const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsAtom1, const MMFFVdW *mmffVdWParamsAtom2) |
RDKIT_FORCEFIELD_EXPORT double | calcUnscaledVdWWellDepth (double R_star_ij, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom) |
RDKIT_FORCEFIELD_EXPORT void | scaleVdWParams (double &R_star_ij, double &wellDepth, const MMFFVdWCollection *mmffVdW, const MMFFVdW *mmffVdWParamsIAtom, const MMFFVdW *mmffVdWParamsJAtom) |
scales the VdW parameters | |
RDKIT_FORCEFIELD_EXPORT double | calcVdWEnergy (const double dist, const double R_star_ij, const double wellDepth) |
calculates and returns the Van der Waals MMFF energy | |
RDKIT_FORCEFIELD_EXPORT double | calcEleEnergy (unsigned int idx1, unsigned int idx2, double dist, double chargeTerm, std::uint8_t dielModel, bool is1_4) |
calculates and returns the electrostatic MMFF energy | |
RDKIT_FORCEFIELD_EXPORT double | calcOopChi (const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint) |
calculates and returns the Wilson angle (in degrees) | |
RDKIT_FORCEFIELD_EXPORT double | calcOopBendForceConstant (const MMFFOop *mmffOopParams) |
returns the out-of-plane force constant koop | |
RDKIT_FORCEFIELD_EXPORT double | calcOopBendEnergy (const double chi, const double koop) |
calculates and returns the out-of-plane MMFF energy | |
RDKIT_FORCEFIELD_EXPORT std::pair< double, double > | calcStbnForceConstants (const MMFFStbn *mmffStbnParams) |
returns the std::pair of stretch-bend force constants for an angle | |
RDKIT_FORCEFIELD_EXPORT std::pair< double, double > | calcStretchBendEnergy (const double deltaDist1, const double deltaDist2, const double deltaTheta, const std::pair< double, double > forceConstants) |
calculates and returns the stretch-bending MMFF energy | |
RDKIT_FORCEFIELD_EXPORT double | calcTorsionCosPhi (const RDGeom::Point3D &iPoint, const RDGeom::Point3D &jPoint, const RDGeom::Point3D &kPoint, const RDGeom::Point3D &lPoint) |
calculates and returns the cosine of a torsion angle | |
RDKIT_FORCEFIELD_EXPORT std::tuple< double, double, double > | calcTorsionForceConstant (const MMFFTor *mmffTorParams) |
returns the 3-tuple of a torsion angle force constants | |
RDKIT_FORCEFIELD_EXPORT double | calcTorsionEnergy (const double V1, const double V2, const double V3, const double cosPhi) |
calculates and returns the torsional MMFF energy | |
RDKIT_FORCEFIELD_EXPORT void | calcTorsionGrad (RDGeom::Point3D *r, RDGeom::Point3D *t, double *d, double **g, double &sinTerm, double &cosPhi) |
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcAngleBendEnergy | ( | const double | theta0, |
const double | ka, | ||
bool | isLinear, | ||
const double | cosTheta ) |
calculates and returns the angle bending MMFF energy
RDKIT_FORCEFIELD_EXPORT void ForceFields::MMFF::Utils::calcAngleBendGrad | ( | RDGeom::Point3D * | r, |
double * | dist, | ||
double ** | g, | ||
double & | dE_dTheta, | ||
double & | cosTheta, | ||
double & | sinTheta ) |
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcAngleForceConstant | ( | const MMFFAngle * | mmffAngleParams | ) |
returns the MMFF force constant for an angle
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcAngleRestValue | ( | const MMFFAngle * | mmffAngleParams | ) |
returns the MMFF rest value for an angle
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcBondForceConstant | ( | const MMFFBond * | mmffBondParams | ) |
returns the MMFF force constant for a bond
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcBondRestLength | ( | const MMFFBond * | mmffBondParams | ) |
returns the MMFF rest length for a bond
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcBondStretchEnergy | ( | const double | r0, |
const double | kb, | ||
const double | distance ) |
calculates and returns the bond stretching MMFF energy
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcCosTheta | ( | RDGeom::Point3D | p1, |
RDGeom::Point3D | p2, | ||
RDGeom::Point3D | p3, | ||
double | dist1, | ||
double | dist2 ) |
calculates and returns the cosine of the angle between points p1, p2, p3
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcEleEnergy | ( | unsigned int | idx1, |
unsigned int | idx2, | ||
double | dist, | ||
double | chargeTerm, | ||
std::uint8_t | dielModel, | ||
bool | is1_4 ) |
calculates and returns the electrostatic MMFF energy
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcOopBendEnergy | ( | const double | chi, |
const double | koop ) |
calculates and returns the out-of-plane MMFF energy
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcOopBendForceConstant | ( | const MMFFOop * | mmffOopParams | ) |
returns the out-of-plane force constant koop
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcOopChi | ( | const RDGeom::Point3D & | iPoint, |
const RDGeom::Point3D & | jPoint, | ||
const RDGeom::Point3D & | kPoint, | ||
const RDGeom::Point3D & | lPoint ) |
calculates and returns the Wilson angle (in degrees)
RDKIT_FORCEFIELD_EXPORT std::pair< double, double > ForceFields::MMFF::Utils::calcStbnForceConstants | ( | const MMFFStbn * | mmffStbnParams | ) |
returns the std::pair of stretch-bend force constants for an angle
RDKIT_FORCEFIELD_EXPORT std::pair< double, double > ForceFields::MMFF::Utils::calcStretchBendEnergy | ( | const double | deltaDist1, |
const double | deltaDist2, | ||
const double | deltaTheta, | ||
const std::pair< double, double > | forceConstants ) |
calculates and returns the stretch-bending MMFF energy
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcTorsionCosPhi | ( | const RDGeom::Point3D & | iPoint, |
const RDGeom::Point3D & | jPoint, | ||
const RDGeom::Point3D & | kPoint, | ||
const RDGeom::Point3D & | lPoint ) |
calculates and returns the cosine of a torsion angle
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcTorsionEnergy | ( | const double | V1, |
const double | V2, | ||
const double | V3, | ||
const double | cosPhi ) |
calculates and returns the torsional MMFF energy
RDKIT_FORCEFIELD_EXPORT std::tuple< double, double, double > ForceFields::MMFF::Utils::calcTorsionForceConstant | ( | const MMFFTor * | mmffTorParams | ) |
returns the 3-tuple of a torsion angle force constants
RDKIT_FORCEFIELD_EXPORT void ForceFields::MMFF::Utils::calcTorsionGrad | ( | RDGeom::Point3D * | r, |
RDGeom::Point3D * | t, | ||
double * | d, | ||
double ** | g, | ||
double & | sinTerm, | ||
double & | cosPhi ) |
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcUnscaledVdWMinimum | ( | const MMFFVdWCollection * | mmffVdW, |
const MMFFVdW * | mmffVdWParamsAtom1, | ||
const MMFFVdW * | mmffVdWParamsAtom2 ) |
calculates and returns the unscaled minimum distance (R*ij) for a MMFF VdW contact
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcUnscaledVdWWellDepth | ( | double | R_star_ij, |
const MMFFVdW * | mmffVdWParamsIAtom, | ||
const MMFFVdW * | mmffVdWParamsJAtom ) |
calculates and returns the unscaled well depth (epsilon) for a MMFF VdW contact
RDKIT_FORCEFIELD_EXPORT double ForceFields::MMFF::Utils::calcVdWEnergy | ( | const double | dist, |
const double | R_star_ij, | ||
const double | wellDepth ) |
calculates and returns the Van der Waals MMFF energy
RDKIT_FORCEFIELD_EXPORT void ForceFields::MMFF::Utils::scaleVdWParams | ( | double & | R_star_ij, |
double & | wellDepth, | ||
const MMFFVdWCollection * | mmffVdW, | ||
const MMFFVdW * | mmffVdWParamsIAtom, | ||
const MMFFVdW * | mmffVdWParamsJAtom ) |
scales the VdW parameters