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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Contains classes and functions related to molecular force fields. More...
Namespaces | |
| AtomProperty | |
| Provides keys for built-in Chem::Atom properties. | |
| BondProperty | |
| Provides keys for built-in Chem::Bond properties. | |
| InteractionType | |
| Provides flags for the specification of a set of force field interaction types. | |
| MMFF94ParameterSet | |
| Provides constants for the specification of a MMFF94 parameter set variant. | |
| MolecularGraphProperty | |
| Provides keys for built-in Chem::MolecularGraph properties. | |
| UFFAtomType | |
| Provides constants for the specification of numeric Universal Force Field (UFF) atom types. | |
Classes | |
| class | ElasticPotential |
| Stores parameters for an elastic potential (harmonic distance restraint) between a pair of atoms. More... | |
| class | Error |
| Base class of the ForceField subsystem exception hierarchy. More... | |
| class | ParameterizationFailed |
| Thrown when force field parameterization has failed. More... | |
| struct | GradientVectorTraits |
| Generic primary traits template providing zero-initialization for a 3D gradient vector container of type GV. More... | |
| struct | GradientVectorTraits< Math::VectorArray< V > > |
| ForceField::GradientVectorTraits specialization for containers of type Math::VectorArray. More... | |
| struct | GradientVectorTraits< std::vector< V > > |
ForceField::GradientVectorTraits specialization for containers of type std::vector. More... | |
| class | MMFF94AngleBendingInteraction |
| Stores parameters for a single MMFF94 angle-bending interaction defined over an atom triplet. More... | |
| class | MMFF94AngleBendingInteractionParameterizer |
| Detects and parameterizes the MMFF94 angle-bending interactions of a molecular graph. More... | |
| class | MMFF94AngleBendingParameterTable |
| Data structure for the storage and lookup of MMFF94 angle-bending interaction parameters. More... | |
| class | MMFF94AromaticAtomTypeDefinitionTable |
| Data structure for the storage and lookup of MMFF94 aromatic atom type definitions. More... | |
| class | MMFF94AromaticSSSRSubset |
| Implements the extraction of all rings in the SSSR of a molecular graph that are considered aromatic according to the MMFF94 aromaticity model. More... | |
| class | MMFF94AtomTypePropertyTable |
| Data structure for the storage and lookup of structural and chemical property data associated with numeric MMFF94 atom types. More... | |
| class | MMFF94AtomTyper |
| Assigns MMFF94 symbolic and numeric atom types to the atoms of a molecular graph. More... | |
| class | MMFF94BondChargeIncrementTable |
| Data structure for the storage and lookup of MMFF94 bond charge increments. More... | |
| class | MMFF94BondStretchingInteraction |
| Stores parameters for a single MMFF94 bond-stretching interaction between two bonded atoms. More... | |
| class | MMFF94BondStretchingInteractionParameterizer |
| Detects and parameterizes the MMFF94 bond-stretching interactions of a molecular graph. More... | |
| class | MMFF94BondStretchingParameterTable |
| Data structure for the storage and lookup of MMFF94 bond-stretching interaction parameters. More... | |
| class | MMFF94BondStretchingRuleParameterTable |
| Data structure for the storage and lookup of MMFF94 bond-stretching interaction fallback parameters. More... | |
| class | MMFF94BondTyper |
| Assigns MMFF94 bond type indices to the bonds of a molecular graph. More... | |
| class | MMFF94ChargeCalculator |
| Calculator for the MMFF94 partial atomic charges of a molecular graph. More... | |
| class | MMFF94DefaultStretchBendParameterTable |
| Data structure for the storage and lookup of MMFF94 stretch-bend interaction fallback parameters. More... | |
| class | MMFF94ElectrostaticInteraction |
| Stores parameters for a single MMFF94 electrostatic interaction between two non-bonded atoms. More... | |
| class | MMFF94ElectrostaticInteractionParameterizer |
| Detects and parameterizes the MMFF94 electrostatic interactions of a molecular graph. More... | |
| class | MMFF94EnergyCalculator |
| Calculates the total MMFF94 force field energy for a set of atom 3D coordinates. More... | |
| class | MMFF94FormalAtomChargeDefinitionTable |
| Data structure for the storage and lookup of formal charge definitions used by the MMFF94 charge model. More... | |
| class | MMFF94GradientCalculator |
| Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates. More... | |
| class | MMFF94HeavyToHydrogenAtomTypeMap |
| Data structure for the storage and lookup of heavy-to-hydrogen symbolic MMFF94 atom type mappings. More... | |
| class | MMFF94InteractionData |
| Container holding the full set of MMFF94 interaction parameter records for a molecular graph. More... | |
| class | MMFF94InteractionParameterizer |
| Highly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization. More... | |
| class | MMFF94OutOfPlaneBendingInteraction |
| Stores parameters for a single MMFF94 out-of-plane bending interaction at a trigonal center. More... | |
| class | MMFF94OutOfPlaneBendingInteractionParameterizer |
| Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph. More... | |
| class | MMFF94OutOfPlaneBendingParameterTable |
| Data structure for the storage and lookup of MMFF94 out-of-plane bending interaction force constants. More... | |
| class | MMFF94PartialBondChargeIncrementTable |
| Data structure for the storage and lookup of MMFF94 per-atom partial bond charge increment and formal charge adjustment factors. More... | |
| class | MMFF94PrimaryToParameterAtomTypeMap |
| Data structure for the storage and lookup of primary numeric MMFF94 atom type to fallback parameter atom type list mappings. More... | |
| class | MMFF94StretchBendInteraction |
| Stores paramters for a single MMFF94 stretch-bend coupling interaction. More... | |
| class | MMFF94StretchBendInteractionParameterizer |
| Detects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph. More... | |
| class | MMFF94StretchBendParameterTable |
| Data structure for the storage and lookup of MMFF94 stretch-bend interaction parameters. More... | |
| class | MMFF94SymbolicAtomTypePatternTable |
| Data structure storing SMARTS substructure patterns used to assign symbolic MMFF94 atom types during atom typing. More... | |
| class | MMFF94SymbolicToNumericAtomTypeMap |
| Lookup table mapping each symbolic MMFF94 atom type to its corresponding numeric MMFF94 atom type. More... | |
| class | MMFF94TorsionInteraction |
| Stores parameters for a single MMFF94 torsion interaction over an atom quadruplet i-j-k-l. More... | |
| class | MMFF94TorsionInteractionParameterizer |
| Detects and parameterizes the MMFF94 torsion interactions of a molecular graph. More... | |
| class | MMFF94TorsionParameterTable |
| Data structure for the storage and lookup of MMFF94 torsion interaction parameters. More... | |
| class | MMFF94VanDerWaalsInteraction |
| Stores parameters for a single MMFF94 Van der Waals interaction between two non-bonded atoms. More... | |
| class | MMFF94VanDerWaalsInteractionParameterizer |
| Detects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph. More... | |
| class | MMFF94VanDerWaalsParameterTable |
| Data structure for the storage and lookup of MMFF94 interaction parameters. More... | |
| class | UFFAtomTypePropertyTable |
| Data structure for the storage and lookup of various properties associated with numeric UFF atom types. More... | |
Typedefs | |
| typedef Util::Array< ElasticPotential > | ElasticPotentialList |
| Data structure for the storage of elastic potential parameter set records. More... | |
| typedef std::function< bool(const Chem::Atom &, const Chem::Atom &)> | InteractionFilterFunction2 |
| Generic wrapper for storing user-defined two-atom interaction filtering functions (see [FUNWRP]). More... | |
| typedef std::function< bool(const Chem::Atom &, const Chem::Atom &, const Chem::Atom &)> | InteractionFilterFunction3 |
| Generic wrapper for storing user-defined three-atom interaction filtering functions (see [FUNWRP]). More... | |
| typedef std::function< bool(const Chem::Atom &, const Chem::Atom &, const Chem::Atom &, const Chem::Atom &)> | InteractionFilterFunction4 |
| Generic wrapper for storing user-defined four-atom interaction filtering functions (see [FUNWRP]). More... | |
| typedef Util::Array< MMFF94AngleBendingInteraction > | MMFF94AngleBendingInteractionList |
| Data structure for the storage of MMFF94 angle-bending interaction parameter records. More... | |
| typedef Util::Array< MMFF94BondStretchingInteraction > | MMFF94BondStretchingInteractionList |
| Data structure for the storage of MMFF94 bond-stretching interaction parameter records. More... | |
| typedef Util::Array< MMFF94ElectrostaticInteraction > | MMFF94ElectrostaticInteractionList |
| Data structure for the storage of MMFF94 electrostatic interaction parameter records. More... | |
| typedef Util::Array< MMFF94OutOfPlaneBendingInteraction > | MMFF94OutOfPlaneBendingInteractionList |
| Data structure for the storage of MMFF94 out-of-plane bending interaction parameter records. More... | |
| typedef std::function< unsigned int(const Chem::Atom &)> | MMFF94NumericAtomTypeFunction |
| Generic wrapper class used to store a user-defined numeric MMFF94 atom type retrieval function. More... | |
| typedef std::function< const std::string &(const Chem::Atom &)> | MMFF94SymbolicAtomTypeFunction |
| Generic wrapper class used to store a user-defined symbolic MMFF94 atom type retrieval function. More... | |
| typedef std::function< double(const Chem::Atom &)> | MMFF94AtomChargeFunction |
| Generic wrapper class used to store a user-defined MMFF94 partial atom charge retrieval function. More... | |
| typedef std::function< unsigned int(const Chem::Bond &)> | MMFF94BondTypeIndexFunction |
| Generic wrapper class used to store a user-defined MMFF94 bond type index retrieval function. More... | |
| typedef std::function< const Chem::FragmentList::SharedPointer &(const Chem::MolecularGraph &)> | MMFF94RingSetFunction |
| Generic wrapper class used to store a user-defined MMFF94 ring set retrieval function. More... | |
| typedef Util::Array< MMFF94StretchBendInteraction > | MMFF94StretchBendInteractionList |
| Data structure for the storage of MMFF94 stretch-bend coupling interaction parameter records. More... | |
| typedef Util::Array< MMFF94TorsionInteraction > | MMFF94TorsionInteractionList |
| Data structure for the storage of MMFF94 torsion interaction parameter records. More... | |
| typedef Util::Array< MMFF94VanDerWaalsInteraction > | MMFF94VanDerWaalsInteractionList |
| Data structure for the storage of MMFF94 Van der Waals interaction parameter records. More... | |
| typedef std::function< std::size_t(const Chem::Atom &, const Chem::Atom &, const Chem::MolecularGraph &)> | TopologicalAtomDistanceFunction |
| Generic wrapper class used to store a user-defined topological atom-pair distance function. More... | |
Functions | |
| CDPL_FORCEFIELD_API const std::string & | getMMFF94SymbolicType (const Chem::Atom &atom) |
| Returns the value of the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API void | setMMFF94SymbolicType (Chem::Atom &atom, const std::string &type) |
| Sets the value of the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom to type. More... | |
| CDPL_FORCEFIELD_API void | clearMMFF94SymbolicType (Chem::Atom &atom) |
| Clears the value of the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API bool | hasMMFF94SymbolicType (const Chem::Atom &atom) |
| Tells whether the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom is set. More... | |
| CDPL_FORCEFIELD_API unsigned int | getMMFF94NumericType (const Chem::Atom &atom) |
| Returns the value of the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API void | setMMFF94NumericType (Chem::Atom &atom, unsigned int type) |
| Sets the value of the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom to type. More... | |
| CDPL_FORCEFIELD_API void | clearMMFF94NumericType (Chem::Atom &atom) |
| Clears the value of the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API bool | hasMMFF94NumericType (const Chem::Atom &atom) |
| Tells whether the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom is set. More... | |
| CDPL_FORCEFIELD_API double | getMMFF94Charge (const Chem::Atom &atom) |
| Returns the value of the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API void | setMMFF94Charge (Chem::Atom &atom, double charge) |
| Sets the value of the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom to charge. More... | |
| CDPL_FORCEFIELD_API void | clearMMFF94Charge (Chem::Atom &atom) |
| Clears the value of the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API bool | hasMMFF94Charge (const Chem::Atom &atom) |
| Tells whether the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom is set. More... | |
| CDPL_FORCEFIELD_API unsigned int | getUFFType (const Chem::Atom &atom) |
| Returns the value of the ForceField::AtomProperty::UFF_TYPE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API void | setUFFType (Chem::Atom &atom, unsigned int type) |
| Sets the value of the ForceField::AtomProperty::UFF_TYPE property of the atom atom to type. More... | |
| CDPL_FORCEFIELD_API void | clearUFFType (Chem::Atom &atom) |
| Clears the value of the ForceField::AtomProperty::UFF_TYPE property of the atom atom. More... | |
| CDPL_FORCEFIELD_API bool | hasUFFType (const Chem::Atom &atom) |
| Tells whether the ForceField::AtomProperty::UFF_TYPE property of the atom atom is set. More... | |
| CDPL_FORCEFIELD_API unsigned int | perceiveUFFType (const Chem::Atom &atom, const Chem::MolecularGraph &molgraph) |
| Perceives the UFF atom type of the atom atom in the context of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API unsigned int | getMMFF94TypeIndex (const Chem::Bond &bond) |
| Returns the value of the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond. More... | |
| CDPL_FORCEFIELD_API void | setMMFF94TypeIndex (Chem::Bond &bond, unsigned int type_idx) |
| Sets the value of the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond to type_idx. More... | |
| CDPL_FORCEFIELD_API void | clearMMFF94TypeIndex (Chem::Bond &bond) |
| Clears the value of the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond. More... | |
| CDPL_FORCEFIELD_API bool | hasMMFF94TypeIndex (const Chem::Bond &bond) |
| Tells whether the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond is set. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcElasticPotentialEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the energies calculated for the elastic potentials specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcElasticPotentialEnergy (const ElasticPotential &pot, const CoordsArray &coords) |
| Calculates the energy of a single elastic potential pot for the supplied atom coordinates coords. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcElasticPotentialEnergy (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, const ValueType &force_const, const ValueType &ref_length) |
| Calculates the energy \( E_{ij} \) of an elastic potential applied on a pair of atoms i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcElasticPotentialGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the energies and gradient contributions calculated for the elastic potentials specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcElasticPotentialGradient (const ElasticPotential &pot, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy and gradient contribution of a single elastic potential pot for the supplied atom coordinates coords. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcElasticPotentialGradient (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, GradVec &atom1_grad, GradVec &atom2_grad, const ValueType &force_const, const ValueType &ref_length) |
| Calculates the elastic potential energy gradient \( \nabla E_{ij} \) for a pair of atoms i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94BondStretchingEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the bond-stretching interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94BondStretchingEnergy (const MMFF94BondStretchingInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single bond-stretching interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94BondStretchingEnergy (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, const ValueType &force_const, const ValueType &ref_length) |
| Calculates the bond stretching interaction energy \( EB_{ij} \) for the bond i-j. More... | |
| template<typename ValueType > | |
| ValueType | calcMMFF94BondStretchingEnergy (const ValueType &r_ij, const ValueType &force_const, const ValueType &ref_length) |
| Calculates the bond stretching interaction energy \( EB_{ij} \) for the bond i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94AngleBendingEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the angle-bending interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94AngleBendingEnergy (const MMFF94AngleBendingInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single angle-bending interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94AngleBendingEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, bool linear, const ValueType &force_const, const ValueType &ref_angle) |
| Calculates the angle bending interaction energy \( EA_{ijk} \) for two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94AngleBendingEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const ValueType &r_ij, const ValueType &r_jk, bool linear, const ValueType &force_const, const ValueType &ref_angle) |
| Calculates the angle bending interaction energy \( EA_{ijk} \) for two bonds i-j and j-k. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94StretchBendEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the stretch-bend coupling interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94StretchBendEnergy (const MMFF94StretchBendInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single stretch-bend coupling interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94StretchBendEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const ValueType &ijk_force_const, const ValueType &kji_force_const, const ValueType &ref_angle, const ValueType &ref_length1, const ValueType &ref_length2) |
| Calculates the stretch-bend interaction energy \( EBA_{ijk} \) for two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94StretchBendEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const ValueType &r_ij, const ValueType &r_jk, const ValueType &ijk_force_const, const ValueType &kji_force_const, const ValueType &ref_angle, const ValueType &ref_length1, const ValueType &ref_length2) |
| Calculates the stretch-bend interaction energy \( EBA_{ijk} \) for two bonds i-j and j-k. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94OutOfPlaneBendingEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the out-of-plane bending interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94OutOfPlaneBendingEnergy (const MMFF94OutOfPlaneBendingInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single out-of-plane bending interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94OutOfPlaneBendingEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const CoordsVec &oop_atom_pos, const ValueType &force_const) |
| Calculates the out-of-plane bending interaction energy \( EOOP_{ijk;l} \) for the bond j-l and the plane i-j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94OutOfPlaneBendingEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const CoordsVec &oop_atom_pos, const ValueType &r_jl, const ValueType &force_const) |
| Calculates the out-of-plane bending interaction energy \( EOOP_{ijk;l} \) for the bond j-l and the plane i-j-k. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94TorsionEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the torsion interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94TorsionEnergy (const MMFF94TorsionInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single torsion interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94TorsionEnergy (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom1_pos, const CoordsVec &ctr_atom2_pos, const CoordsVec &term_atom2_pos, const ValueType &tor_param1, const ValueType &tor_param2, const ValueType &tor_param3) |
| Calculates the torsion interaction energy \( ET_{ijkl} \) for the central bond j-k and the connected bonds i-j and k-l. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94ElectrostaticEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the electrostatic interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94ElectrostaticEnergy (const MMFF94ElectrostaticInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single electrostatic interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94ElectrostaticEnergy (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, const ValueType &atom1_chg, const ValueType &atom2_chg, const ValueType &scale_fact, const ValueType &de_const, const ValueType &dist_expo) |
| Calculates the electrostatic interaction energy \( EQ_{ij} \) for the atom pair i-j. More... | |
| template<typename ValueType > | |
| ValueType | calcMMFF94ElectrostaticEnergy (const ValueType &r_ij, const ValueType &atom1_chg, const ValueType &atom2_chg, const ValueType &scale_fact, const ValueType &de_const, const ValueType &dist_expo) |
| Calculates the electrostatic interaction energy \( EQ_{ij} \) for the atom pair i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray > | |
| ValueType | calcMMFF94VanDerWaalsEnergy (Iter beg, const Iter &end, const CoordsArray &coords) |
| Accumulates the Van der Waals interaction energies calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray > | |
| ValueType | calcMMFF94VanDerWaalsEnergy (const MMFF94VanDerWaalsInteraction &iaction, const CoordsArray &coords) |
| Calculates the energy of a single Van der Waals interaction iaction. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcMMFF94VanDerWaalsEnergy (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, const ValueType &e_IJ, const ValueType &r_IJ, const ValueType &r_IJ_7) |
| Calculates the Van der Waals interaction energy \( E_{vdW_{ij}} \) for the atom pair i-j. More... | |
| template<typename ValueType > | |
| ValueType | calcMMFF94VanDerWaalsEnergy (const ValueType &r_ij, const ValueType &e_IJ, const ValueType &r_IJ, const ValueType &r_IJ_7) |
| Calculates the Van der Waals interaction energy \( E_{vdW_{ij}} \) for the atom pair i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94BondStretchingGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the bond-stretching interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94BondStretchingGradient (const MMFF94BondStretchingInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single bond-stretching interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94BondStretchingGradient (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, GradVec &atom1_grad, GradVec &atom2_grad, const ValueType &force_const, const ValueType &ref_length) |
| Calculates the bond stretching interaction energy gradient \( \nabla EB_{ij} \) for the bond i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94AngleBendingGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the angle-bending interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94AngleBendingGradient (const MMFF94AngleBendingInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single angle-bending interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94AngleBendingGradient (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, GradVec &term_atom1_grad, GradVec &ctr_atom_grad, GradVec &term_atom2_grad, bool linear, const ValueType &force_const, const ValueType &ref_angle) |
| Calculates the angle bending interaction energy gradient \( \nabla EA_{ijk} \) for two bonds i-j and j-k. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94StretchBendGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the stretch-bend coupling interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94StretchBendGradient (const MMFF94StretchBendInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single stretch-bend coupling interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94StretchBendGradient (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, GradVec &term_atom1_grad, GradVec &ctr_atom_grad, GradVec &term_atom2_grad, const ValueType &ijk_force_const, const ValueType &kji_force_const, const ValueType &ref_angle, const ValueType &ref_length1, const ValueType &ref_length2) |
| Calculates the stretch-bend interaction energy gradient \( \nabla EBA_{ijk} \) for two bonds i-j and j-k. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94OutOfPlaneBendingGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the out-of-plane bending interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94OutOfPlaneBendingGradient (const MMFF94OutOfPlaneBendingInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single out-of-plane bending interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94OutOfPlaneBendingGradient (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const CoordsVec &oop_atom_pos, GradVec &term_atom1_grad, GradVec &ctr_atom_grad, GradVec &term_atom2_grad, GradVec &oop_atom_grad, const ValueType &force_const) |
| Calculates the out-of-plane bending interaction energy gradient \( \nabla EOOP_{ijk;l} \) for the bond j-l and the plane i-j-k. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94TorsionGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the torsion interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94TorsionGradient (const MMFF94TorsionInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single torsion interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94TorsionGradient (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom1_pos, const CoordsVec &ctr_atom2_pos, const CoordsVec &term_atom2_pos, GradVec &term_atom1_grad, GradVec &ctr_atom1_grad, GradVec &ctr_atom2_grad, GradVec &term_atom2_grad, const ValueType &tor_param1, const ValueType &tor_param2, const ValueType &tor_param3) |
| Calculates the torsion interaction energy gradient \( \nabla ET_{ijkl} \) for the central bond j-k and the connected bonds i-j and k-l. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94ElectrostaticGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the electrostatic interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94ElectrostaticGradient (const MMFF94ElectrostaticInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single electrostatic interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94ElectrostaticGradient (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, GradVec &atom1_grad, GradVec &atom2_grad, const ValueType &atom1_chg, const ValueType &atom2_chg, const ValueType &scale_fact, const ValueType &de_const, const ValueType &dist_expo) |
| Calculates the electrostatic interaction energy gradient \( \nabla EQ_{ij} \) for the atom pair i-j. More... | |
| template<typename ValueType , typename Iter , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94VanDerWaalsGradient (Iter beg, const Iter &end, const CoordsArray &coords, GradVector &grad) |
| Accumulates the Van der Waals interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range. More... | |
| template<typename ValueType , typename CoordsArray , typename GradVector > | |
| ValueType | calcMMFF94VanDerWaalsGradient (const MMFF94VanDerWaalsInteraction &iaction, const CoordsArray &coords, GradVector &grad) |
| Calculates the energy of a single Van der Waals interaction iaction and accumulates the corresponding per-atom gradient contributions. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcMMFF94VanDerWaalsGradient (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, GradVec &atom1_grad, GradVec &atom2_grad, const ValueType &e_IJ, const ValueType &r_IJ, const ValueType &r_IJ_7) |
| Calculates the Van der Waals interaction energy gradient \( \nabla E_{vdW_{ij}} \) for the atom pair i-j. More... | |
| CDPL_FORCEFIELD_API const Chem::FragmentList::SharedPointer & | getMMFF94AromaticRings (const Chem::MolecularGraph &molgraph) |
| Returns the value of the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API void | setMMFF94AromaticRings (Chem::MolecularGraph &molgraph, const Chem::FragmentList::SharedPointer &rings) |
| Sets the value of the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph to rings. More... | |
| CDPL_FORCEFIELD_API void | clearMMFF94AromaticRings (Chem::MolecularGraph &molgraph) |
| Clears the value of the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API bool | hasMMFF94AromaticRings (const Chem::MolecularGraph &molgraph) |
| Tells whether the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph is set. More... | |
| CDPL_FORCEFIELD_API Chem::FragmentList::SharedPointer | perceiveMMFF94AromaticRings (const Chem::MolecularGraph &molgraph) |
| Perceives the list of MMFF94 aromatic rings of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API Chem::FragmentList::SharedPointer | perceiveMMFF94AromaticRings (Chem::MolecularGraph &molgraph, bool overwrite) |
| Perceives and (optionally) stores the list of MMFF94 aromatic rings of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API void | assignMMFF94AtomTypes (Chem::MolecularGraph &molgraph, bool strict, bool overwrite) |
| Assigns MMFF94 atom types to the atoms of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API void | assignMMFF94BondTypeIndices (Chem::MolecularGraph &molgraph, bool strict, bool overwrite) |
| Assigns MMFF94 bond type indices to the bonds of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API void | calcMMFF94AtomCharges (Chem::MolecularGraph &molgraph, bool strict, bool overwrite) |
| Calculates and assigns MMFF94 partial atomic charges to the atoms of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API void | assignUFFAtomTypes (Chem::MolecularGraph &molgraph, bool overwrite) |
| Assigns UFF atom types to the atoms of the molecular graph molgraph. More... | |
| CDPL_FORCEFIELD_API void | filterInteractions (const MMFF94InteractionData &ia_data, MMFF94InteractionData &filtered_ia_data, const Util::BitSet &inc_atom_mask) |
| Filters an MMFF94 interaction data set, retaining only those interactions that exclusively reference atoms in inc_atom_mask. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcSquaredDistance (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos) |
| Calculates the squared distance \( r_{ij}^2 \) between two atoms i and j. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcDistance (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos) |
| Calculates the distance \( r_{ij} \) between two atoms i and j. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcBondLengthsAndAngleCos (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, ValueType &bond_length1, ValueType &bond_length2) |
| Calculates bond lengths \( r_{ij} \) and \( r_{jk} \) and the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcBondLengthsAndAngle (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, ValueType &bond_length1, ValueType &bond_length2) |
| Calculates bond lengths \( r_{ij} \) and \( r_{jk} \) and the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcBondAngleCos (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos) |
| Calculates the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcBondAngleCos (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const ValueType &r_ij, const ValueType &r_jk) |
| Calculates the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcBondAngle (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos) |
| Calculates the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcBondAngle (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const ValueType &r_ij, const ValueType &r_jk) |
| Calculates the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcOutOfPlaneAngle (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const CoordsVec &oop_atom_pos) |
| Calculates the out-of-plane angle \( \chi_{ijk;l} \) between the bond j-l and the plane defined by the atoms i-j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcOutOfPlaneAngle (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const CoordsVec &oop_atom_pos, const ValueType &r_jl) |
| Calculates the out-of-plane angle \( \chi_{ijk;l} \) between the bond j-l and the plane defined by the atoms i-j-k. More... | |
| template<typename ValueType , typename CoordsVec > | |
| ValueType | calcDihedralAngleCos (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom1_pos, const CoordsVec &ctr_atom2_pos, const CoordsVec &term_atom2_pos) |
| Calculates the cosine of the dihedral angle \( \Phi_{ijkl} \) between the planes defined by the atom triplets i-j-k and j-k-l. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcDistanceDerivatives (const CoordsVec &atom1_pos, const CoordsVec &atom2_pos, GradVec &atom1_deriv, GradVec &atom2_deriv) |
| Calculates the partial derivatives \( \frac{\partial r_{ij}}{\partial \vec{p_x}} \) of the distance \( r_{ij} \) between two atoms i and j. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcBondAngleCosDerivatives (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, GradVec &term_atom1_deriv, GradVec &ctr_atom_deriv, GradVec &term_atom2_deriv) |
| Calculates the partial derivatives \( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_x}} \) of the of the cosine of the angle \( \vartheta_{ijk} \) between the bonds i-j and j-k. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcDihedralAngleCosDerivatives (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom1_pos, const CoordsVec &ctr_atom2_pos, const CoordsVec &term_atom2_pos, GradVec &term_atom1_deriv, GradVec &ctr_atom1_deriv, GradVec &ctr_atom2_deriv, GradVec &term_atom2_deriv) |
| Calculates the partial derivatives \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_x}} \) of the cosine of the angle \( \Phi_{ijkl} \) between the planes defined by the atom triplets i-j-k and j-k-l. More... | |
| template<typename ValueType , typename CoordsVec , typename GradVec > | |
| ValueType | calcOutOfPlaneAngleCosDerivatives (const CoordsVec &term_atom1_pos, const CoordsVec &ctr_atom_pos, const CoordsVec &term_atom2_pos, const CoordsVec &oop_atom_pos, GradVec &term_atom1_deriv, GradVec &ctr_atom_deriv, GradVec &term_atom2_deriv, GradVec &oop_atom_deriv) |
| Calculates the partial derivatives \( \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_x}} \) of the cosine of the angle \( \omega_{ijk;l} \) between the bond j-l and the normal of the plane defined by the atoms i-j-k. More... | |
Contains classes and functions related to molecular force fields.
Data structure for the storage of elastic potential parameter set records.
| typedef std::function<bool(const Chem::Atom&, const Chem::Atom&)> CDPL::ForceField::InteractionFilterFunction2 |
Generic wrapper for storing user-defined two-atom interaction filtering functions (see [FUNWRP]).
The function is invoked with the two interacting atoms and is expected to return true if the interaction should be considered, and false if it should be skipped.
| typedef std::function<bool(const Chem::Atom&, const Chem::Atom&, const Chem::Atom&)> CDPL::ForceField::InteractionFilterFunction3 |
Generic wrapper for storing user-defined three-atom interaction filtering functions (see [FUNWRP]).
The function is invoked with the three interacting atoms (typically used for angle-bending and stretch-bend interactions) and is expected to return true if the interaction should be considered, and false if it should be skipped.
| typedef std::function<bool(const Chem::Atom&, const Chem::Atom&, const Chem::Atom&, const Chem::Atom&)> CDPL::ForceField::InteractionFilterFunction4 |
Generic wrapper for storing user-defined four-atom interaction filtering functions (see [FUNWRP]).
The function is invoked with the four interacting atoms (typically used for torsion and out-of-plane bending interactions) and is expected to return true if the interaction should be considered, and false if it should be skipped.
| typedef Util::Array<MMFF94AngleBendingInteraction> CDPL::ForceField::MMFF94AngleBendingInteractionList |
Data structure for the storage of MMFF94 angle-bending interaction parameter records.
| typedef Util::Array<MMFF94BondStretchingInteraction> CDPL::ForceField::MMFF94BondStretchingInteractionList |
Data structure for the storage of MMFF94 bond-stretching interaction parameter records.
| typedef Util::Array<MMFF94ElectrostaticInteraction> CDPL::ForceField::MMFF94ElectrostaticInteractionList |
Data structure for the storage of MMFF94 electrostatic interaction parameter records.
| typedef Util::Array<MMFF94OutOfPlaneBendingInteraction> CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionList |
Data structure for the storage of MMFF94 out-of-plane bending interaction parameter records.
| typedef std::function<unsigned int(const Chem::Atom&)> CDPL::ForceField::MMFF94NumericAtomTypeFunction |
Generic wrapper class used to store a user-defined numeric MMFF94 atom type retrieval function.
| typedef std::function<const std::string&(const Chem::Atom&)> CDPL::ForceField::MMFF94SymbolicAtomTypeFunction |
Generic wrapper class used to store a user-defined symbolic MMFF94 atom type retrieval function.
| typedef std::function<double(const Chem::Atom&)> CDPL::ForceField::MMFF94AtomChargeFunction |
Generic wrapper class used to store a user-defined MMFF94 partial atom charge retrieval function.
| typedef std::function<unsigned int(const Chem::Bond&)> CDPL::ForceField::MMFF94BondTypeIndexFunction |
Generic wrapper class used to store a user-defined MMFF94 bond type index retrieval function.
| typedef std::function<const Chem::FragmentList::SharedPointer&(const Chem::MolecularGraph&)> CDPL::ForceField::MMFF94RingSetFunction |
Generic wrapper class used to store a user-defined MMFF94 ring set retrieval function.
| typedef Util::Array<MMFF94StretchBendInteraction> CDPL::ForceField::MMFF94StretchBendInteractionList |
Data structure for the storage of MMFF94 stretch-bend coupling interaction parameter records.
Data structure for the storage of MMFF94 torsion interaction parameter records.
| typedef Util::Array<MMFF94VanDerWaalsInteraction> CDPL::ForceField::MMFF94VanDerWaalsInteractionList |
Data structure for the storage of MMFF94 Van der Waals interaction parameter records.
| typedef std::function<std::size_t(const Chem::Atom&, const Chem::Atom&, const Chem::MolecularGraph&)> CDPL::ForceField::TopologicalAtomDistanceFunction |
Generic wrapper class used to store a user-defined topological atom-pair distance function.
| CDPL_FORCEFIELD_API const std::string& CDPL::ForceField::getMMFF94SymbolicType | ( | const Chem::Atom & | atom | ) |
Returns the value of the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::setMMFF94SymbolicType | ( | Chem::Atom & | atom, |
| const std::string & | type | ||
| ) |
Sets the value of the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom to type.
| atom | The atom for which to set the property value. |
| type | The new symbolic MMFF94 atom type. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::clearMMFF94SymbolicType | ( | Chem::Atom & | atom | ) |
Clears the value of the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| CDPL_FORCEFIELD_API bool CDPL::ForceField::hasMMFF94SymbolicType | ( | const Chem::Atom & | atom | ) |
Tells whether the ForceField::AtomProperty::MMFF94_SYMBOLIC_TYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
true if the symbolic MMFF94 atom type is set, and false otherwise. | CDPL_FORCEFIELD_API unsigned int CDPL::ForceField::getMMFF94NumericType | ( | const Chem::Atom & | atom | ) |
Returns the value of the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::setMMFF94NumericType | ( | Chem::Atom & | atom, |
| unsigned int | type | ||
| ) |
Sets the value of the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom to type.
| atom | The atom for which to set the property value. |
| type | The new numeric MMFF94 atom type. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::clearMMFF94NumericType | ( | Chem::Atom & | atom | ) |
Clears the value of the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| CDPL_FORCEFIELD_API bool CDPL::ForceField::hasMMFF94NumericType | ( | const Chem::Atom & | atom | ) |
Tells whether the ForceField::AtomProperty::MMFF94_NUMERIC_TYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
true if the numeric MMFF94 atom type is set, and false otherwise. | CDPL_FORCEFIELD_API double CDPL::ForceField::getMMFF94Charge | ( | const Chem::Atom & | atom | ) |
Returns the value of the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom.
| atom | The atom for which to return the property value. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::setMMFF94Charge | ( | Chem::Atom & | atom, |
| double | charge | ||
| ) |
Sets the value of the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom to charge.
| atom | The atom for which to set the property value. |
| charge | The new MMFF94 partial atomic charge. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::clearMMFF94Charge | ( | Chem::Atom & | atom | ) |
Clears the value of the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom.
| atom | The atom for which to clear the property value. |
| CDPL_FORCEFIELD_API bool CDPL::ForceField::hasMMFF94Charge | ( | const Chem::Atom & | atom | ) |
Tells whether the ForceField::AtomProperty::MMFF94_CHARGE property of the atom atom is set.
| atom | The atom for which to query the property value. |
true if the MMFF94 partial atomic charge is set, and false otherwise. | CDPL_FORCEFIELD_API unsigned int CDPL::ForceField::getUFFType | ( | const Chem::Atom & | atom | ) |
Returns the value of the ForceField::AtomProperty::UFF_TYPE property of the atom atom.
| atom | The atom for which to return the property value. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::setUFFType | ( | Chem::Atom & | atom, |
| unsigned int | type | ||
| ) |
Sets the value of the ForceField::AtomProperty::UFF_TYPE property of the atom atom to type.
| atom | The atom for which to set the property value. |
| type | The new numeric UFF atom type. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::clearUFFType | ( | Chem::Atom & | atom | ) |
Clears the value of the ForceField::AtomProperty::UFF_TYPE property of the atom atom.
| atom | The atom for which to clear the property value. |
| CDPL_FORCEFIELD_API bool CDPL::ForceField::hasUFFType | ( | const Chem::Atom & | atom | ) |
Tells whether the ForceField::AtomProperty::UFF_TYPE property of the atom atom is set.
| atom | The atom for which to query the property value. |
true if the numeric UFF atom type is set, and false otherwise. | CDPL_FORCEFIELD_API unsigned int CDPL::ForceField::perceiveUFFType | ( | const Chem::Atom & | atom, |
| const Chem::MolecularGraph & | molgraph | ||
| ) |
Perceives the UFF atom type of the atom atom in the context of the molecular graph molgraph.
| atom | The atom whose UFF type is to be perceived. |
| molgraph | The molecular graph providing the atom environment for type perception. |
| CDPL_FORCEFIELD_API unsigned int CDPL::ForceField::getMMFF94TypeIndex | ( | const Chem::Bond & | bond | ) |
Returns the value of the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond.
| bond | The bond for which to return the property value. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::setMMFF94TypeIndex | ( | Chem::Bond & | bond, |
| unsigned int | type_idx | ||
| ) |
Sets the value of the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond to type_idx.
| bond | The bond for which to set the property value. |
| type_idx | The new MMFF94 bond type index. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::clearMMFF94TypeIndex | ( | Chem::Bond & | bond | ) |
Clears the value of the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond.
| bond | The bond for which to clear the property value. |
| CDPL_FORCEFIELD_API bool CDPL::ForceField::hasMMFF94TypeIndex | ( | const Chem::Bond & | bond | ) |
Tells whether the ForceField::BondProperty::MMFF94_TYPE_INDEX property of the bond bond is set.
| bond | The bond for which to query the property value. |
true if the MMFF94 bond type index is set, and false otherwise. | ValueType CDPL::ForceField::calcElasticPotentialEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the energies calculated for the elastic potentials specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::ElasticPotential instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first elastic potential parameter record. |
| end | Iterator pointing one past the last elastic potential parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcElasticPotentialEnergy | ( | const ElasticPotential & | pot, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single elastic potential pot for the supplied atom coordinates coords.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| pot | The parameters of the elastic potential to evaluate. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcElasticPotentialEnergy | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_length | ||
| ) |
Calculates the energy \( E_{ij} \) of an elastic potential applied on a pair of atoms i-j.
\( E_{ij} = k_{ij} \: \Delta r_{ij}^2 \)
where
\( k_{ij} \) = the force constant of the elastic potential.
\( \Delta r_{ij} \) = \( r_{ij} - r_{ij}^0 \), the difference between actual and reference distance of the atoms i and j.
| atom1_pos | The position of atom i. |
| atom2_pos | The position of atom j. |
| force_const | The force constant \( k_{ij} \). |
| ref_length | The reference distance \( r_{ij}^0 \). |
| ValueType CDPL::ForceField::calcElasticPotentialGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the energies and gradient contributions calculated for the elastic potentials specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::ElasticPotential instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first elastic potential parameter record. |
| end | Iterator pointing one past the last elastic potential parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcElasticPotentialGradient | ( | const ElasticPotential & | pot, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy and gradient contribution of a single elastic potential pot for the supplied atom coordinates coords.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| pot | The parameters of the elastic potential to evaluate. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcElasticPotentialGradient | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| GradVec & | atom1_grad, | ||
| GradVec & | atom2_grad, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_length | ||
| ) |
Calculates the elastic potential energy gradient \( \nabla E_{ij} \) for a pair of atoms i-j.
Energy function:
\( E_{ij} = k_{ij} \: \Delta r_{ij}^2 \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial E_{ij}}{\partial \vec{p_x}} = \frac{\partial E_{ij}}{\partial \Delta r_{ij}} \: \frac{\partial \Delta r_{ij}}{\partial \vec{p_x}} \)
\( \frac{\partial E_{ij}}{\partial \Delta r_{ij}} = 2 \: \Delta r_{ij} \: k_{ij} \)
for the calculation of the partial derivatives \( \frac{\partial \Delta r_{ij}}{\partial \vec{p_x}} \) see calcDistanceDerivatives().
where
\( k_{ij} \) = the force constant of the elastic potential.
\( \Delta r_{ij} \) = \( r_{ij} - r_{ij}^0 \), the difference between actual and reference distance of the atoms i and j.
\( \vec{p_x} \) = coordinates of the atoms i and j.
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| atom2_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| force_const | The force constant \( k_{ij} \). |
| ref_length | The reference distance \( r_{ij}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the bond-stretching interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94BondStretchingInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingEnergy | ( | const MMFF94BondStretchingInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single bond-stretching interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 bond-stretching interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingEnergy | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_length | ||
| ) |
Calculates the bond stretching interaction energy \( EB_{ij} \) for the bond i-j.
\( EB_{ij} = 143.9325 \: \frac{kb_{IJ}}{2} \: \Delta r_{ij}^2 \: (1 + cs \: \Delta r_{ij} + \frac{7}{12} \: cs^2 \: \Delta r_{ij}^2) \)
where
\( kb_{IJ} \) = the bond stretching force constant in \( \frac{md}{Ang} \) for bonded atoms i and j of types I and J.
\( \Delta r_{ij} \) = \( r_{ij} - r_{IJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms i and j of types I and J (see calcDistance()).
\( cs \) = \( -2 \: Ang^{-1} \), the "cubic stretch" constant.
Note: throughout this description, the indices i, j, k, ... represent atoms; I, J, K, ... denote the corresponding numerical MMFF atom types (or, occasionally, the atomic species).
| atom1_pos | The position of atom i. |
| atom2_pos | The position of atom j. |
| force_const | The bond stretching force constant \( kb_{IJ} \). |
| ref_length | The reference bond length \( r_{IJ}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingEnergy | ( | const ValueType & | r_ij, |
| const ValueType & | force_const, | ||
| const ValueType & | ref_length | ||
| ) |
Calculates the bond stretching interaction energy \( EB_{ij} \) for the bond i-j.
\( EB_{ij} = 143.9325 \: \frac{kb_{IJ}}{2} \: \Delta r_{ij}^2 \: (1 + cs \: \Delta r_{ij} + \frac{7}{12} \: cs^2 \: \Delta r_{ij}^2) \)
where
\( kb_{IJ} \) = the bond stretching force constant in \( \frac{md}{Ang} \) for bonded atoms i and j of types I and J.
\( \Delta r_{ij} \) = \( r_{ij} - r_{IJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms i and j of types I and J (see calcDistance()).
\( cs \) = \( -2 \: Ang^{-1} \), the "cubic stretch" constant.
Note: throughout this description, the indices i, j, k, ... represent atoms; I, J, K, ... denote the corresponding numerical MMFF atom types (or, occasionally, the atomic species).
| r_ij | The length of the bond between atom i and j. |
| force_const | The bond stretching force constant \( kb_{IJ} \). |
| ref_length | The reference bond length \( r_{IJ}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the angle-bending interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94AngleBendingInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingEnergy | ( | const MMFF94AngleBendingInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single angle-bending interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 angle-bending interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| bool | linear, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_angle | ||
| ) |
Calculates the angle bending interaction energy \( EA_{ijk} \) for two bonds i-j and j-k.
\( EA_{ijk} = 0.043844 \: \frac{ka_{IJK}}{2} \: \Delta \vartheta_{ijk}^2 \: (1 + cb \: \Delta \vartheta_{ijk}) \)
where
\( ka_{IJK} \) = angle bending force constant in \( \frac{md Ang}{rad^2} \) for the angle between atoms i, j and k of atom types I, J and K.
\( \Delta \vartheta_{ijk} \) = \( \vartheta_{ijk} - \vartheta_{IJK}^0 \), the difference between actual and reference i-j-k bond angles in degrees (see calcBondAngle()).
\( cb \) = \( -0.007 \: deg^{-1} \), the "cubic-bend" constant.
For linear or near-linear bond angles such as those which occur in alkynes, nitriles, isonitriles, azides, and diazo compounds, the form used in DREIDING and UFF is employed:
\( EA_{ijk} = 143.9325 \: ka_{IJK} \:(1 + \cos(\vartheta_{ijk})) \)
where \( ka_{IJK} \) and \( \vartheta_{ijk} \) are defined as above.
| term_atom1_pos | The position of atom i. |
| ctr_atom_pos | The position of the central atom j. |
| term_atom2_pos | The position of atom k. |
| linear | If true, the bond angle is linear. |
| force_const | The angle bending force constant \( ka_{IJK} \). |
| ref_angle | The reference bond angle \( \vartheta_{IJK}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const ValueType & | r_ij, | ||
| const ValueType & | r_jk, | ||
| bool | linear, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_angle | ||
| ) |
Calculates the angle bending interaction energy \( EA_{ijk} \) for two bonds i-j and j-k.
\( EA_{ijk} = 0.043844 \: \frac{ka_{IJK}}{2} \: \Delta \vartheta_{ijk}^2 \: (1 + cb \: \Delta \vartheta_{ijk}) \)
where
\( ka_{IJK} \) = angle bending force constant in \( \frac{md Ang}{rad^2} \) for the angle between atoms i, j and k of atom types I, J and K.
\( \Delta \vartheta_{ijk} \) = \( \vartheta_{ijk} - \vartheta_{IJK}^0 \), the difference between actual and reference i-j-k bond angles in degrees (see calcBondAngle()).
\( cb \) = \( -0.007 \: deg^{-1} \), the "cubic-bend" constant.
For linear or near-linear bond angles such as those which occur in alkynes, nitriles, isonitriles, azides, and diazo compounds, the form used in DREIDING and UFF is employed:
\( EA_{ijk} = 143.9325 \: ka_{IJK} \:(1 + \cos(\vartheta_{ijk})) \)
where \( ka_{IJK} \) and \( \vartheta_{ijk} \) are defined as above.
| term_atom1_pos | The position of atom i. |
| ctr_atom_pos | The position of the central atom j. |
| term_atom2_pos | The position of atom k. |
| r_ij | The length of the bond between atom i and j. |
| r_jk | The length of the bond between atom j and k. |
| linear | If true, the bond angle is linear. |
| force_const | The angle bending force constant \( ka_{IJK} \). |
| ref_angle | The reference bond angle \( \vartheta_{IJK}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94StretchBendEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the stretch-bend coupling interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94StretchBendInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94StretchBendEnergy | ( | const MMFF94StretchBendInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single stretch-bend coupling interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 stretch-bend interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94StretchBendEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const ValueType & | ijk_force_const, | ||
| const ValueType & | kji_force_const, | ||
| const ValueType & | ref_angle, | ||
| const ValueType & | ref_length1, | ||
| const ValueType & | ref_length2 | ||
| ) |
Calculates the stretch-bend interaction energy \( EBA_{ijk} \) for two bonds i-j and j-k.
\( EBA_{ijk} = 2.51210 \: (kba_{IJK} \: \Delta r_{ij} + kba_{KJI} \: \Delta r_{kj}) \: \Delta \vartheta_{ijk} \)
where
\( kba_{IJK} \) = force constant in \( \frac{md}{rad} \) for i-j stretch coupled to i-j-k bend.
\( kba_{KJI} \) = force constant in \( \frac{md}{rad} \) for k-j stretch coupled to i-j-k bend.
\( \Delta r_{ij} \) = \( r_{ij} - r_{IJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms i and j of types I and J.
\( \Delta r_{kj} \) = \( r_{kj} - r_{KJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms k and j of types K and J.
\( \Delta \vartheta_{ijk} \) = \( \vartheta_{ijk} - \vartheta_{IJK}^0 \), the difference between actual and reference i-j-k bond angles in degrees.
For the calculation of \( r_{ij} \), \( r_{kj} \), and \( \vartheta_{ijk} \) see calcBondLengthsAndAngle().
Currently, stretch-bend interactions are omitted when the i-j-k interaction corresponds to a linear bond angle.
| term_atom1_pos | The position of atom i. |
| ctr_atom_pos | The position of the central atom j. |
| term_atom2_pos | The position of atom k. |
| ijk_force_const | The stretch-bend force constant \( kba_{IJK} \). |
| kji_force_const | The stretch-bend force constant \( kba_{KJI} \). |
| ref_angle | The reference bond angle \( \vartheta_{IJK}^0 \). |
| ref_length1 | The reference bond length \( r_{IJ}^0 \). |
| ref_length2 | The reference bond length \( r_{KJ}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94StretchBendEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const ValueType & | r_ij, | ||
| const ValueType & | r_jk, | ||
| const ValueType & | ijk_force_const, | ||
| const ValueType & | kji_force_const, | ||
| const ValueType & | ref_angle, | ||
| const ValueType & | ref_length1, | ||
| const ValueType & | ref_length2 | ||
| ) |
Calculates the stretch-bend interaction energy \( EBA_{ijk} \) for two bonds i-j and j-k.
\( EBA_{ijk} = 2.51210 \: (kba_{IJK} \: \Delta r_{ij} + kba_{KJI} \: \Delta r_{kj}) \: \Delta \vartheta_{ijk} \)
where
\( kba_{IJK} \) = force constant in \( \frac{md}{rad} \) for i-j stretch coupled to i-j-k bend.
\( kba_{KJI} \) = force constant in \( \frac{md}{rad} \) for k-j stretch coupled to i-j-k bend.
\( \Delta r_{ij} \) = \( r_{ij} - r_{IJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms i and j of types I and J.
\( \Delta r_{kj} \) = \( r_{kj} - r_{KJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms k and j of types K and J.
\( \Delta \vartheta_{ijk} \) = \( \vartheta_{ijk} - \vartheta_{IJK}^0 \), the difference between actual and reference i-j-k bond angles in degrees.
For the calculation of \( r_{ij} \), \( r_{kj} \), and \( \vartheta_{ijk} \) see calcBondLengthsAndAngle().
Currently, stretch-bend interactions are omitted when the i-j-k interaction corresponds to a linear bond angle.
| term_atom1_pos | The position of atom i. |
| ctr_atom_pos | The position of the central atom j. |
| term_atom2_pos | The position of atom k. |
| r_ij | The length of the bond between atom i and j. |
| r_jk | The length of the bond between atom j and k. |
| ijk_force_const | The stretch-bend force constant \( kba_{IJK} \). |
| kji_force_const | The stretch-bend force constant \( kba_{KJI} \). |
| ref_angle | The reference bond angle \( \vartheta_{IJK}^0 \). |
| ref_length1 | The reference bond length \( r_{IJ}^0 \). |
| ref_length2 | The reference bond length \( r_{KJ}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the out-of-plane bending interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94OutOfPlaneBendingInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingEnergy | ( | const MMFF94OutOfPlaneBendingInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single out-of-plane bending interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 out-of-plane bending interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const CoordsVec & | oop_atom_pos, | ||
| const ValueType & | force_const | ||
| ) |
Calculates the out-of-plane bending interaction energy \( EOOP_{ijk;l} \) for the bond j-l and the plane i-j-k.
\( EOOP_{ijk;l} = 0.043844 \: \frac{koop_{IJK \colon L}}{2} \: \chi_{ijk;l}^2 \)
where
\( koop_{IJK \colon L} \) = out-of-plane bending force constant in \( \frac{md Ang}{rad^2} \).
\( \chi_{ijk;l} \) = angle in degrees between the bond j-l and the plane i-j-k, where j is the central atom (see calcOutOfPlaneAngle()).
| term_atom1_pos | The position of atom i. |
| ctr_atom_pos | The position of the central atom j. |
| term_atom2_pos | The position of atom k. |
| oop_atom_pos | The position of the out-of-plane atom l. |
| force_const | The out-of-plane bending force constant \( koop_{IJK \colon L} \). |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const CoordsVec & | oop_atom_pos, | ||
| const ValueType & | r_jl, | ||
| const ValueType & | force_const | ||
| ) |
Calculates the out-of-plane bending interaction energy \( EOOP_{ijk;l} \) for the bond j-l and the plane i-j-k.
\( EOOP_{ijk;l} = 0.043844 \: \frac{koop_{IJK \colon L}}{2} \: \chi_{ijk;l}^2 \)
where
\( koop_{IJK \colon L} \) = out-of-plane bending force constant in \( \frac{md Ang}{rad^2} \).
\( \chi_{ijk;l} \) = angle in degrees between the bond j-l and the plane i-j-k, where j is the central atom (see calcOutOfPlaneAngle()).
| term_atom1_pos | The position of atom i. |
| ctr_atom_pos | The position of the central atom j. |
| term_atom2_pos | The position of atom k. |
| oop_atom_pos | The position of the out-of-plane atom l. |
| r_jl | The length of the bond between atom j and atom l. |
| force_const | The out-of-plane bending force constant \( koop_{IJK \colon L} \). |
| ValueType CDPL::ForceField::calcMMFF94TorsionEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the torsion interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94TorsionInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94TorsionEnergy | ( | const MMFF94TorsionInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single torsion interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 torsion interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94TorsionEnergy | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom1_pos, | ||
| const CoordsVec & | ctr_atom2_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const ValueType & | tor_param1, | ||
| const ValueType & | tor_param2, | ||
| const ValueType & | tor_param3 | ||
| ) |
Calculates the torsion interaction energy \( ET_{ijkl} \) for the central bond j-k and the connected bonds i-j and k-l.
\( ET_{ijkl} = 0.5 \: (V_1 \: (1 + \cos(\Phi_{ijkl})) + V_2 \: (1 - \cos(2 \: \Phi_{ijkl})) + V_3 \: (1 + \cos(3 \: \Phi_{ijkl}))) \)
where \( \Phi_{ijkl} \) is the i-j-k-l dihedral angle. The constants \( V_1 \), \( V_2 \) and \( V_3 \) depend on the atom types I, J, K and L for atoms i, j, k and l, where i-j, j-k and k-l are bonded pairs and i is not equal to l.
For the calculation of \( \cos(\Phi_{ijkl}) \) see calcDihedralAngleCos().
| term_atom1_pos | The position of the terminal atom i. |
| ctr_atom1_pos | The position of the central atom j. |
| ctr_atom2_pos | The position of the central atom k. |
| term_atom2_pos | The position of the terminal atom l. |
| tor_param1 | The torsion parameter \( V_1 \). |
| tor_param2 | The torsion parameter \( V_2 \). |
| tor_param3 | The torsion parameter \( V_3 \). |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the electrostatic interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94ElectrostaticInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticEnergy | ( | const MMFF94ElectrostaticInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single electrostatic interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 electrostatic interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticEnergy | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| const ValueType & | atom1_chg, | ||
| const ValueType & | atom2_chg, | ||
| const ValueType & | scale_fact, | ||
| const ValueType & | de_const, | ||
| const ValueType & | dist_expo | ||
| ) |
Calculates the electrostatic interaction energy \( EQ_{ij} \) for the atom pair i-j.
\( EQ_{ij} = S \: 332.0716 \: \frac{q_i \: q_j}{D \: (R_{ij} + \delta)^n} \)
where
\( S \) = a scaling factor depending on the topological distance of i-j.
\( q_i \) and \( q_j \) = Partial atomic charges.
\( D \) = Dielectric constant.
\( R_{ij} \) = Interatomic distance (Å) (see calcDistance()).
\( \delta \) = Electrostatic buffering constant (0.05 Å).
\( n \) = Exponent (normally 1, but can be 2 for distance-dependent dielectric constant).
Note: 1-4 electrostatic interactions are scaled by 0.75 (thus, the electrostatic energy term becomes \( EQ_{14} \: 0.75 \)).
| atom1_pos | The position of atom i. |
| atom2_pos | The position of atom j. |
| atom1_chg | The partial atom charge \( q_i \) of atom i. |
| atom2_chg | The partial atom charge \( q_j \) of atom j. |
| scale_fact | The scaling factor for \( S \) depending on the topological i-j distance. |
| de_const | The dielectric constant \( D \). |
| dist_expo | The exponent \( n \). |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticEnergy | ( | const ValueType & | r_ij, |
| const ValueType & | atom1_chg, | ||
| const ValueType & | atom2_chg, | ||
| const ValueType & | scale_fact, | ||
| const ValueType & | de_const, | ||
| const ValueType & | dist_expo | ||
| ) |
Calculates the electrostatic interaction energy \( EQ_{ij} \) for the atom pair i-j.
\( EQ_{ij} = S \: 332.0716 \: \frac{q_i \: q_j}{D \: (R_{ij} + \delta)^n} \)
where
\( S \) = a scaling factor depending on the topological distance of i-j.
\( q_i \) and \( q_j \) = Partial atomic charges.
\( D \) = Dielectric constant.
\( R_{ij} \) = Interatomic distance (Å) (see calcDistance()).
\( \delta \) = Electrostatic buffering constant (0.05 Å).
\( n \) = Exponent (normally 1, but can be 2 for distance-dependent dielectric constant).
Note: 1-4 electrostatic interactions are scaled by 0.75 (thus, the electrostatic energy term becomes \( EQ_{14} \: 0.75 \)).
| r_ij | The interatomic distance \( R_{ij} \) of atom i and atom j. |
| atom1_chg | The partial atom charge \( q_i \) of atom i. |
| atom2_chg | The partial atom charge \( q_j \) of atom j. |
| scale_fact | The scaling factor for \( S \) depending on the topological i-j distance. |
| de_const | The dielectric constant \( D \). |
| dist_expo | The exponent \( n \). |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsEnergy | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords | ||
| ) |
Accumulates the Van der Waals interaction energies calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94VanDerWaalsInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsEnergy | ( | const MMFF94VanDerWaalsInteraction & | iaction, |
| const CoordsArray & | coords | ||
| ) |
Calculates the energy of a single Van der Waals interaction iaction.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| iaction | The MMFF94 Van der Waals interaction parameter record. |
| coords | The atom 3D coordinates for which the energy shall be calculated. |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsEnergy | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| const ValueType & | e_IJ, | ||
| const ValueType & | r_IJ, | ||
| const ValueType & | r_IJ_7 | ||
| ) |
Calculates the Van der Waals interaction energy \( E_{vdW_{ij}} \) for the atom pair i-j.
\( E_{vdW_{ij}} = \varepsilon_{IJ} \: (\frac{1.07 \: R_{IJ}^*}{(R_{ij} + 0.07 \: R_{IJ}^*)})^7 \: (\frac{1.12 \: R_{IJ}^{*^7}}{(R_{ij}^7 + 0.12 \: R_{IJ}^{*^7})} - 2) \;\;\;\; (1) \)
where
\( R_{ij} \) = the interatomic distance (see calcDistance()).
\( R_{II}^* = A_I \: \alpha_I^{PEXP} \;\;\;\; (2) \)
\( R_{IJ}^* = 0.5 \: (R_{II}^* + R_{JJ}^*) \: (1 + AFACT(1 - \exp(-BFACT \: \gamma_{IJ}^2))) \;\;\;\; (3) \)
\( \gamma_{IJ} = \frac{(R_{II}^* - R_{JJ}^*)}{(R_{II}^* + R_{JJ}^*)} \;\;\;\; (4) \)
\( \varepsilon_{IJ} = \frac{181.16 \: G_I \: GJ \: \alpha_I \: \alpha_J}{((\alpha_I / N_I)^{1/2} + (\alpha_J / N_J)^{1/2})} \: \frac{1}{R_{IJ}^{*^6}} \;\;\;\; (5) \)
MMFF employs a "Buffered 14-7" form (eq 1) together with an expression which relates the minimum-energy separation \( R_{II}^* \) to the atomic polarizability \( \alpha_I \) (eq 2), a specially formulated combination rule (eqs 3, 4), and a Slater-Kirkwood expression for the well depth \( \varepsilon_{IJ} \) (eq 5): The first non-comment line in the parameter file "MMFFVDW.PAR" contains five floating point numbers which define the variables PEXP, AFACT, BFACT, DARAD, and DAEPS, respectively. PEXP (currently 0.25), AFACT (currently 0.2) and BFACT (currently 12.0) are used in the equations shown above; DARAD and DAEPS are used as follows:
When either i or j is a hydrogen-bond donor, MMFF uses the simple arithmetic mean \( 0.5 \: (R_{II}^* + R_{JJ}^*) \) instead of eq 3 to obtain \( R_{IJ}^* \). If the i-j interaction is a donor-acceptor interaction, MMFF also scales \( R_{IJ}^* \) as given by eq 3 by DARAD (currently 0.8) and \( \varepsilon_{IJ} \) as given by eq 5 by DAEPS (currently 0.5).
| atom1_pos | The position of atom i. |
| atom2_pos | The position of atom j. |
| e_IJ | The precalculated value \( \varepsilon_{IJ} \). |
| r_IJ | The precalculated value \( R_{IJ}^* \). |
| r_IJ_7 | The precalculated value \( R_{IJ}^{*^7} \). |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsEnergy | ( | const ValueType & | r_ij, |
| const ValueType & | e_IJ, | ||
| const ValueType & | r_IJ, | ||
| const ValueType & | r_IJ_7 | ||
| ) |
Calculates the Van der Waals interaction energy \( E_{vdW_{ij}} \) for the atom pair i-j.
\( E_{vdW_{ij}} = \varepsilon_{IJ} \: (\frac{1.07 \: R_{IJ}^*}{(R_{ij} + 0.07 \: R_{IJ}^*)})^7 \: (\frac{1.12 \: R_{IJ}^{*^7}}{(R_{ij}^7 + 0.12 \: R_{IJ}^{*^7})} - 2) \;\;\;\; (1) \)
where
\( R_{ij} \) = the interatomic distance (see calcDistance()).
\( R_{II}^* = A_I \: \alpha_I^{PEXP} \;\;\;\; (2) \)
\( R_{IJ}^* = 0.5 \: (R_{II}^* + R_{JJ}^*) \: (1 + AFACT(1 - \exp(-BFACT \: \gamma_{IJ}^2))) \;\;\;\; (3) \)
\( \gamma_{IJ} = \frac{(R_{II}^* - R_{JJ}^*)}{(R_{II}^* + R_{JJ}^*)} \;\;\;\; (4) \)
\( \varepsilon_{IJ} = \frac{181.16 \: G_I \: GJ \: \alpha_I \: \alpha_J}{((\alpha_I / N_I)^{1/2} + (\alpha_J / N_J)^{1/2})} \: \frac{1}{R_{IJ}^{*^6}} \;\;\;\; (5) \)
MMFF employs a "Buffered 14-7" form (eq 1) together with an expression which relates the minimum-energy separation \( R_{II}^* \) to the atomic polarizability \( \alpha_I \) (eq 2), a specially formulated combination rule (eqs 3, 4), and a Slater-Kirkwood expression for the well depth \( \varepsilon_{IJ} \) (eq 5): The first non-comment line in the parameter file "MMFFVDW.PAR" contains five floating point numbers which define the variables PEXP, AFACT, BFACT, DARAD, and DAEPS, respectively. PEXP (currently 0.25), AFACT (currently 0.2) and BFACT (currently 12.0) are used in the equations shown above; DARAD and DAEPS are used as follows:
When either i or j is a hydrogen-bond donor, MMFF uses the simple arithmetic mean \( 0.5 \: (R_{II}^* + R_{JJ}^*) \) instead of eq 3 to obtain \( R_{IJ}^* \). If the i-j interaction is a donor-acceptor interaction, MMFF also scales \( R_{IJ}^* \) as given by eq 3 by DARAD (currently 0.8) and \( \varepsilon_{IJ} \) as given by eq 5 by DAEPS (currently 0.5).
| r_ij | The interatomic distance \( R_{ij} \) of atom i and atom j. |
| e_IJ | The precalculated value \( \varepsilon_{IJ} \). |
| r_IJ | The precalculated value \( R_{IJ}^* \). |
| r_IJ_7 | The precalculated value \( R_{IJ}^{*^7} \). |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the bond-stretching interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94BondStretchingInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingGradient | ( | const MMFF94BondStretchingInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single bond-stretching interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 bond-stretching interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94BondStretchingGradient | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| GradVec & | atom1_grad, | ||
| GradVec & | atom2_grad, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_length | ||
| ) |
Calculates the bond stretching interaction energy gradient \( \nabla EB_{ij} \) for the bond i-j.
Energy function:
\( EB_{ij} = 143.9325 \: \frac{kb_{IJ}}{2} \: \Delta r_{ij}^2 \: (1 + cs \: \Delta r_{ij} + \frac{7}{12} \: cs^2 \: \Delta r_{ij}^2) \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial EB_{ij}}{\partial \vec{p_x}} = \frac{\partial EB_{ij}}{\partial \Delta r_{ij}} \: \frac{\partial \Delta r_{ij}}{\partial \vec{p_x}} \)
\( \frac{\partial EB_{ij}}{\partial \Delta r_{ij}} = (167.92125 \: \Delta r_{ij}^3 \: cs^2 + 215.89875 \: \Delta r_{ij}^2 \: cs + 143.9325 \: \Delta r_{ij}) \: kb_{IJ} \)
for the calculation of the partial derivatives \( \frac{\partial \Delta r_{ij}}{\partial \vec{p_x}} \) see calcDistanceDerivatives().
where
\( kb_{IJ} \) = the bond stretching force constant in \( \frac{md}{Ang} \) for bonded atoms i and j of types I and J.
\( \Delta r_{ij} \) = \( r_{ij} - r_{IJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms i and j of types I and J.
\( cs \) = \( -2 \: Ang^{-1} \), the "cubic stretch" constant.
\( \vec{p_x} \) = coordinates of the involved atoms i and j.
Note: throughout this description, the indices i, j, k, ... represent atoms; I, J, K, ... denote the corresponding numerical MMFF atom types (or, occasionally, the atomic species).
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| atom2_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| force_const | The bond stretching force constant \( kb_{IJ} \). |
| ref_length | The reference bond length \( r_{IJ}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the angle-bending interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94AngleBendingInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingGradient | ( | const MMFF94AngleBendingInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single angle-bending interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 angle-bending interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94AngleBendingGradient | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| GradVec & | term_atom1_grad, | ||
| GradVec & | ctr_atom_grad, | ||
| GradVec & | term_atom2_grad, | ||
| bool | linear, | ||
| const ValueType & | force_const, | ||
| const ValueType & | ref_angle | ||
| ) |
Calculates the angle bending interaction energy gradient \( \nabla EA_{ijk} \) for two bonds i-j and j-k.
Energy function employed for the non-linear case:
\( EA_{ijk} = 0.043844 \: \frac{ka_{IJK}}{2} \: \Delta \vartheta_{ijk}^2 \: (1 + cb \: \Delta \vartheta_{ijk}) \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial EA_{ijk}}{\partial \vec{p_x}} = \frac{\partial EA_{ijk}}{\partial \vartheta_{ijk}} \: \frac{\partial \vartheta_{ijk}}{\partial \cos(\vartheta_{ijk})} \: \frac{\partial \cos(\vartheta_{ijk})}{\vec{p_x}} \)
\( \frac{\partial EA_{ijk}}{\partial \vartheta_{ijk}} = -ka_{IJK} \: (86.58992538 \: \vartheta_{ijk}^2 - 3.022558594 \: \vartheta_{ijk} \: \vartheta_{IJK}^0 - 143.9313616 \: \vartheta_{ijk} + 0.02637679965 \: \vartheta_{IJK}^{0^2} + 2.512076157 \: \vartheta_{IJK}^0) \)
\( \frac{\partial \vartheta_{ijk}}{\partial \cos(\vartheta_{ijk})} = \frac{-1}{\sqrt{1 - \cos(\vartheta_{ijk})^2}} \)
for the calculation of the partial derivatives \( \frac{\partial \cos(\vartheta_{ijk})}{\vec{p_x}} \) see calcBondAngleCosDerivatives().
For linear or near-linear bond angles such as those which occur in alkynes, nitriles, isonitriles, azides, and diazo compounds, the energy function form used in DREIDING and UFF is employed:
\( EA_{ijk} = 143.9325 \: ka_{IJK} \:(1 + \cos(\vartheta_{ijk})) \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial EA_{ijk}}{\partial \vec{p_x}} = 143.9325 \: ka_{IJK} \: \frac{\partial \cos(\vartheta_{ijk})}{\vec{p_x}} \)
where
\( ka_{IJK} \) = angle bending force constant in \( \frac{md Ang}{rad^2} \) for the angle between atoms i, j and k of atom types I, J and K.
\( \Delta \vartheta_{ijk} \) = \( \vartheta_{ijk} - \vartheta_{IJK}^0 \), the difference between actual and reference i-j-k bond angles in degrees.
\( cb \) = \( -0.007 \: deg^{-1} \), the "cubic-bend" constant.
\( \vec{p_x} \) = coordinates of the involved atoms i, j and k.
| term_atom1_pos | The position \( \vec{p_i} \) of atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of atom k. |
| term_atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| ctr_atom_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| term_atom2_grad | The output variable storing the accumulated energy gradient contributions for atom k. |
| linear | If true, the bond angle is linear. |
| force_const | The angle bending force constant \( ka_{IJK} \). |
| ref_angle | The reference bond angle \( \vartheta_{IJK}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94StretchBendGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the stretch-bend coupling interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94StretchBendInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94StretchBendGradient | ( | const MMFF94StretchBendInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single stretch-bend coupling interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 stretch-bend interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94StretchBendGradient | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| GradVec & | term_atom1_grad, | ||
| GradVec & | ctr_atom_grad, | ||
| GradVec & | term_atom2_grad, | ||
| const ValueType & | ijk_force_const, | ||
| const ValueType & | kji_force_const, | ||
| const ValueType & | ref_angle, | ||
| const ValueType & | ref_length1, | ||
| const ValueType & | ref_length2 | ||
| ) |
Calculates the stretch-bend interaction energy gradient \( \nabla EBA_{ijk} \) for two bonds i-j and j-k.
Energy function:
\( EBA_{ijk} = 2.51210 \: (kba_{IJK} \: \Delta r_{ij} + kba_{KJI} \: \Delta r_{kj}) \: \Delta \vartheta_{ijk} \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial EBA_{ijk}}{\partial \vec{p_x}} = 2.5121 \: \Delta \vartheta_{ijk} \: (kba_{IJK} \: \frac{\partial \Delta r_{ij}}{\partial \vec{p_x}} + kba_{KJI} \: \frac{\partial \Delta r_{kj}}{\partial \vec{p_x}}) + 2.5121 \: \frac{\partial \Delta \vartheta_{ijk}}{\partial \vec{p_x}} \: (kba_{IJK} \: \Delta r_{ij} + kba_{KJI} \: \Delta r_{kj}) \)
\( \frac{\partial \Delta \vartheta_{ijk}}{\partial \vec{p_x}} = \frac{\partial \Delta \vartheta_{ijk}}{\partial \vartheta_{ijk}} \: \frac{\partial \vartheta_{ijk}}{\partial \cos(\vartheta_{ijk})} \: \frac{\partial \cos(\vartheta_{ijk})}{\vec{p_x}} \)
\( \frac{\partial \Delta \vartheta_{ijk}}{\partial \vartheta_{ijk}} = \frac{180}{\pi} \)
\( \frac{\partial \vartheta_{ijk}}{\partial \cos(\vartheta_{ijk})} = \frac{-1}{\sqrt{1 - \cos(\vartheta_{ijk})^2}} \)
for the calculation of the partial derivatives \( \frac{\partial \cos(\vartheta_{ijk})}{\vec{p_x}} \) see calcBondAngleCosDerivatives() and for the calculation of \( \frac{\partial \Delta r_{ij}}{\partial \vec{p_x}} \) see calcDistanceDerivatives().
where
\( kba_{IJK} \) = force constant in \( \frac{md}{rad} \) for i-j stretch coupled to i-j-k bend.
\( kba_{KJI} \) = force constant in \( \frac{md}{rad} \) for k-j stretch coupled to i-j-k bend.
\( \Delta r_{ij} \) = \( r_{ij} - r_{IJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms i and j of types I and J.
\( \Delta r_{kj} \) = \( r_{kj} - r_{KJ}^0 \), the difference in angstroms between actual and reference bond lengths between bonded atoms k and j of types K and J.
\( \Delta \vartheta_{ijk} \) = \( \vartheta_{ijk} \: \frac{180}{\pi} - \vartheta_{IJK}^0 \), the difference between actual and reference i-j-k bond angles in degrees.
\( \vec{p_x} \) = coordinates of the involved atoms i, j and k.
Currently, stretch-bend interactions are omitted when the i-j-k interaction corresponds to a linear bond angle.
| term_atom1_pos | The position \( \vec{p_i} \) of atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of atom k. |
| term_atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| ctr_atom_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| term_atom2_grad | The output variable storing the accumulated energy gradient contributions for atom k. |
| ijk_force_const | The stretch-bend force constant \( kba_{IJK} \). |
| kji_force_const | The stretch-bend force constant \( kba_{KJI} \). |
| ref_angle | The reference bond angle \( \vartheta_{IJK}^0 \). |
| ref_length1 | The reference bond length \( r_{IJ}^0 \). |
| ref_length2 | The reference bond length \( r_{KJ}^0 \). |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the out-of-plane bending interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94OutOfPlaneBendingInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingGradient | ( | const MMFF94OutOfPlaneBendingInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single out-of-plane bending interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 out-of-plane bending interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94OutOfPlaneBendingGradient | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const CoordsVec & | oop_atom_pos, | ||
| GradVec & | term_atom1_grad, | ||
| GradVec & | ctr_atom_grad, | ||
| GradVec & | term_atom2_grad, | ||
| GradVec & | oop_atom_grad, | ||
| const ValueType & | force_const | ||
| ) |
Calculates the out-of-plane bending interaction energy gradient \( \nabla EOOP_{ijk;l} \) for the bond j-l and the plane i-j-k.
Energy function:
\( EOOP_{ijk;l} = 0.043844 \: \frac{koop_{IJK \colon L}}{2} \: (\chi_{ijk;l} \: \frac{180}{\pi})^2 \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial EOOP_{ijk;l}}{\partial \vec{p_x}} = \frac{\partial EOOP_{ijk;l}}{\partial \chi_{ijk;l}} \: \frac{\partial \chi_{ijk;l}}{\partial \cos(\alpha_{ijk;l})} \: \frac{\partial \cos(\alpha_{ijk;l})}{\partial \vec{p_x}} \)
\( \frac{\partial EOOP_{ijk;l}}{\partial \chi_{ijk;l}} = 0.043844 \: (\frac{180}{\pi})^2 \: \chi_{ijk;l} \: koop_{IJK \colon L} \)
\( \chi_{ijk;l} = \frac{\pi}{2} - \alpha_{ijk;l} \)
\( \frac{\partial \chi_{ijk;l}}{\partial \cos(\alpha_{ijk;l})} = \frac{-1}{\sqrt{1 - \cos(\alpha_{ijk;l})^2}} \)
for the calculation of the partial derivatives \( \frac{\partial \cos(\alpha_{ijk;l})}{\partial \vec{p_x}} \) see calcOutOfPlaneAngleCosDerivatives().
where
\( koop_{IJK \colon L} \) = out-of-plane bending force constant in \( \frac{md Ang}{rad^2} \).
\( \chi_{ijk;l} \) = angle in radians between the bond j-l and the plane i-j-k, where j is the central atom.
\( \vec{p_x} \) = coordinates of the involved atoms i, j, k and l.
| term_atom1_pos | The position \( \vec{p_i} \) of atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of atom k. |
| oop_atom_pos | The position \( \vec{p_l} \) of the out-of-plane atom l. |
| term_atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| ctr_atom_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| term_atom2_grad | The output variable storing the accumulated energy gradient contributions for atom k. |
| oop_atom_grad | The output variable storing the accumulated energy gradient contributions for atom l. |
| force_const | The out-of-plane bending force constant \( koop_{IJK \colon L} \). |
| ValueType CDPL::ForceField::calcMMFF94TorsionGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the torsion interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94TorsionInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94TorsionGradient | ( | const MMFF94TorsionInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single torsion interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 torsion interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94TorsionGradient | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom1_pos, | ||
| const CoordsVec & | ctr_atom2_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| GradVec & | term_atom1_grad, | ||
| GradVec & | ctr_atom1_grad, | ||
| GradVec & | ctr_atom2_grad, | ||
| GradVec & | term_atom2_grad, | ||
| const ValueType & | tor_param1, | ||
| const ValueType & | tor_param2, | ||
| const ValueType & | tor_param3 | ||
| ) |
Calculates the torsion interaction energy gradient \( \nabla ET_{ijkl} \) for the central bond j-k and the connected bonds i-j and k-l.
Energy function:
\( ET_{ijkl} = 0.5 \: (V_1 \: (1 + \cos(\Phi_{ijkl})) + V_2 \: (1 - \cos(2 \: \Phi_{ijkl})) + V_3 \: (1 + \cos(3 \: \Phi_{ijkl}))) \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial ET_{ijkl}}{\partial \vec{p_x}} = \frac{\partial ET_{ijkl}}{\partial \Phi_{ijkl}} \: \frac{\partial \Phi_{ijkl}}{\partial \cos(\Phi_{ijkl})} \: \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_x}} \)
\( \frac{\partial ET_{ijkl}}{\partial \Phi_{ijkl}} = V_2 \: \sin(2 \: \Phi_{ijkl}) - 0.5 \: V_1 \: \sin(\Phi_{ijkl}) - 1.5 \: V_3 \: \sin(3 \: \Phi_{ijkl}) \)
\( \frac{\partial \Phi_{ijkl}}{\partial \cos(\Phi_{ijkl})} = \frac{-1}{\sqrt{1 - \cos(\Phi_{ijkl})^2}} \)
for the calculation of the partial derivatives \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_x}} \) see calcDihedralAngleCosDerivatives().
where
\( \Phi_{ijkl} \) is the i-j-k-l dihedral angle. The constants \( V_1 \), \( V_2 \) and \( V_3 \) depend on the atom types I, J, K and L for atoms i, j, k and l, where i-j, j-k and k-l are bonded pairs and i is not equal to l.
\( \vec{p_x} \) = coordinates of the involved atoms i, j, k and l.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom1_pos | The position \( \vec{p_j} \) of the central atom j. |
| ctr_atom2_pos | The position \( \vec{p_k} \) of the central atom k. |
| term_atom2_pos | The position \( \vec{p_l} \) of the terminal atom l. |
| term_atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| ctr_atom1_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| ctr_atom2_grad | The output variable storing the accumulated energy gradient contributions for atom k. |
| term_atom2_grad | The output variable storing the accumulated energy gradient contributions for atom l. |
| tor_param1 | The torsion parameter \( V_1 \). |
| tor_param2 | The torsion parameter \( V_2 \). |
| tor_param3 | The torsion parameter \( V_3 \). |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the electrostatic interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94ElectrostaticInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticGradient | ( | const MMFF94ElectrostaticInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single electrostatic interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 electrostatic interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94ElectrostaticGradient | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| GradVec & | atom1_grad, | ||
| GradVec & | atom2_grad, | ||
| const ValueType & | atom1_chg, | ||
| const ValueType & | atom2_chg, | ||
| const ValueType & | scale_fact, | ||
| const ValueType & | de_const, | ||
| const ValueType & | dist_expo | ||
| ) |
Calculates the electrostatic interaction energy gradient \( \nabla EQ_{ij} \) for the atom pair i-j.
Energy function:
\( EQ_{ij} = S \: 332.0716 \: \frac{q_i \: q_j}{D \: (R_{ij} + \delta)^n} \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial EQ_{ij}}{\partial \vec{p_x}} = \frac{\partial EQ_{ij}}{\partial R_{ij}} \: \frac{\partial R_{ij}}{\partial \vec{p_x}} \)
\( \frac{\partial EQ_{ij}}{\partial R_{ij}} = -S \: 332.0716 \: n \: \frac{q_i \: q_j}{D \: (R_{ij} + \delta)^{n + 1}} \)
for the calculation of the partial derivatives \( \frac{\partial R_{ij}}{\partial \vec{p_x}} \) see calcDistanceDerivatives().
where
\( S \) = a scaling factor depending on the topological distance of i-j.
\( q_i \) and \( q_j \) = partial atomic charges.
\( D \) = dielectric constant.
\( R_{ij} \) = interatomic distance (Å).
\( \delta \) = electrostatic buffering constant (0.05 Å).
\( n \) = exponent (normally 1, but can be 2 for distance-dependent dielectric constant).
\( \vec{p_x} \) = coordinates of the involved atoms i and j.
Note: 1-4 electrostatic interactions are scaled by 0.75 (thus, the electrostatic gradient term becomes \( EQ_{14} \: 0.75 \)).
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| atom2_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| atom1_chg | The partial atom charge \( q_i \) of atom i. |
| atom2_chg | The partial atom charge \( q_j \) of atom j. |
| scale_fact | The scaling factor for \( S \) depending on the topological i-j distance. |
| de_const | The dielectric constant \( D \). |
| dist_expo | The exponent \( n \). |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsGradient | ( | Iter | beg, |
| const Iter & | end, | ||
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Accumulates the Van der Waals interaction energies and the corresponding per-atom gradient contributions calculated for the interactions specified by the iterators in the given range.
| ValueType | The energy/atom coordinate value type. |
| Iter | The iterator type yielding ForceField::MMFF94VanDerWaalsInteraction instances. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| beg | Iterator pointing to the first interaction parameter record. |
| end | Iterator pointing one past the last interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsGradient | ( | const MMFF94VanDerWaalsInteraction & | iaction, |
| const CoordsArray & | coords, | ||
| GradVector & | grad | ||
| ) |
Calculates the energy of a single Van der Waals interaction iaction and accumulates the corresponding per-atom gradient contributions.
| ValueType | The energy/atom coordinate value type. |
| CoordsArray | The array type storing the atom 3D coordinates. |
| GradVector | The array type storing the atom gradient vectors. |
| iaction | The MMFF94 Van der Waals interaction parameter record. |
| coords | The atom 3D coordinates for which the energies/gradients shall be calculated. |
| grad | The atom gradient vector array receiving the accumulated contributions. |
| ValueType CDPL::ForceField::calcMMFF94VanDerWaalsGradient | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| GradVec & | atom1_grad, | ||
| GradVec & | atom2_grad, | ||
| const ValueType & | e_IJ, | ||
| const ValueType & | r_IJ, | ||
| const ValueType & | r_IJ_7 | ||
| ) |
Calculates the Van der Waals interaction energy gradient \( \nabla E_{vdW_{ij}} \) for the atom pair i-j.
Energy function:
\( E_{vdW_{ij}} = \varepsilon_{IJ} \: (\frac{1.07 \: R_{IJ}^*}{(R_{ij} + 0.07 \: R_{IJ}^*)})^7 \: (\frac{1.12 \: R_{IJ}^{*^7}}{(R_{ij}^7 + 0.12 \: R_{IJ}^{*^7})} - 2) \;\;\;\; (1) \)
The partial derivatives with respect to the atom coordinates \( \vec{p_x} \) are calculated by:
\( \frac{\partial E_{vdW_{ij}}}{\partial \vec{p_x}} = \frac{\partial E_{vdW_{ij}}}{\partial R_{ij}} \: \frac{\partial R_{ij}}{\partial \vec{p_x}} \)
\( \frac{\partial E_{vdW_{ij}}}{\partial R_{ij}} = \frac{-R_{IJ}^{*^7} \: \varepsilon_{IJ}}{(R_{ij} + 0.07 \: R_{IJ}^*)^8 \: (R_{ij}^7 + 0.12 \: R_{IJ}^{*^7})^2} \: (-22.48094067 \: R_{ij}^{14} + 19.78322779 \: R_{ij}^7 \: R_{IJ}^{*^7} + 0.8812528743 \: R_{ij}^6 \: R_{IJ}^{*^8} + 1.186993667 \: R_{IJ}^{*^{14}}) \)
for the calculation of the partial derivatives \( \frac{\partial R_{ij}}{\partial \vec{p_x}} \) see calcDistanceDerivatives().
where
\( R_{ij} \) = the interatomic distance.
\( R_{II}^* = A_I \: \alpha_I^{PEXP} \;\;\;\; (2) \)
\( R_{IJ}^* = 0.5 \: (R_{II}^* + R_{JJ}^*) \: (1 + AFACT(1 - \exp(-BFACT \: \gamma_{IJ}^2))) \;\;\;\; (3) \)
\( \gamma_{IJ} = \frac{(R_{II}^* - R_{JJ}^*)}{(R_{II}^* + R_{JJ}^*)} \;\;\;\; (4) \)
\( \varepsilon_{IJ} = \frac{181.16 \: G_I \: GJ \: \alpha_I \: \alpha_J}{((\alpha_I / N_I)^{1/2} + (\alpha_J / N_J)^{1/2})} \: \frac{1}{R_{IJ}^{*6}} \;\;\;\; (5) \)
\( \vec{p_x} \) = coordinates of the involved atoms i and j.
MMFF employs a "Buffered 14-7" form (eq 1) together with an expression which relates the minimum-gradient separation \( R_{II}^* \) to the atomic polarizability \( \alpha_I \) (eq 2), a specially formulated combination rule (eqs 3, 4), and a Slater-Kirkwood expression for the well depth \( \varepsilon_{IJ} \) (eq 5): The first non-comment line in the parameter file "MMFFVDW.PAR" contains five floating point numbers which define the variables PEXP, AFACT, BFACT, DARAD, and DAEPS, respectively. PEXP (currently 0.25), AFACT (currently 0.2) and BFACT (currently 12.0) are used in the equations shown above; DARAD and DAEPS are used as follows:
When either i or j is a hydrogen-bond donor, MMFF uses the simple arithmetic mean \( 0.5 \: (R_{II}^* + R_{JJ}^*) \) instead of eq 3 to obtain \( R_{IJ}^* \). If the i-j interaction is a donor-acceptor interaction, MMFF also scales \( R_{IJ}^* \) as given by eq 3 by DARAD (currently 0.8) and \( \varepsilon_{IJ} \) as given by eq 5 by DAEPS (currently 0.5).
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| atom1_grad | The output variable storing the accumulated energy gradient contributions for atom i. |
| atom2_grad | The output variable storing the accumulated energy gradient contributions for atom j. |
| e_IJ | The precalculated value \( \varepsilon_{IJ} \). |
| r_IJ | The precalculated value \( R_{IJ}^* \). |
| r_IJ_7 | The precalculated value \( R_{IJ}^{*^7} \). |
| CDPL_FORCEFIELD_API const Chem::FragmentList::SharedPointer& CDPL::ForceField::getMMFF94AromaticRings | ( | const Chem::MolecularGraph & | molgraph | ) |
Returns the value of the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to return the property value. |
const shared pointer to the list of MMFF94 aromatic rings. | CDPL_FORCEFIELD_API void CDPL::ForceField::setMMFF94AromaticRings | ( | Chem::MolecularGraph & | molgraph, |
| const Chem::FragmentList::SharedPointer & | rings | ||
| ) |
Sets the value of the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph to rings.
| molgraph | The molecular graph for which to set the property value. |
| rings | The new list of MMFF94 aromatic rings. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::clearMMFF94AromaticRings | ( | Chem::MolecularGraph & | molgraph | ) |
Clears the value of the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph.
| molgraph | The molecular graph for which to clear the property value. |
| CDPL_FORCEFIELD_API bool CDPL::ForceField::hasMMFF94AromaticRings | ( | const Chem::MolecularGraph & | molgraph | ) |
Tells whether the ForceField::MolecularGraphProperty::MMFF94_AROMATIC_RINGS property of the molecular graph molgraph is set.
| molgraph | The molecular graph for which to query the property value. |
true if the property is set, and false otherwise. | CDPL_FORCEFIELD_API Chem::FragmentList::SharedPointer CDPL::ForceField::perceiveMMFF94AromaticRings | ( | const Chem::MolecularGraph & | molgraph | ) |
Perceives the list of MMFF94 aromatic rings of the molecular graph molgraph.
| molgraph | The molecular graph. |
| CDPL_FORCEFIELD_API Chem::FragmentList::SharedPointer CDPL::ForceField::perceiveMMFF94AromaticRings | ( | Chem::MolecularGraph & | molgraph, |
| bool | overwrite | ||
| ) |
Perceives and (optionally) stores the list of MMFF94 aromatic rings of the molecular graph molgraph.
| molgraph | The molecular graph to inspect/modify. |
| overwrite | Specifies whether an already existing value of the property should be replaced. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::assignMMFF94AtomTypes | ( | Chem::MolecularGraph & | molgraph, |
| bool | strict, | ||
| bool | overwrite | ||
| ) |
Assigns MMFF94 atom types to the atoms of the molecular graph molgraph.
| molgraph | The molecular graph whose atoms will be typed. |
| strict | If true, atoms for which no MMFF94 type could be perceived cause an error to be reported. Otherwise, perception never fails and problematic atoms are assigned a suitable fallback type. |
| overwrite | Specifies whether already assigned atom type properties should be replaced. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::assignMMFF94BondTypeIndices | ( | Chem::MolecularGraph & | molgraph, |
| bool | strict, | ||
| bool | overwrite | ||
| ) |
Assigns MMFF94 bond type indices to the bonds of the molecular graph molgraph.
| molgraph | The molecular graph whose bonds will be typed. |
| strict | If true, strict parameterization will be peformed that might fail. Otherwise, bonds with parameterization problems receive the type index 0. |
| overwrite | Specifies whether already assigned bond type index properties should be replaced. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::calcMMFF94AtomCharges | ( | Chem::MolecularGraph & | molgraph, |
| bool | strict, | ||
| bool | overwrite | ||
| ) |
Calculates and assigns MMFF94 partial atomic charges to the atoms of the molecular graph molgraph.
| molgraph | The molecular graph for which to assign atom charges. |
| strict | If true, strict parameterization is performed (and may fail). Otherwise, in case of parameterization problems, fallback strategies take effect. |
| overwrite | Specifies whether already assigned charge properties should be replaced. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::assignUFFAtomTypes | ( | Chem::MolecularGraph & | molgraph, |
| bool | overwrite | ||
| ) |
Assigns UFF atom types to the atoms of the molecular graph molgraph.
| molgraph | The molecular graph whose atoms will be typed. |
| overwrite | Specifies whether already assigned atom type properties should be replaced. |
| CDPL_FORCEFIELD_API void CDPL::ForceField::filterInteractions | ( | const MMFF94InteractionData & | ia_data, |
| MMFF94InteractionData & | filtered_ia_data, | ||
| const Util::BitSet & | inc_atom_mask | ||
| ) |
Filters an MMFF94 interaction data set, retaining only those interactions that exclusively reference atoms in inc_atom_mask.
| ia_data | The input interaction data set. |
| filtered_ia_data | The output interaction data set receiving the retained interactions. |
| inc_atom_mask | A bit set whose set bits correspond to the indices of atoms that may appear in a retained interaction. |
| ValueType CDPL::ForceField::calcSquaredDistance | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos | ||
| ) |
Calculates the squared distance \( r_{ij}^2 \) between two atoms i and j.
\( r_{ij}^2 = |\vec{v_{ij}}|^2 \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| ValueType CDPL::ForceField::calcDistance | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos | ||
| ) |
Calculates the distance \( r_{ij} \) between two atoms i and j.
\( r_{ij} = |\vec{v_{ij}}| \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| ValueType CDPL::ForceField::calcBondLengthsAndAngleCos | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| ValueType & | bond_length1, | ||
| ValueType & | bond_length2 | ||
| ) |
Calculates bond lengths \( r_{ij} \) and \( r_{jk} \) and the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k.
\( r_{ij} = |\vec{v_{ij}}| \)
\( r_{jk} = |\vec{v_{jk}}| \)
\( \cos(\vartheta_{ijk}) = \frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{r_{ij} \: r_{jk}} \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| bond_length1 | Output variable for the bond length \( r_{ij} \). |
| bond_length2 | Output variable for the bond length \( r_{jk} \). |
| ValueType CDPL::ForceField::calcBondLengthsAndAngle | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| ValueType & | bond_length1, | ||
| ValueType & | bond_length2 | ||
| ) |
Calculates bond lengths \( r_{ij} \) and \( r_{jk} \) and the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k.
\( r_{ij} = |\vec{v_{ij}}| \)
\( r_{jk} = |\vec{v_{jk}}| \)
\( \vartheta_{ijk} = \arccos(\frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{r_{ij} \: r_{jk}}) \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| bond_length1 | Output variable for the bond length \( r_{ij} \). |
| bond_length2 | Output variable for the bond length \( r_{jk} \). |
| ValueType CDPL::ForceField::calcBondAngleCos | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos | ||
| ) |
Calculates the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k.
\( \cos(\vartheta_{ijk}) = \frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{|\vec{v_{ij}}| \: |\vec{v_{jk}}|} \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| ValueType CDPL::ForceField::calcBondAngleCos | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const ValueType & | r_ij, | ||
| const ValueType & | r_jk | ||
| ) |
Calculates the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k.
\( \cos(\vartheta_{ijk}) = \frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{|\vec{v_{ij}}| \: |\vec{v_{jk}}|} \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| r_ij | The length of the bond between atom i and j. |
| r_jk | The length of the bond between atom j and k. |
| ValueType CDPL::ForceField::calcBondAngle | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos | ||
| ) |
Calculates the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k.
\( \vartheta_{ijk} = \arccos(\frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{|\vec{v_{ij}}| \: |\vec{v_{jk}}|}) \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| ValueType CDPL::ForceField::calcBondAngle | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const ValueType & | r_ij, | ||
| const ValueType & | r_jk | ||
| ) |
Calculates the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k.
\( \vartheta_{ijk} = \arccos(\frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{|\vec{v_{ij}}| \: |\vec{v_{jk}}|}) \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| r_ij | The length of the bond between atom i and j. |
| r_jk | The length of the bond between atom j and k. |
| ValueType CDPL::ForceField::calcOutOfPlaneAngle | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const CoordsVec & | oop_atom_pos | ||
| ) |
Calculates the out-of-plane angle \( \chi_{ijk;l} \) between the bond j-l and the plane defined by the atoms i-j-k.
\( \chi_{ijk;l} = \frac{\pi}{2} - \arccos(\frac{\vec{n_{ijk}} \cdot \vec{v_{jl}}}{|\vec{n_{ijk}}| \: |\vec{v_{jl}}|}) \)
where
\( \vec{v_{ji}} = \vec{p_i} - \vec{p_j} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{v_{jl}} = \vec{p_l} - \vec{p_j} \)
\( \vec{n_{ijk}} = \vec{v_{ji}} \times \vec{v_{jk}} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
\( \vec{p_l} \) = coordinates of atom l.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| oop_atom_pos | The position \( \vec{p_l} \) of the out-of-plane atom l. |
| ValueType CDPL::ForceField::calcOutOfPlaneAngle | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const CoordsVec & | oop_atom_pos, | ||
| const ValueType & | r_jl | ||
| ) |
Calculates the out-of-plane angle \( \chi_{ijk;l} \) between the bond j-l and the plane defined by the atoms i-j-k.
\( \chi_{ijk;l} = \frac{\pi}{2} - \arccos(\frac{\vec{n_{ijk}} \cdot \vec{v_{jl}}}{|\vec{n_{ijk}}| \: |\vec{v_{jl}}|}) \)
where
\( \vec{v_{ji}} = \vec{p_i} - \vec{p_j} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{v_{jl}} = \vec{p_l} - \vec{p_j} \)
\( \vec{n_{ijk}} = \vec{v_{ji}} \times \vec{v_{jk}} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
\( \vec{p_l} \) = coordinates of atom l.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| oop_atom_pos | The position \( \vec{p_l} \) of the out-of-plane atom l. |
| r_jl | The length of the bond between atom j and atom l. |
| ValueType CDPL::ForceField::calcDihedralAngleCos | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom1_pos, | ||
| const CoordsVec & | ctr_atom2_pos, | ||
| const CoordsVec & | term_atom2_pos | ||
| ) |
Calculates the cosine of the dihedral angle \( \Phi_{ijkl} \) between the planes defined by the atom triplets i-j-k and j-k-l.
\( \cos(\Phi_{ijkl}) = \frac{\vec{n_{ijk}} \cdot \vec{n_{jkl}}}{|\vec{n_{ijk}}| \: |\vec{n_{jkl}}|} \)
where
\( \vec{v_{ji}} = \vec{p_i} - \vec{p_j} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{v_{lk}} = \vec{p_k} - \vec{p_l} \)
\( \vec{n_{ijk}} = \vec{v_{ji}} \times \vec{v_{jk}} \)
\( \vec{n_{jkl}} = \vec{v_{jk}} \times \vec{v_{lk}} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
\( \vec{p_l} \) = coordinates of atom l.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom1_pos | The position \( \vec{p_j} \) of the central atom j. |
| ctr_atom2_pos | The position \( \vec{p_k} \) of the central atom k. |
| term_atom2_pos | The position \( \vec{p_l} \) of the terminal atom l. |
| ValueType CDPL::ForceField::calcDistanceDerivatives | ( | const CoordsVec & | atom1_pos, |
| const CoordsVec & | atom2_pos, | ||
| GradVec & | atom1_deriv, | ||
| GradVec & | atom2_deriv | ||
| ) |
Calculates the partial derivatives \( \frac{\partial r_{ij}}{\partial \vec{p_x}} \) of the distance \( r_{ij} \) between two atoms i and j.
\( \frac{\partial r_{ij}}{\partial \vec{p_i}} = \frac{-\vec{v_{ij}}}{r_{ij}} \)
\( \frac{\partial r_{ij}}{\partial \vec{p_j}} = \frac{\vec{v_{ij}}}{r_{ij}} \)
\( r_{ij} = |\vec{v_{ij}}| \)
where
\( \vec{v_{ij}} = \vec{p_j} - \vec{p_i} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
| atom1_pos | The position \( \vec{p_i} \) of atom i. |
| atom2_pos | The position \( \vec{p_j} \) of atom j. |
| atom1_deriv | Output variable for the calculated partial derivative \( \frac{\partial r_{ij}}{\partial \vec{p_i}} \) at the given atom positions. |
| atom2_deriv | Output variable for the calculated partial derivative \( \frac{\partial r_{ij}}{\partial \vec{p_j}} \) at the given atom positions. |
| ValueType CDPL::ForceField::calcBondAngleCosDerivatives | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| GradVec & | term_atom1_deriv, | ||
| GradVec & | ctr_atom_deriv, | ||
| GradVec & | term_atom2_deriv | ||
| ) |
Calculates the partial derivatives \( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_x}} \) of the of the cosine of the angle \( \vartheta_{ijk} \) between the bonds i-j and j-k.
\( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_i}} = \frac{\vec{v_{jk}}}{r_{ji} \: r_{jk}} - \frac{\vec{v_{ji}} \: (\vec{v_{ji}} \cdot \vec{v_{jk}})}{r_{ji}^3 \: r_{jk}} \)
\( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_k}} = \frac{\vec{v_{ji}}}{r_{ji} \: r_{jk}} - \frac{\vec{v_{jk}} \: (\vec{v_{ji}} \cdot \vec{v_{jk}})}{r_{ji} \: r_{jk}^3} \)
\( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_j}} = -(\frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_i}} + \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_k}}) \)
\( \cos(\vartheta_{ijk}) = \frac{\vec{v_{ij}} \cdot \vec{v_{jk}}}{r_{ij} \: r_{jk}} \)
where
\( \vec{v_{ji}} = \vec{p_i} - \vec{p_j} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( r_{ji} = |\vec{v_{ji}}| \)
\( r_{jk} = |\vec{v_{jk}}| \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
| term_atom1_pos | The position \( \vec{p_i} \) of atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of atom k. |
| term_atom1_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_i}} \) at the given atom positions. |
| ctr_atom_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_j}} \) at the given atom positions. |
| term_atom2_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\vartheta_{ijk})}{\partial \vec{p_k}} \) at the given atom positions. |
| ValueType CDPL::ForceField::calcDihedralAngleCosDerivatives | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom1_pos, | ||
| const CoordsVec & | ctr_atom2_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| GradVec & | term_atom1_deriv, | ||
| GradVec & | ctr_atom1_deriv, | ||
| GradVec & | ctr_atom2_deriv, | ||
| GradVec & | term_atom2_deriv | ||
| ) |
Calculates the partial derivatives \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_x}} \) of the cosine of the angle \( \Phi_{ijkl} \) between the planes defined by the atom triplets i-j-k and j-k-l.
\( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_i}} = \vec{v_{jk}} \times \vec{a} \)
\( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_j}} = \vec{r_{ki}} \times \vec{a} - \vec{v_{lk}} \times \vec{b} \)
\( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_l}} = \vec{v_{jk}} \times \vec{b} \)
\( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_k}} = -(\frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_i}} + \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_j}} + \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_l}}) \)
\( \cos(\Phi_{ijkl}) = \frac{\vec{n_{ijk}} \cdot \vec{n_{jkl}}}{|\vec{n_{ijk}}| \: |\vec{n_{jkl}}|} \)
where
\( \vec{v_{ji}} = \vec{p_i} - \vec{p_j} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{v_{lk}} = \vec{p_k} - \vec{p_l} \)
\( \vec{r_{ki}} = \vec{p_i} - \vec{p_k} \)
\( \vec{n_{ijk}} = \vec{v_{ji}} \times \vec{v_{jk}} \)
\( \vec{n_{jkl}} = \vec{v_{jk}} \times \vec{v_{lk}} \)
\( \vec{a} = \frac{\frac{\vec{n_{jkl}}}{|\vec{n_{jkl}}|} - \cos(\Phi_{ijkl}) \: \frac{\vec{n_{ijk}}}{|\vec{n_{ijk}}|}}{|\vec{n_{ijk}}|} \)
\( \vec{b} = \frac{\frac{\vec{n_{ijk}}}{|\vec{n_{ijk}}|} - \cos(\Phi_{ijkl}) \: \frac{\vec{n_{jkl}}}{|\vec{n_{jkl}}|}}{|\vec{n_{jkl}}|} \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
\( \vec{p_l} \) = coordinates of atom l.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom1_pos | The position \( \vec{p_j} \) of the central atom j. |
| ctr_atom2_pos | The position \( \vec{p_k} \) of the central atom k. |
| term_atom2_pos | The position \( \vec{p_l} \) of the terminal atom l. |
| term_atom1_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_i}} \) at the given atom positions. |
| ctr_atom1_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_j}} \) at the given atom positions. |
| ctr_atom2_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_k}} \) at the given atom positions. |
| term_atom2_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\Phi_{ijkl})}{\partial \vec{p_l}} \) at the given atom positions. |
| ValueType CDPL::ForceField::calcOutOfPlaneAngleCosDerivatives | ( | const CoordsVec & | term_atom1_pos, |
| const CoordsVec & | ctr_atom_pos, | ||
| const CoordsVec & | term_atom2_pos, | ||
| const CoordsVec & | oop_atom_pos, | ||
| GradVec & | term_atom1_deriv, | ||
| GradVec & | ctr_atom_deriv, | ||
| GradVec & | term_atom2_deriv, | ||
| GradVec & | oop_atom_deriv | ||
| ) |
Calculates the partial derivatives \( \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_x}} \) of the cosine of the angle \( \omega_{ijk;l} \) between the bond j-l and the normal of the plane defined by the atoms i-j-k.
\( \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_i}} = \frac{\vec{v_{jk}} \times \vec{v_{jl}}}{|\vec{n_{ijk}}| \: r_{jl}} - \cos(\omega_{ijk;l}) \: \frac{M_1 \cdot \vec{n_{ijk}}}{|\vec{n_{ijk}}|^2} \)
\( \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_k}} = \frac{\vec{v_{jl}} \times \vec{v_{ji}}}{|\vec{n_{ijk}}| \: r_{jl}} - \cos(\omega_{ijk;l}) \: \frac{M_2 \cdot \vec{n_{ijk}}}{|\vec{n_{ijk}}|^2} \)
\( \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_l}} = \frac{-1}{|\vec{n_{ijk}}| \: r_{jl}} \: (\frac{\vec{v_{jl}} (\vec{n_{ijk}} \cdot \vec{v_{jl}})}{r_{jl}^2} + \vec{r_{kl}} \times \vec{v_{il}} + \vec{v_{jl}} \times \vec{v_{ji}} + \vec{v_{jk}} \times \vec{v_{jl}}) \)
\( \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_j}} = -(\frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_i}} + \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_k}} + \frac{\partial \cos(\omega_{ijk;l})}{\partial \vec{p_l}}) \)
\( \cos(\omega_{ijk;l}) = \frac{\vec{n_{ijk}} \cdot \vec{v_{jl}}}{|\vec{n_{ijk}}| \: r_{jl}} \)
where
\( M_1 = \begin{vmatrix} 0 & -\vec{v_{jk}}.z & \vec{v_{jk}}.y \\ \vec{v_{jk}}.z & 0 & -\vec{v_{jk}}.x \\ -\vec{v_{jk}}.y & \vec{v_{jk}}.x & 0 \end{vmatrix} \)
\( M_2 = \begin{vmatrix} 0 & \vec{v_{ji}}.z & -\vec{v_{ji}}.y \\ -\vec{v_{ji}}.z & 0 & \vec{v_{ji}}.x \\ \vec{v_{ji}}.y & -\vec{v_{ji}}.x & 0 \end{vmatrix} \)
\( \vec{v_{ji}} = \vec{p_i} - \vec{p_j} \)
\( \vec{v_{jk}} = \vec{p_k} - \vec{p_j} \)
\( \vec{v_{jl}} = \vec{p_l} - \vec{p_j} \)
\( \vec{r_{kl}} = \vec{p_l} - \vec{p_k} \)
\( \vec{v_{il}} = \vec{p_l} - \vec{p_i} \)
\( \vec{n_{ijk}} = \vec{v_{ji}} \times \vec{v_{jk}} \)
\( r_{jl} = |\vec{v_{jl}}| \)
\( \vec{p_i} \) = coordinates of atom i.
\( \vec{p_j} \) = coordinates of atom j.
\( \vec{p_k} \) = coordinates of atom k.
\( \vec{p_l} \) = coordinates of atom l.
| term_atom1_pos | The position \( \vec{p_i} \) of the terminal atom i. |
| ctr_atom_pos | The position \( \vec{p_j} \) of the central atom j. |
| term_atom2_pos | The position \( \vec{p_k} \) of the terminal atom k. |
| oop_atom_pos | The position \( \vec{p_l} \) of the out-of-plane atom l. |
| term_atom1_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\omega_{ijkl})}{\partial \vec{p_i}} \) at the given atom positions. |
| ctr_atom_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\omega_{ijkl})}{\partial \vec{p_j}} \) at the given atom positions. |
| term_atom2_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\omega_{ijkl})}{\partial \vec{p_k}} \) at the given atom positions. |
| oop_atom_deriv | Output variable for the calculated partial derivative \( \frac{\partial \cos(\omega_{ijkl})}{\partial \vec{p_l}} \) at the given atom positions. |
1.9.1