Contains classes and functions related to molecular force fields. More...

Classes
class	AtomProperty
	Provides keys for built-in Chem.Atom properties. More...

class	BondProperty
	Provides keys for built-in Chem.Bond properties. More...

class	ElasticPotential
	Stores parameters for an elastic potential (harmonic distance restraint) between a pair of atoms. More...

class	ElasticPotentialList
	Data structure for the storage of elastic potential parameter set records. More...

class	Error
	Base class of the ForceField subsystem exception hierarchy. More...

class	InteractionFilterFunction3
	Generic wrapper for storing user-defined three-atom interaction filtering functions (see [FUNWRP]). More...

class	InteractionFilterFunction4
	Generic wrapper for storing user-defined four-atom interaction filtering functions (see [FUNWRP]). More...

class	InteractionType
	Provides flags for the specification of a set of force field interaction types. More...

class	MMFF94AngleBendingInteraction
	Stores parameters for a single MMFF94 angle-bending interaction defined over an atom triplet. More...

class	MMFF94AngleBendingInteractionList
	Data structure for the storage of MMFF94 angle-bending interaction parameter set records. 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	MMFF94AtomChargeFunction
	Generic wrapper class used to store a user-defined MMFF94 partial atom charge retrieval function. 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	MMFF94BondStretchingInteractionList
	Data structure for the storage of MMFF94 bond-stretching interaction parameter set records. 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	MMFF94BondTypeIndexFunction
	Generic wrapper class used to store a user-defined MMFF94 bond type index retrieval function. 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	MMFF94ElectrostaticInteractionList
	Data structure for the storage of MMFF94 electrostatic interaction parameter set records. 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 parameters for a molecular graph. More...

class	MMFF94InteractionParameterizer
	Highly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization. More...

class	MMFF94NumericAtomTypeFunction
	Generic wrapper class used to store a user-defined numeric MMFF94 atom type retrieval function. More...

class	MMFF94OutOfPlaneBendingInteraction
	Stores parameters for a single MMFF94 out-of-plane bending interaction at a trigonal center. More...

class	MMFF94OutOfPlaneBendingInteractionList
	Data structure for the storage of MMFF94 out-of-plane bending interaction parameter set records. 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	MMFF94ParameterSet
	Provides constants for MMFF94 parameter set variant specification. 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	MMFF94RingSetFunction
	Generic wrapper class used to store a user-defined MMFF94 ring set retrieval function. More...

class	MMFF94StretchBendInteraction
	Stores paramters for a single MMFF94 stretch-bend coupling interaction. More...

class	MMFF94StretchBendInteractionList
	Data structure for the storage of MMFF94 stretch-bend coupling interaction parameter set records. More...

class	MMFF94StretchBendInteractionParameterizer

class	MMFF94StretchBendParameterTable
	Data structure for the storage and lookup of MMFF94 stretch-bend interaction parameters. More...

class	MMFF94SymbolicAtomTypeFunction
	Generic wrapper class used to store a user-defined symbolic MMFF94 atom type retrieval function. 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	MMFF94TorsionInteractionList
	Data structure for the storage of MMFF94 torsion interaction parameter set records. 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	MMFF94VanDerWaalsAtomParameters

class	MMFF94VanDerWaalsInteraction
	Stores parameters for a single MMFF94 Van der Waals interaction between two non-bonded atoms. More...

class	MMFF94VanDerWaalsInteractionList
	Data structure for the storage of MMFF94 Van der Waals interaction parameter set records. 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	MolecularGraphProperty
	Provides keys for built-in Chem.MolecularGraph properties. More...

class	ParameterizationFailed
	Thrown when force field parameterization has failed. More...

class	TopologicalAtomDistanceFunction
	Generic wrapper class used to store a user-defined topological atom-pair distance function. More...

class	UFFAtomType
	Provides constants for the specification of numeric Universal Force Field (UFF) atom types. More...

class	UFFAtomTypePropertyTable
	Data structure for the storage and lookup of various properties associated with numeric UFF atom types. More...

Functions
None	setMMFF94AromaticRings (Chem.MolecularGraph molgraph, Chem.FragmentList rings)
	Sets the value of the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph to rings. More...

bool	hasMMFF94AromaticRings (Chem.MolecularGraph molgraph)
	Tells whether the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph is set. More...

Chem.FragmentList	getMMFF94AromaticRings (Chem.MolecularGraph molgraph)
	Returns the value of the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph. More...

None	clearMMFF94AromaticRings (Chem.MolecularGraph molgraph)
	Clears the value of the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph. More...

None	setMMFF94Charge (Chem.Atom atom, float charge)
	Sets the value of the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom to charge. More...

bool	hasMMFF94Charge (Chem.Atom atom)
	Tells whether the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom is set. More...

float	getMMFF94Charge (Chem.Atom atom)
	Returns the value of the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom. More...

None	clearMMFF94Charge (Chem.Atom atom)
	Clears the value of the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom. More...

None	setMMFF94NumericType (Chem.Atom atom, int type)
	Sets the value of the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom to type. More...

bool	hasMMFF94NumericType (Chem.Atom atom)
	Tells whether the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom is set. More...

int	getMMFF94NumericType (Chem.Atom atom)
	Returns the value of the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom. More...

None	clearMMFF94NumericType (Chem.Atom atom)
	Clears the value of the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom. More...

None	setMMFF94SymbolicType (Chem.Atom atom, str type)
	Sets the value of the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom to type. More...

bool	hasMMFF94SymbolicType (Chem.Atom atom)
	Tells whether the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom is set. More...

str	getMMFF94SymbolicType (Chem.Atom atom)
	Returns the value of the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom. More...

None	clearMMFF94SymbolicType (Chem.Atom atom)
	Clears the value of the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom. More...

None	setMMFF94TypeIndex (Chem.Bond bond, int type_idx)
	Sets the value of the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond to type_idx. More...

bool	hasMMFF94TypeIndex (Chem.Bond bond)
	Tells whether the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond is set. More...

int	getMMFF94TypeIndex (Chem.Bond bond)
	Returns the value of the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond. More...

None	clearMMFF94TypeIndex (Chem.Bond bond)
	Clears the value of the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond. More...

None	setUFFType (Chem.Atom atom, int type)
	Sets the value of the ForceField.AtomProperty.UFF_TYPE property of the atom atom to type. More...

bool	hasUFFType (Chem.Atom atom)
	Tells whether the ForceField.AtomProperty.UFF_TYPE property of the atom atom is set. More...

int	getUFFType (Chem.Atom atom)
	Returns the value of the ForceField.AtomProperty.UFF_TYPE property of the atom atom. More...

None	clearUFFType (Chem.Atom atom)
	Clears the value of the ForceField.AtomProperty.UFF_TYPE property of the atom atom. More...

None	assignMMFF94AtomTypes (Chem.MolecularGraph molgraph, bool strict, bool overwrite)
	Assigns MMFF94 atom types to the atoms of the molecular graph molgraph. More...

None	assignMMFF94BondTypeIndices (Chem.MolecularGraph molgraph, bool strict, bool overwrite)
	Assigns MMFF94 bond type indices to the bonds of the molecular graph molgraph. More...

None	assignUFFAtomTypes (Chem.MolecularGraph molgraph, bool overwrite)
	Assigns UFF atom types to the atoms of the molecular graph molgraph. More...

float	calcBondAngleCosDerivatives (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D term_atom1_deriv, Math.Vector3D ctr_atom_deriv, Math.Vector3D 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...

float	calcBondAngleCos (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, float r_ij, float r_jk)
	Calculates the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More...

float	calcBondAngleCos (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos)
	Calculates the cosine of the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More...

float	calcBondAngle (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, float r_ij, float r_jk)
	Calculates the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More...

float	calcBondAngle (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos)
	Calculates the bond angle \( \vartheta_{ijk} \) between the two bonds i-j and j-k. More...

tuple	calcBondLengthsAndAngleCos (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos)

tuple	calcBondLengthsAndAngle (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos)

float	calcDihedralAngleCosDerivatives (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom1_pos, Math.Vector3D ctr_atom2_pos, Math.Vector3D term_atom2_pos, Math.Vector3D term_atom1_deriv, Math.Vector3D ctr_atom1_deriv, Math.Vector3D ctr_atom2_deriv, Math.Vector3D 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...

float	calcDihedralAngleCos (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom1_pos, Math.Vector3D ctr_atom2_pos, Math.Vector3D 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...

float	calcDistanceDerivatives (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, Math.Vector3D atom1_deriv, Math.Vector3D 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...

float	calcDistance (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos)
	Calculates the distance \( r_{ij} \) between two atoms i and j. More...

float	calcElasticPotentialEnergy (ElasticPotential pot, Math.Vector3DArray coords)
	Calculates the energy of a single elastic potential pot for the supplied atom coordinates coords. More...

float	calcElasticPotentialEnergy (ElasticPotentialList list, Math.Vector3DArray coords)

float	calcElasticPotentialEnergy (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, float force_const, float ref_length)
	Calculates the energy \( E_{ij} \) of an elastic potential applied on a pair of atoms i-j. More...

float	calcElasticPotentialGradient (ElasticPotential pot, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the energy and gradient contribution of a single elastic potential pot for the supplied atom coordinates coords. More...

float	calcElasticPotentialGradient (ElasticPotentialList list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcElasticPotentialGradient (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, Math.Vector3D atom1_grad, Math.Vector3D atom2_grad, float force_const, float ref_length)
	Calculates the elastic potential energy gradient \( \nabla E_{ij} \) for a pair of atoms i-j. More...

float	calcMMFF94AngleBendingEnergy (MMFF94AngleBendingInteraction iaction, Math.Vector3DArray coords)
	Calculates the angle-bending interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94AngleBendingEnergy (MMFF94AngleBendingInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94AngleBendingEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, bool linear, float force_const, float ref_angle)
	Calculates the angle bending interaction energy \( EA_{ijk} \) for two bonds i-j and j-k. More...

float	calcMMFF94AngleBendingEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, float r_ij, float r_jk, bool linear, float force_const, float ref_angle)
	Calculates the angle bending interaction energy \( EA_{ijk} \) for two bonds i-j and j-k. More...

float	calcMMFF94AngleBendingGradient (MMFF94AngleBendingInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the angle-bending interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94AngleBendingGradient (MMFF94AngleBendingInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94AngleBendingGradient (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D term_atom1_grad, Math.Vector3D ctr_atom_grad, Math.Vector3D term_atom2_grad, bool linear, float force_const, float ref_angle)
	Calculates the angle bending interaction energy gradient \( \nabla EA_{ijk} \) for two bonds i-j and j-k. More...

None	calcMMFF94AtomCharges (Chem.MolecularGraph molgraph, bool strict, bool overwrite)
	Calculates and assigns MMFF94 partial atomic charges to the atoms of the molecular graph molgraph. More...

float	calcMMFF94BondStretchingEnergy (MMFF94BondStretchingInteraction iaction, Math.Vector3DArray coords)
	Calculates the bond-stretching interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94BondStretchingEnergy (MMFF94BondStretchingInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94BondStretchingEnergy (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, float force_const, float ref_length)
	Calculates the bond stretching interaction energy \( EB_{ij} \) for the bond i-j. More...

float	calcMMFF94BondStretchingEnergy (float r_ij, float force_const, float ref_length)
	Calculates the bond stretching interaction energy \( EB_{ij} \) for the bond i-j. More...

float	calcMMFF94BondStretchingGradient (MMFF94BondStretchingInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the bond-stretching interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94BondStretchingGradient (MMFF94BondStretchingInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94BondStretchingGradient (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, Math.Vector3D atom1_grad, Math.Vector3D atom2_grad, float force_const, float ref_length)
	Calculates the bond stretching interaction energy gradient \( \nabla EB_{ij} \) for the bond i-j. More...

float	calcMMFF94ElectrostaticEnergy (MMFF94ElectrostaticInteraction iaction, Math.Vector3DArray coords)
	Calculates the electrostatic interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94ElectrostaticEnergy (MMFF94ElectrostaticInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94ElectrostaticEnergy (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, float atom1_chg, float atom2_chg, float scale_fact, float de_const, float dist_expo)
	Calculates the electrostatic interaction energy \( EQ_{ij} \) for the atom pair i-j. More...

float	calcMMFF94ElectrostaticEnergy (float r_ij, float atom1_chg, float atom2_chg, float scale_fact, float de_const, float dist_expo)
	Calculates the electrostatic interaction energy \( EQ_{ij} \) for the atom pair i-j. More...

float	calcMMFF94ElectrostaticGradient (MMFF94ElectrostaticInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the electrostatic interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94ElectrostaticGradient (MMFF94ElectrostaticInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94ElectrostaticGradient (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, Math.Vector3D atom1_grad, Math.Vector3D atom2_grad, float atom1_chg, float atom2_chg, float scale_fact, float de_const, float dist_expo)
	Calculates the electrostatic interaction energy gradient \( \nabla EQ_{ij} \) for the atom pair i-j. More...

float	calcMMFF94OutOfPlaneBendingEnergy (MMFF94OutOfPlaneBendingInteraction iaction, Math.Vector3DArray coords)
	Calculates the out-of-plane bending interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94OutOfPlaneBendingEnergy (MMFF94OutOfPlaneBendingInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94OutOfPlaneBendingEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D oop_atom_pos, float 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...

float	calcMMFF94OutOfPlaneBendingEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D oop_atom_pos, float r_jl, float 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...

float	calcMMFF94OutOfPlaneBendingGradient (MMFF94OutOfPlaneBendingInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the out-of-plane bending interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94OutOfPlaneBendingGradient (MMFF94OutOfPlaneBendingInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94OutOfPlaneBendingGradient (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D oop_atom_pos, Math.Vector3D term_atom1_grad, Math.Vector3D ctr_atom_grad, Math.Vector3D term_atom2_grad, Math.Vector3D oop_atom_grad, float 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...

float	calcMMFF94StretchBendEnergy (MMFF94StretchBendInteraction iaction, Math.Vector3DArray coords)
	Calculates the stretch-bend coupling interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94StretchBendEnergy (MMFF94StretchBendInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94StretchBendEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, float ijk_force_const, float kji_force_const, float ref_angle, float ref_length1, float ref_length2)
	Calculates the stretch-bend interaction energy \( EBA_{ijk} \) for two bonds i-j and j-k. More...

float	calcMMFF94StretchBendEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, float r_ij, float r_jk, float ijk_force_const, float kji_force_const, float ref_angle, float ref_length1, float ref_length2)
	Calculates the stretch-bend interaction energy \( EBA_{ijk} \) for two bonds i-j and j-k. More...

float	calcMMFF94StretchBendGradient (MMFF94StretchBendInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the stretch-bend coupling interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94StretchBendGradient (MMFF94StretchBendInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94StretchBendGradient (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D term_atom1_grad, Math.Vector3D ctr_atom_grad, Math.Vector3D term_atom2_grad, float ijk_force_const, float kji_force_const, float ref_angle, float ref_length1, float ref_length2)
	Calculates the stretch-bend interaction energy gradient \( \nabla EBA_{ijk} \) for two bonds i-j and j-k. More...

float	calcMMFF94TorsionEnergy (MMFF94TorsionInteraction iaction, Math.Vector3DArray coords)
	Calculates the torsion interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94TorsionEnergy (MMFF94TorsionInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94TorsionEnergy (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom1_pos, Math.Vector3D ctr_atom2_pos, Math.Vector3D term_atom2_pos, float tor_param1, float tor_param2, float 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...

float	calcMMFF94TorsionGradient (MMFF94TorsionInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the torsion interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94TorsionGradient (MMFF94TorsionInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94TorsionGradient (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom1_pos, Math.Vector3D ctr_atom2_pos, Math.Vector3D term_atom2_pos, Math.Vector3D term_atom1_grad, Math.Vector3D ctr_atom1_grad, Math.Vector3D ctr_atom2_grad, Math.Vector3D term_atom2_grad, float tor_param1, float tor_param2, float 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...

float	calcMMFF94VanDerWaalsEnergy (MMFF94VanDerWaalsInteraction iaction, Math.Vector3DArray coords)
	Calculates the Van der Waals interaction energy of iaction using the geometry from coords. More...

float	calcMMFF94VanDerWaalsEnergy (MMFF94VanDerWaalsInteractionList ia_list, Math.Vector3DArray coords)

float	calcMMFF94VanDerWaalsEnergy (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, float e_IJ, float r_IJ, float r_IJ_7)
	Calculates the Van der Waals interaction energy \( E_{vdW_{ij}} \) for the atom pair i-j. More...

float	calcMMFF94VanDerWaalsEnergy (float r_ij, float e_IJ, float r_IJ, float r_IJ_7)
	Calculates the Van der Waals interaction energy \( E_{vdW_{ij}} \) for the atom pair i-j. More...

float	calcMMFF94VanDerWaalsGradient (MMFF94VanDerWaalsInteraction iaction, Math.Vector3DArray coords, Math.Vector3DArray grad)
	Calculates the Van der Waals interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad. More...

float	calcMMFF94VanDerWaalsGradient (MMFF94VanDerWaalsInteractionList ia_list, Math.Vector3DArray coords, Math.Vector3DArray grad)

float	calcMMFF94VanDerWaalsGradient (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos, Math.Vector3D atom1_grad, Math.Vector3D atom2_grad, float e_IJ, float r_IJ, float r_IJ_7)
	Calculates the Van der Waals interaction energy gradient \( \nabla E_{vdW_{ij}} \) for the atom pair i-j. More...

float	calcOutOfPlaneAngleCosDerivatives (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D oop_atom_pos, Math.Vector3D term_atom1_deriv, Math.Vector3D ctr_atom_deriv, Math.Vector3D term_atom2_deriv, Math.Vector3D 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...

float	calcOutOfPlaneAngle (Math.Vector3D term_atom1_pos, Math.Vector3D ctr_atom_pos, Math.Vector3D term_atom2_pos, Math.Vector3D oop_atom_pos, float 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...

float	calcSquaredDistance (Math.Vector3D atom1_pos, Math.Vector3D atom2_pos)
	Calculates the squared distance \( r_{ij}^2 \) between two atoms i and j. More...

None	filterInteractions (MMFF94InteractionData ia_data, MMFF94InteractionData filtered_ia_data, Util.BitSet inc_atom_mask)
	Filters an MMFF94 interaction data set, retaining only those interactions that exclusively reference atoms in inc_atom_mask. More...

Chem.FragmentList	perceiveMMFF94AromaticRings (Chem.MolecularGraph molgraph)
	Perceives the list of MMFF94 aromatic rings of the molecular graph molgraph. More...

Chem.FragmentList	perceiveMMFF94AromaticRings (Chem.MolecularGraph molgraph, bool overwrite)
	Perceives and (optionally) stores the list of MMFF94 aromatic rings of the molecular graph molgraph. More...

int	perceiveUFFType (Chem.Atom atom, Chem.MolecularGraph molgraph)
	Perceives the UFF atom type of the atom atom in the context of the molecular graph molgraph. More...

Detailed Description

Contains classes and functions related to molecular force fields.

Function Documentation

◆ setMMFF94AromaticRings()

None CDPL.ForceField.setMMFF94AromaticRings	(	Chem.MolecularGraph	molgraph,
		Chem.FragmentList	rings
	)

Sets the value of the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph to rings.

Parameters

molgraph	The molecular graph for which to set the property value.
rings	The new list of MMFF94 aromatic rings.

◆ hasMMFF94AromaticRings()

bool CDPL.ForceField.hasMMFF94AromaticRings ( Chem.MolecularGraph molgraph )

Tells whether the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph is set.

Parameters

molgraph The molecular graph for which to query the property value.

Returns: True if the property is set, and False otherwise.

◆ getMMFF94AromaticRings()

Chem.FragmentList CDPL.ForceField.getMMFF94AromaticRings ( Chem.MolecularGraph molgraph )

Returns the value of the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph.

Parameters

molgraph The molecular graph for which to return the property value.

Returns: A shared reference to the list of MMFF94 aromatic rings.

◆ clearMMFF94AromaticRings()

None CDPL.ForceField.clearMMFF94AromaticRings ( Chem.MolecularGraph molgraph )

Clears the value of the ForceField.MolecularGraphProperty.MMFF94_AROMATIC_RINGS property of the molecular graph molgraph.

Parameters

molgraph The molecular graph for which to clear the property value.

◆ setMMFF94Charge()

None CDPL.ForceField.setMMFF94Charge	(	Chem.Atom	atom,
		float	charge
	)

Sets the value of the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom to charge.

Parameters

atom	The atom for which to set the property value.
charge	The new MMFF94 partial atomic charge.

◆ hasMMFF94Charge()

bool CDPL.ForceField.hasMMFF94Charge ( Chem.Atom atom )

Tells whether the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the MMFF94 partial atomic charge is set, and False otherwise.

◆ getMMFF94Charge()

float CDPL.ForceField.getMMFF94Charge ( Chem.Atom atom )

Returns the value of the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The MMFF94 partial atomic charge.

◆ clearMMFF94Charge()

None CDPL.ForceField.clearMMFF94Charge ( Chem.Atom atom )

Clears the value of the ForceField.AtomProperty.MMFF94_CHARGE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ setMMFF94NumericType()

None CDPL.ForceField.setMMFF94NumericType	(	Chem.Atom	atom,
		int	type
	)

Sets the value of the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new numeric MMFF94 atom type.

◆ hasMMFF94NumericType()

bool CDPL.ForceField.hasMMFF94NumericType ( Chem.Atom atom )

Tells whether the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the numeric MMFF94 atom type is set, and False otherwise.

◆ getMMFF94NumericType()

int CDPL.ForceField.getMMFF94NumericType ( Chem.Atom atom )

Returns the value of the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The numeric MMFF94 atom type.

◆ clearMMFF94NumericType()

None CDPL.ForceField.clearMMFF94NumericType ( Chem.Atom atom )

Clears the value of the ForceField.AtomProperty.MMFF94_NUMERIC_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ setMMFF94SymbolicType()

None CDPL.ForceField.setMMFF94SymbolicType	(	Chem.Atom	atom,
		str	type
	)

Sets the value of the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new symbolic MMFF94 atom type.

◆ hasMMFF94SymbolicType()

bool CDPL.ForceField.hasMMFF94SymbolicType ( Chem.Atom atom )

Tells whether the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the symbolic MMFF94 atom type is set, and False otherwise.

◆ getMMFF94SymbolicType()

str CDPL.ForceField.getMMFF94SymbolicType ( Chem.Atom atom )

Returns the value of the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The symbolic MMFF94 atom type.

◆ clearMMFF94SymbolicType()

None CDPL.ForceField.clearMMFF94SymbolicType ( Chem.Atom atom )

Clears the value of the ForceField.AtomProperty.MMFF94_SYMBOLIC_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ setMMFF94TypeIndex()

None CDPL.ForceField.setMMFF94TypeIndex	(	Chem.Bond	bond,
		int	type_idx
	)

Sets the value of the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond to type_idx.

Parameters

bond	The bond for which to set the property value.
type_idx	The new MMFF94 bond type index.

◆ hasMMFF94TypeIndex()

bool CDPL.ForceField.hasMMFF94TypeIndex ( Chem.Bond bond )

Tells whether the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond is set.

Parameters

bond	The bond for which to query the property value.

Returns: True if the MMFF94 bond type index is set, and False otherwise.

◆ getMMFF94TypeIndex()

int CDPL.ForceField.getMMFF94TypeIndex ( Chem.Bond bond )

Returns the value of the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond.

Parameters

bond	The bond for which to return the property value.

Returns: The MMFF94 bond type index.

◆ clearMMFF94TypeIndex()

None CDPL.ForceField.clearMMFF94TypeIndex ( Chem.Bond bond )

Clears the value of the ForceField.BondProperty.MMFF94_TYPE_INDEX property of the bond bond.

Parameters

bond	The bond for which to clear the property value.

◆ setUFFType()

None CDPL.ForceField.setUFFType	(	Chem.Atom	atom,
		int	type
	)

Sets the value of the ForceField.AtomProperty.UFF_TYPE property of the atom atom to type.

Parameters

atom	The atom for which to set the property value.
type	The new numeric UFF atom type.

◆ hasUFFType()

bool CDPL.ForceField.hasUFFType ( Chem.Atom atom )

Tells whether the ForceField.AtomProperty.UFF_TYPE property of the atom atom is set.

Parameters

atom	The atom for which to query the property value.

Returns: True if the numeric UFF atom type is set, and False otherwise.

◆ getUFFType()

int CDPL.ForceField.getUFFType ( Chem.Atom atom )

Returns the value of the ForceField.AtomProperty.UFF_TYPE property of the atom atom.

Parameters

atom	The atom for which to return the property value.

Returns: The numeric UFF atom type.

◆ clearUFFType()

None CDPL.ForceField.clearUFFType ( Chem.Atom atom )

Clears the value of the ForceField.AtomProperty.UFF_TYPE property of the atom atom.

Parameters

atom	The atom for which to clear the property value.

◆ assignMMFF94AtomTypes()

None CDPL.ForceField.assignMMFF94AtomTypes	(	Chem.MolecularGraph	molgraph,
		bool	strict,
		bool	overwrite
	)

Assigns MMFF94 atom types to the atoms of the molecular graph molgraph.

Parameters

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.

◆ assignMMFF94BondTypeIndices()

None CDPL.ForceField.assignMMFF94BondTypeIndices	(	Chem.MolecularGraph	molgraph,
		bool	strict,
		bool	overwrite
	)

Assigns MMFF94 bond type indices to the bonds of the molecular graph molgraph.

Parameters

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.

◆ assignUFFAtomTypes()

None CDPL.ForceField.assignUFFAtomTypes	(	Chem.MolecularGraph	molgraph,
		bool	overwrite
	)

Assigns UFF atom types to the atoms of the molecular graph molgraph.

Parameters

molgraph	The molecular graph whose atoms will be typed.
overwrite	Specifies whether already assigned atom type properties should be replaced.

◆ calcBondAngleCosDerivatives()

float CDPL.ForceField.calcBondAngleCosDerivatives	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	term_atom1_deriv,
		Math.Vector3D	ctr_atom_deriv,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated cosine of the bond angle \( \vartheta_{ijk} \).

◆ calcBondAngleCos() [1/2]

float CDPL.ForceField.calcBondAngleCos	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		float	r_ij,
		float	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.

Parameters

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.

Returns: The calculated cosine of the bond angle \( \vartheta_{ijk} \).

◆ calcBondAngleCos() [2/2]

float CDPL.ForceField.calcBondAngleCos	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated cosine of the bond angle \( \vartheta_{ijk} \).

◆ calcBondAngle() [1/2]

float CDPL.ForceField.calcBondAngle	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		float	r_ij,
		float	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.

Parameters

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.

Returns: The calculated bond angle \( \vartheta_{ijk} \).

◆ calcBondAngle() [2/2]

float CDPL.ForceField.calcBondAngle	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated bond angle \( \vartheta_{ijk} \).

◆ calcBondLengthsAndAngleCos()

tuple CDPL.ForceField.calcBondLengthsAndAngleCos	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos
	)

Parameters

term_atom1_pos
ctr_atom_pos
term_atom2_pos

Returns

◆ calcBondLengthsAndAngle()

tuple CDPL.ForceField.calcBondLengthsAndAngle	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos
	)

Parameters

term_atom1_pos
ctr_atom_pos
term_atom2_pos

Returns

◆ calcDihedralAngleCosDerivatives()

float CDPL.ForceField.calcDihedralAngleCosDerivatives	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom1_pos,
		Math.Vector3D	ctr_atom2_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	term_atom1_deriv,
		Math.Vector3D	ctr_atom1_deriv,
		Math.Vector3D	ctr_atom2_deriv,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated cosine of the dihedral angle \( \Phi_{ijkl} \).

◆ calcDihedralAngleCos()

float CDPL.ForceField.calcDihedralAngleCos	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom1_pos,
		Math.Vector3D	ctr_atom2_pos,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated cosine of the dihedral angle \( \Phi_{ijkl} \).

◆ calcDistanceDerivatives()

float CDPL.ForceField.calcDistanceDerivatives	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		Math.Vector3D	atom1_deriv,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated distance \( r_{ij} \).

◆ calcDistance()

float CDPL.ForceField.calcDistance	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	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.

Parameters

atom1_pos	The position \( \vec{p_i} \) of atom i.
atom2_pos	The position \( \vec{p_j} \) of atom j.

Returns: The calculated distance \( r_{ij} \).

◆ calcElasticPotentialEnergy() [1/3]

float CDPL.ForceField.calcElasticPotentialEnergy	(	ElasticPotential	pot,
		Math.Vector3DArray	coords
	)

Calculates the energy of a single elastic potential pot for the supplied atom coordinates coords.

Parameters

pot	The parameters of the elastic potential to evaluate.
coords	The atom 3D coordinates for which the energy shall be calculated.

Returns: The calculated elastic potential energy.

Since: 1.1

◆ calcElasticPotentialEnergy() [2/3]

float CDPL.ForceField.calcElasticPotentialEnergy	(	ElasticPotentialList	list,
		Math.Vector3DArray	coords
	)

Parameters

list
coords

Returns

◆ calcElasticPotentialEnergy() [3/3]

float CDPL.ForceField.calcElasticPotentialEnergy	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		float	force_const,
		float	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.

Parameters

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 \( r_{ij}^0 \).

Returns: The calculated elastic potential energy \( E_{ij} \).

Since: 1.1

◆ calcElasticPotentialGradient() [1/3]

float CDPL.ForceField.calcElasticPotentialGradient	(	ElasticPotential	pot,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the energy and gradient contribution of a single elastic potential pot for the supplied atom coordinates coords.

Parameters

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.

Returns: The calculated elastic potential energy.

Note: Gradient contributions for the two atoms are added to the corresponding entries of grad.

Since: 1.1

◆ calcElasticPotentialGradient() [2/3]

float CDPL.ForceField.calcElasticPotentialGradient	(	ElasticPotentialList	list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

list
coords
grad

Returns

◆ calcElasticPotentialGradient() [3/3]

float CDPL.ForceField.calcElasticPotentialGradient	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		Math.Vector3D	atom1_grad,
		Math.Vector3D	atom2_grad,
		float	force_const,
		float	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.

Parameters

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 \( r_{ij}^0 \).

Returns: The calculated elastic potential energy \( E_{ij} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

Since: 1.1

◆ calcMMFF94AngleBendingEnergy() [1/4]

float CDPL.ForceField.calcMMFF94AngleBendingEnergy	(	MMFF94AngleBendingInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the angle-bending interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 angle-bending interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The angle-bending interaction energy of iaction.

◆ calcMMFF94AngleBendingEnergy() [2/4]

float CDPL.ForceField.calcMMFF94AngleBendingEnergy	(	MMFF94AngleBendingInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94AngleBendingEnergy() [3/4]

float CDPL.ForceField.calcMMFF94AngleBendingEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		bool	linear,
		float	force_const,
		float	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.

Parameters

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 \( \vartheta_{IJK}^0 \).

Returns: The calculated angle bending interaction energy \( EA_{ijk} \).

◆ calcMMFF94AngleBendingEnergy() [4/4]

float CDPL.ForceField.calcMMFF94AngleBendingEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		float	r_ij,
		float	r_jk,
		bool	linear,
		float	force_const,
		float	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.

Parameters

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 \( \vartheta_{IJK}^0 \).

Returns: The calculated angle bending interaction energy \( EA_{ijk} \).

◆ calcMMFF94AngleBendingGradient() [1/3]

float CDPL.ForceField.calcMMFF94AngleBendingGradient	(	MMFF94AngleBendingInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the angle-bending interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 angle-bending interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The angle-bending interaction energy of iaction.

◆ calcMMFF94AngleBendingGradient() [2/3]

float CDPL.ForceField.calcMMFF94AngleBendingGradient	(	MMFF94AngleBendingInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94AngleBendingGradient() [3/3]

float CDPL.ForceField.calcMMFF94AngleBendingGradient	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	term_atom1_grad,
		Math.Vector3D	ctr_atom_grad,
		Math.Vector3D	term_atom2_grad,
		bool	linear,
		float	force_const,
		float	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.

Parameters

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 \( \vartheta_{IJK}^0 \).

Returns: The calculated angle bending interaction energy \( EA_{ijk} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcMMFF94AtomCharges()

None 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.

Parameters

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.

◆ calcMMFF94BondStretchingEnergy() [1/4]

float CDPL.ForceField.calcMMFF94BondStretchingEnergy	(	MMFF94BondStretchingInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the bond-stretching interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 bond-stretching interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The bond-stretching interaction energy of iaction.

◆ calcMMFF94BondStretchingEnergy() [2/4]

float CDPL.ForceField.calcMMFF94BondStretchingEnergy	(	MMFF94BondStretchingInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94BondStretchingEnergy() [3/4]

float CDPL.ForceField.calcMMFF94BondStretchingEnergy	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		float	force_const,
		float	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).

Parameters

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 \( r_{IJ}^0 \).

Returns: The calculated bond stretching interaction energy \( EB_{ij} \).

◆ calcMMFF94BondStretchingEnergy() [4/4]

float CDPL.ForceField.calcMMFF94BondStretchingEnergy	(	float	r_ij,
		float	force_const,
		float	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).

Parameters

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 \( r_{IJ}^0 \).

Returns: The calculated bond stretching interaction energy \( EB_{ij} \).

◆ calcMMFF94BondStretchingGradient() [1/3]

float CDPL.ForceField.calcMMFF94BondStretchingGradient	(	MMFF94BondStretchingInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the bond-stretching interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 bond-stretching interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The bond-stretching interaction energy of iaction.

◆ calcMMFF94BondStretchingGradient() [2/3]

float CDPL.ForceField.calcMMFF94BondStretchingGradient	(	MMFF94BondStretchingInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94BondStretchingGradient() [3/3]

float CDPL.ForceField.calcMMFF94BondStretchingGradient	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		Math.Vector3D	atom1_grad,
		Math.Vector3D	atom2_grad,
		float	force_const,
		float	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).

Parameters

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 \( r_{IJ}^0 \).

Returns: The calculated bond stretching interaction energy \( EB_{ij} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcMMFF94ElectrostaticEnergy() [1/4]

float CDPL.ForceField.calcMMFF94ElectrostaticEnergy	(	MMFF94ElectrostaticInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the electrostatic interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 electrostatic interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The electrostatic interaction energy of iaction.

◆ calcMMFF94ElectrostaticEnergy() [2/4]

float CDPL.ForceField.calcMMFF94ElectrostaticEnergy	(	MMFF94ElectrostaticInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94ElectrostaticEnergy() [3/4]

float CDPL.ForceField.calcMMFF94ElectrostaticEnergy	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		float	atom1_chg,
		float	atom2_chg,
		float	scale_fact,
		float	de_const,
		float	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 \( EQ_{14} \: 0.75 \)).

Parameters

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 \( n \).

Returns: The calculated electrostatic interaction energy \( EQ_{ij} \).

◆ calcMMFF94ElectrostaticEnergy() [4/4]

float CDPL.ForceField.calcMMFF94ElectrostaticEnergy	(	float	r_ij,
		float	atom1_chg,
		float	atom2_chg,
		float	scale_fact,
		float	de_const,
		float	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 \( EQ_{14} \: 0.75 \)).

Parameters

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 \( n \).

Returns: The calculated electrostatic interaction energy \( EQ_{ij} \).

◆ calcMMFF94ElectrostaticGradient() [1/3]

float CDPL.ForceField.calcMMFF94ElectrostaticGradient	(	MMFF94ElectrostaticInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the electrostatic interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 electrostatic interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The electrostatic interaction energy of iaction.

◆ calcMMFF94ElectrostaticGradient() [2/3]

float CDPL.ForceField.calcMMFF94ElectrostaticGradient	(	MMFF94ElectrostaticInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94ElectrostaticGradient() [3/3]

float CDPL.ForceField.calcMMFF94ElectrostaticGradient	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		Math.Vector3D	atom1_grad,
		Math.Vector3D	atom2_grad,
		float	atom1_chg,
		float	atom2_chg,
		float	scale_fact,
		float	de_const,
		float	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 \( EQ_{14} \: 0.75 \)).

Parameters

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 \( n \).

Returns: The calculated electrostatic interaction energy \( EQ_{ij} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcMMFF94OutOfPlaneBendingEnergy() [1/4]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingEnergy	(	MMFF94OutOfPlaneBendingInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the out-of-plane bending interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 out-of-plane bending interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The out-of-plane bending interaction energy of iaction.

◆ calcMMFF94OutOfPlaneBendingEnergy() [2/4]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingEnergy	(	MMFF94OutOfPlaneBendingInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94OutOfPlaneBendingEnergy() [3/4]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	oop_atom_pos,
		float	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()).

Parameters

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 \( koop_{IJK \colon L} \).

Returns: The calculated out-of-plane bending interaction energy \( EOOP_{ijk;l} \).

◆ calcMMFF94OutOfPlaneBendingEnergy() [4/4]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	oop_atom_pos,
		float	r_jl,
		float	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()).

Parameters

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 \( koop_{IJK \colon L} \).

Returns: The calculated out-of-plane bending interaction energy \( EOOP_{ijk;l} \).

◆ calcMMFF94OutOfPlaneBendingGradient() [1/3]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingGradient	(	MMFF94OutOfPlaneBendingInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the out-of-plane bending interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 out-of-plane bending interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The out-of-plane bending interaction energy of iaction.

◆ calcMMFF94OutOfPlaneBendingGradient() [2/3]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingGradient	(	MMFF94OutOfPlaneBendingInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94OutOfPlaneBendingGradient() [3/3]

float CDPL.ForceField.calcMMFF94OutOfPlaneBendingGradient	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	oop_atom_pos,
		Math.Vector3D	term_atom1_grad,
		Math.Vector3D	ctr_atom_grad,
		Math.Vector3D	term_atom2_grad,
		Math.Vector3D	oop_atom_grad,
		float	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.

Parameters

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 \( koop_{IJK \colon L} \).

Returns: The calculated out-of-plane bending interaction energy \( EOOP_{ijk;l} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcMMFF94StretchBendEnergy() [1/4]

float CDPL.ForceField.calcMMFF94StretchBendEnergy	(	MMFF94StretchBendInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the stretch-bend coupling interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 stretch-bend interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The stretch-bend interaction energy of iaction.

◆ calcMMFF94StretchBendEnergy() [2/4]

float CDPL.ForceField.calcMMFF94StretchBendEnergy	(	MMFF94StretchBendInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94StretchBendEnergy() [3/4]

float CDPL.ForceField.calcMMFF94StretchBendEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		float	ijk_force_const,
		float	kji_force_const,
		float	ref_angle,
		float	ref_length1,
		float	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.

Parameters

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 \( r_{KJ}^0 \).

Returns: The calculated stretch-bend interaction energy \( EBA_{ijk} \).

◆ calcMMFF94StretchBendEnergy() [4/4]

float CDPL.ForceField.calcMMFF94StretchBendEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		float	r_ij,
		float	r_jk,
		float	ijk_force_const,
		float	kji_force_const,
		float	ref_angle,
		float	ref_length1,
		float	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.

Parameters

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 \( r_{KJ}^0 \).

Returns: The calculated stretch-bend interaction energy \( EBA_{ijk} \).

◆ calcMMFF94StretchBendGradient() [1/3]

float CDPL.ForceField.calcMMFF94StretchBendGradient	(	MMFF94StretchBendInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the stretch-bend coupling interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 stretch-bend interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The stretch-bend interaction energy of iaction.

◆ calcMMFF94StretchBendGradient() [2/3]

float CDPL.ForceField.calcMMFF94StretchBendGradient	(	MMFF94StretchBendInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94StretchBendGradient() [3/3]

float CDPL.ForceField.calcMMFF94StretchBendGradient	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	term_atom1_grad,
		Math.Vector3D	ctr_atom_grad,
		Math.Vector3D	term_atom2_grad,
		float	ijk_force_const,
		float	kji_force_const,
		float	ref_angle,
		float	ref_length1,
		float	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.

Parameters

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 \( r_{KJ}^0 \).

Returns: The calculated stretch-bend interaction energy \( EBA_{ijk} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcMMFF94TorsionEnergy() [1/3]

float CDPL.ForceField.calcMMFF94TorsionEnergy	(	MMFF94TorsionInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the torsion interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 torsion interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The torsion interaction energy of iaction.

◆ calcMMFF94TorsionEnergy() [2/3]

float CDPL.ForceField.calcMMFF94TorsionEnergy	(	MMFF94TorsionInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94TorsionEnergy() [3/3]

float CDPL.ForceField.calcMMFF94TorsionEnergy	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom1_pos,
		Math.Vector3D	ctr_atom2_pos,
		Math.Vector3D	term_atom2_pos,
		float	tor_param1,
		float	tor_param2,
		float	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().

Parameters

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 \( V_3 \).

Returns: The calculated torsion interaction energy \( ET_{ijkl} \).

◆ calcMMFF94TorsionGradient() [1/3]

float CDPL.ForceField.calcMMFF94TorsionGradient	(	MMFF94TorsionInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the torsion interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 torsion interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The torsion interaction energy of iaction.

◆ calcMMFF94TorsionGradient() [2/3]

float CDPL.ForceField.calcMMFF94TorsionGradient	(	MMFF94TorsionInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94TorsionGradient() [3/3]

float CDPL.ForceField.calcMMFF94TorsionGradient	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom1_pos,
		Math.Vector3D	ctr_atom2_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	term_atom1_grad,
		Math.Vector3D	ctr_atom1_grad,
		Math.Vector3D	ctr_atom2_grad,
		Math.Vector3D	term_atom2_grad,
		float	tor_param1,
		float	tor_param2,
		float	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.

Parameters

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 \( V_3 \).

Returns: The calculated torsion interaction energy \( ET_{ijkl} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcMMFF94VanDerWaalsEnergy() [1/4]

float CDPL.ForceField.calcMMFF94VanDerWaalsEnergy	(	MMFF94VanDerWaalsInteraction	iaction,
		Math.Vector3DArray	coords
	)

Calculates the Van der Waals interaction energy of iaction using the geometry from coords.

Parameters

iaction	The MMFF94 Van der Waals interaction record.
coords	The atom-coordinates array providing the geometry.

Returns: The Van der Waals interaction energy of iaction.

◆ calcMMFF94VanDerWaalsEnergy() [2/4]

float CDPL.ForceField.calcMMFF94VanDerWaalsEnergy	(	MMFF94VanDerWaalsInteractionList	ia_list,
		Math.Vector3DArray	coords
	)

Parameters

ia_list
coords

Returns

◆ calcMMFF94VanDerWaalsEnergy() [3/4]

float CDPL.ForceField.calcMMFF94VanDerWaalsEnergy	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		float	e_IJ,
		float	r_IJ,
		float	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).

Parameters

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 \( R_{IJ}^{*^7} \).

Returns: The calculated Van der Waals interaction energy \( E_{vdW_{ij}} \).

◆ calcMMFF94VanDerWaalsEnergy() [4/4]

float CDPL.ForceField.calcMMFF94VanDerWaalsEnergy	(	float	r_ij,
		float	e_IJ,
		float	r_IJ,
		float	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).

Parameters

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 \( R_{IJ}^{*^7} \).

Returns: The calculated Van der Waals interaction energy \( E_{vdW_{ij}} \).

◆ calcMMFF94VanDerWaalsGradient() [1/3]

float CDPL.ForceField.calcMMFF94VanDerWaalsGradient	(	MMFF94VanDerWaalsInteraction	iaction,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Calculates the Van der Waals interaction energy of iaction and accumulates the corresponding atom-position gradient contribution into grad.

Parameters

iaction	The MMFF94 Van der Waals interaction record.
coords	The atom-coordinates array providing the geometry.
grad	The gradient vector to accumulate into.

Returns: The Van der Waals interaction energy of iaction.

◆ calcMMFF94VanDerWaalsGradient() [2/3]

float CDPL.ForceField.calcMMFF94VanDerWaalsGradient	(	MMFF94VanDerWaalsInteractionList	ia_list,
		Math.Vector3DArray	coords,
		Math.Vector3DArray	grad
	)

Parameters

ia_list
coords
grad

Returns

◆ calcMMFF94VanDerWaalsGradient() [3/3]

float CDPL.ForceField.calcMMFF94VanDerWaalsGradient	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	atom2_pos,
		Math.Vector3D	atom1_grad,
		Math.Vector3D	atom2_grad,
		float	e_IJ,
		float	r_IJ,
		float	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).

Parameters

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 \( R_{IJ}^{*^7} \).

Returns: The calculated Van der Waals interaction energy \( E_{vdW_{ij}} \).

Note: The calculated partial energy derivative (see above) for an atom gets added to the corresponding output variable!

◆ calcOutOfPlaneAngleCosDerivatives()

float CDPL.ForceField.calcOutOfPlaneAngleCosDerivatives	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	oop_atom_pos,
		Math.Vector3D	term_atom1_deriv,
		Math.Vector3D	ctr_atom_deriv,
		Math.Vector3D	term_atom2_deriv,
		Math.Vector3D	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.

Parameters

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.

Returns: The calculated cosine of the angle \( \omega_{ijk;l} \).

◆ calcOutOfPlaneAngle()

float CDPL.ForceField.calcOutOfPlaneAngle	(	Math.Vector3D	term_atom1_pos,
		Math.Vector3D	ctr_atom_pos,
		Math.Vector3D	term_atom2_pos,
		Math.Vector3D	oop_atom_pos,
		float	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.

Parameters

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.

Returns: The calculated out-of-plane angle \( \chi_{ijk;l} \).

◆ calcSquaredDistance()

float CDPL.ForceField.calcSquaredDistance	(	Math.Vector3D	atom1_pos,
		Math.Vector3D	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.

Parameters

atom1_pos	The position \( \vec{p_i} \) of atom i.
atom2_pos	The position \( \vec{p_j} \) of atom j.

Returns: The calculated squared distance \( r_{ij}^2 \).

◆ filterInteractions()

None CDPL.ForceField.filterInteractions	(	MMFF94InteractionData	ia_data,
		MMFF94InteractionData	filtered_ia_data,
		Util.BitSet	inc_atom_mask
	)

Filters an MMFF94 interaction data set, retaining only those interactions that exclusively reference atoms in inc_atom_mask.

Parameters

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.

◆ perceiveMMFF94AromaticRings() [1/2]

Chem.FragmentList CDPL.ForceField.perceiveMMFF94AromaticRings ( Chem.MolecularGraph molgraph )

Perceives the list of MMFF94 aromatic rings of the molecular graph molgraph.

Parameters

molgraph The molecular graph.

Returns: A shared reference to the perceived list of MMFF94 aromatic rings.

◆ perceiveMMFF94AromaticRings() [2/2]

Chem.FragmentList CDPL.ForceField.perceiveMMFF94AromaticRings	(	Chem.MolecularGraph	molgraph,
		bool	overwrite
	)

Perceives and (optionally) stores the list of MMFF94 aromatic rings of the molecular graph molgraph.

Parameters

molgraph	The molecular graph to inspect/modify.
overwrite	Specifies whether an already existing value of the property should be replaced.

Returns: A shared reference to the perceived (or pre-existing) list of MMFF94 aromatic rings.

◆ perceiveUFFType()

int CDPL.ForceField.perceiveUFFType	(	Chem.Atom	atom,
		Chem.MolecularGraph	molgraph
	)

Perceives the UFF atom type of the atom atom in the context of the molecular graph molgraph.

Parameters

atom	The atom whose UFF type is to be perceived.
molgraph	The molecular graph providing the atom environment for type perception.

Returns: The perceived numeric UFF atom type (see namespace ForceField.UFFAtomType).

Classes

Functions

Detailed Description

Function Documentation

◆ setMMFF94AromaticRings()

◆ hasMMFF94AromaticRings()

◆ getMMFF94AromaticRings()

◆ clearMMFF94AromaticRings()

◆ setMMFF94Charge()

◆ hasMMFF94Charge()

◆ getMMFF94Charge()

◆ clearMMFF94Charge()

◆ setMMFF94NumericType()

◆ hasMMFF94NumericType()

◆ getMMFF94NumericType()

◆ clearMMFF94NumericType()

◆ setMMFF94SymbolicType()

◆ hasMMFF94SymbolicType()

◆ getMMFF94SymbolicType()

◆ clearMMFF94SymbolicType()

◆ setMMFF94TypeIndex()

◆ hasMMFF94TypeIndex()

◆ getMMFF94TypeIndex()

◆ clearMMFF94TypeIndex()

◆ setUFFType()

◆ hasUFFType()

◆ getUFFType()

◆ clearUFFType()

◆ assignMMFF94AtomTypes()

◆ assignMMFF94BondTypeIndices()

◆ assignUFFAtomTypes()

◆ calcBondAngleCosDerivatives()

◆ calcBondAngleCos() [1/2]

◆ calcBondAngleCos() [2/2]

◆ calcBondAngle() [1/2]

◆ calcBondAngle() [2/2]

◆ calcBondLengthsAndAngleCos()

◆ calcBondLengthsAndAngle()

◆ calcDihedralAngleCosDerivatives()

◆ calcDihedralAngleCos()

◆ calcDistanceDerivatives()

◆ calcDistance()

◆ calcElasticPotentialEnergy() [1/3]

◆ calcElasticPotentialEnergy() [2/3]

◆ calcElasticPotentialEnergy() [3/3]

◆ calcElasticPotentialGradient() [1/3]

◆ calcElasticPotentialGradient() [2/3]

◆ calcElasticPotentialGradient() [3/3]

◆ calcMMFF94AngleBendingEnergy() [1/4]

◆ calcMMFF94AngleBendingEnergy() [2/4]

◆ calcMMFF94AngleBendingEnergy() [3/4]

◆ calcMMFF94AngleBendingEnergy() [4/4]

◆ calcMMFF94AngleBendingGradient() [1/3]

◆ calcMMFF94AngleBendingGradient() [2/3]

◆ calcMMFF94AngleBendingGradient() [3/3]

◆ calcMMFF94AtomCharges()

◆ calcMMFF94BondStretchingEnergy() [1/4]

◆ calcMMFF94BondStretchingEnergy() [2/4]

◆ calcMMFF94BondStretchingEnergy() [3/4]

◆ calcMMFF94BondStretchingEnergy() [4/4]

◆ calcMMFF94BondStretchingGradient() [1/3]

◆ calcMMFF94BondStretchingGradient() [2/3]

◆ calcMMFF94BondStretchingGradient() [3/3]

◆ calcMMFF94ElectrostaticEnergy() [1/4]

◆ calcMMFF94ElectrostaticEnergy() [2/4]

◆ calcMMFF94ElectrostaticEnergy() [3/4]

◆ calcMMFF94ElectrostaticEnergy() [4/4]

◆ calcMMFF94ElectrostaticGradient() [1/3]

◆ calcMMFF94ElectrostaticGradient() [2/3]

◆ calcMMFF94ElectrostaticGradient() [3/3]

◆ calcMMFF94OutOfPlaneBendingEnergy() [1/4]

◆ calcMMFF94OutOfPlaneBendingEnergy() [2/4]

◆ calcMMFF94OutOfPlaneBendingEnergy() [3/4]

◆ calcMMFF94OutOfPlaneBendingEnergy() [4/4]

◆ calcMMFF94OutOfPlaneBendingGradient() [1/3]

◆ calcMMFF94OutOfPlaneBendingGradient() [2/3]

◆ calcMMFF94OutOfPlaneBendingGradient() [3/3]

◆ calcMMFF94StretchBendEnergy() [1/4]

◆ calcMMFF94StretchBendEnergy() [2/4]

◆ calcMMFF94StretchBendEnergy() [3/4]