One-stop MMFF94 parameterizer that combines atom typing, bond typing, partial-charge assignment and per-interaction-type parameter look-up into a single parameterize() call. More...

#include <MMFF94InteractionParameterizer.hpp>

Public Types
typedef std::shared_ptr< MMFF94InteractionParameterizer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94InteractionParameterizer` instances. More...

Public Member Functions
	MMFF94InteractionParameterizer (unsigned int param_set=MMFF94ParameterSet::STATIC)
	Constructs the parameterizer with the default tables for the chosen MMFF94 parameter set. More...

	MMFF94InteractionParameterizer (const MMFF94InteractionParameterizer &parameterizer)
	Constructs a copy of the parameterizer parameterizer. More...

void	setBondStretchingFilterFunction (const InteractionFilterFunction2 &func)
	Installs a filter that decides whether a candidate bond-stretching interaction is kept. More...

void	setAngleBendingFilterFunction (const InteractionFilterFunction3 &func)
	Installs a filter that decides whether a candidate angle-bending interaction is kept. More...

void	setStretchBendFilterFunction (const InteractionFilterFunction3 &func)
	Installs a filter that decides whether a candidate stretch-bend interaction is kept. More...

void	setOutOfPlaneBendingFilterFunction (const InteractionFilterFunction4 &func)
	Installs a filter that decides whether a candidate out-of-plane bending interaction is kept. More...

void	setTorsionFilterFunction (const InteractionFilterFunction4 &func)
	Installs a filter that decides whether a candidate torsion interaction is kept. More...

void	setElectrostaticFilterFunction (const InteractionFilterFunction2 &func)
	Installs a filter that decides whether a candidate electrostatic interaction is kept. More...

void	setVanDerWaalsFilterFunction (const InteractionFilterFunction2 &func)
	Installs a filter that decides whether a candidate van-der-Waals interaction is kept. More...

void	clearFilterFunctions ()
	Removes every previously installed interaction-filter function. More...

void	setSymbolicAtomTypePatternTable (const MMFF94SymbolicAtomTypePatternTable::SharedPointer &table)
	Sets the symbolic-atom-type pattern table to use during atom typing. More...

void	setHeavyToHydrogenAtomTypeMap (const MMFF94HeavyToHydrogenAtomTypeMap::SharedPointer &map)
	Sets the heavy-to-hydrogen atom-type map used to derive hydrogen atom types from their non-hydrogen neighbors. More...

void	setSymbolicToNumericAtomTypeMap (const MMFF94SymbolicToNumericAtomTypeMap::SharedPointer &map)
	Sets the symbolic-to-numeric atom-type map used to convert symbolic types to numeric ones. More...

void	setAromaticAtomTypeDefinitionTable (const MMFF94AromaticAtomTypeDefinitionTable::SharedPointer &table)
	Sets the aromatic-atom-type definition table used to override types of aromatic atoms. More...

void	setAtomTypePropertyTable (const MMFF94AtomTypePropertyTable::SharedPointer &table)
	Sets the atom-type property table used to resolve per-numeric-type properties. More...

void	setFormalAtomChargeDefinitionTable (const MMFF94FormalAtomChargeDefinitionTable::SharedPointer &table)
	Sets the formal-atomic-charge definition table used during charge assignment. More...

void	setBondChargeIncrementTable (const MMFF94BondChargeIncrementTable::SharedPointer &table)
	Sets the bond charge-increment table used during partial-charge calculation. More...

void	setPartialBondChargeIncrementTable (const MMFF94PartialBondChargeIncrementTable::SharedPointer &table)
	Sets the partial bond charge-increment table used during partial-charge calculation. More...

void	setPrimaryToParameterAtomTypeMap (const MMFF94PrimaryToParameterAtomTypeMap::SharedPointer &map)
	Sets the primary-to-parameter atom-type map used by the parameter look-ups. More...

void	setAngleBendingParameterTable (const MMFF94AngleBendingParameterTable::SharedPointer &table)
	Sets the angle-bending parameter table to use. More...

void	setBondStretchingParameterTable (const MMFF94BondStretchingParameterTable::SharedPointer &table)
	Sets the bond-stretching parameter table to use. More...

void	setBondStretchingRuleParameterTable (const MMFF94BondStretchingRuleParameterTable::SharedPointer &table)
	Sets the bond-stretching rule parameter table used as a fallback when no explicit bond-stretching entry is available. More...

void	setStretchBendParameterTable (const MMFF94StretchBendParameterTable::SharedPointer &table)
	Sets the stretch-bend parameter table to use. More...

void	setDefaultStretchBendParameterTable (const MMFF94DefaultStretchBendParameterTable::SharedPointer &table)
	Sets the default stretch-bend parameter table used as a periodic-row fallback. More...

void	setOutOfPlaneBendingParameterTable (const MMFF94OutOfPlaneBendingParameterTable::SharedPointer &table)
	Sets the out-of-plane bending parameter table to use. More...

void	setTorsionParameterTable (const MMFF94TorsionParameterTable::SharedPointer &table)
	Sets the torsion parameter table to use. More...

void	setVanDerWaalsParameterTable (const MMFF94VanDerWaalsParameterTable::SharedPointer &table)
	Sets the van-der-Waals parameter table to use. More...

void	setDielectricConstant (double de_const)
	Sets the dielectric constant used by the electrostatic interaction parameterizer. More...

void	setDistanceExponent (double dist_expo)
	Sets the distance exponent used by the electrostatic interaction parameterizer. More...

void	setParameterSet (unsigned int param_set)
	Switches the active MMFF94 parameter-set variant and reinstalls the matching default tables. More...

MMFF94InteractionParameterizer &	operator= (const MMFF94InteractionParameterizer &parameterizer)
	Copies the state of parameterizer. More...

void	parameterize (const Chem::MolecularGraph &molgraph, MMFF94InteractionData &ia_data, unsigned int ia_types=InteractionType::ALL, bool strict=true)
	Parameterizes the MMFF94 force field interactions for molgraph and stores them in ia_data. More...

Detailed Description

One-stop MMFF94 parameterizer that combines atom typing, bond typing, partial-charge assignment and per-interaction-type parameter look-up into a single parameterize() call.

The constructor installs default parameter tables and atom-/bond-typing helpers for the selected ForceField::MMFF94ParameterSet variant (STATIC, DYNAMIC, etc.); every table, map and filter function can be overridden via the corresponding setter. Calling parameterize() runs atom typing, bond typing, formal/partial-charge assignment, aromaticity perception and topological-distance calculation, then dispatches to the seven per-interaction MMFF94*InteractionParameterizer members and stores the resulting interaction lists in the supplied ForceField::MMFF94InteractionData object.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94InteractionParameterizer> CDPL::ForceField::MMFF94InteractionParameterizer::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94InteractionParameterizer instances.

Constructor & Destructor Documentation

◆ MMFF94InteractionParameterizer() [1/2]

CDPL::ForceField::MMFF94InteractionParameterizer::MMFF94InteractionParameterizer ( unsigned int param_set = MMFF94ParameterSet::STATIC )

Constructs the parameterizer with the default tables for the chosen MMFF94 parameter set.

Parameters

param_set The parameter-set variant (see namespace ForceField::MMFF94ParameterSet).

◆ MMFF94InteractionParameterizer() [2/2]

CDPL::ForceField::MMFF94InteractionParameterizer::MMFF94InteractionParameterizer ( const MMFF94InteractionParameterizer & parameterizer )

Constructs a copy of the parameterizer parameterizer.

Parameters

parameterizer The parameterizer to copy.

Member Function Documentation

◆ setBondStretchingFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setBondStretchingFilterFunction ( const InteractionFilterFunction2 & func )

Installs a filter that decides whether a candidate bond-stretching interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ setAngleBendingFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setAngleBendingFilterFunction ( const InteractionFilterFunction3 & func )

Installs a filter that decides whether a candidate angle-bending interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ setStretchBendFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setStretchBendFilterFunction ( const InteractionFilterFunction3 & func )

Installs a filter that decides whether a candidate stretch-bend interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ setOutOfPlaneBendingFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setOutOfPlaneBendingFilterFunction ( const InteractionFilterFunction4 & func )

Installs a filter that decides whether a candidate out-of-plane bending interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ setTorsionFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setTorsionFilterFunction ( const InteractionFilterFunction4 & func )

Installs a filter that decides whether a candidate torsion interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ setElectrostaticFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setElectrostaticFilterFunction ( const InteractionFilterFunction2 & func )

Installs a filter that decides whether a candidate electrostatic interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ setVanDerWaalsFilterFunction()

void CDPL::ForceField::MMFF94InteractionParameterizer::setVanDerWaalsFilterFunction ( const InteractionFilterFunction2 & func )

Installs a filter that decides whether a candidate van-der-Waals interaction is kept.

Parameters

func	The filter functor (returns `true` to keep the interaction).

◆ clearFilterFunctions()

void CDPL::ForceField::MMFF94InteractionParameterizer::clearFilterFunctions ( )

Removes every previously installed interaction-filter function.

◆ setSymbolicAtomTypePatternTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setSymbolicAtomTypePatternTable ( const MMFF94SymbolicAtomTypePatternTable::SharedPointer & table )

Sets the symbolic-atom-type pattern table to use during atom typing.

Parameters

table The new symbolic-atom-type pattern table.

◆ setHeavyToHydrogenAtomTypeMap()

void CDPL::ForceField::MMFF94InteractionParameterizer::setHeavyToHydrogenAtomTypeMap ( const MMFF94HeavyToHydrogenAtomTypeMap::SharedPointer & map )

Sets the heavy-to-hydrogen atom-type map used to derive hydrogen atom types from their non-hydrogen neighbors.

Parameters

map	The new heavy-to-hydrogen atom-type map.

◆ setSymbolicToNumericAtomTypeMap()

void CDPL::ForceField::MMFF94InteractionParameterizer::setSymbolicToNumericAtomTypeMap ( const MMFF94SymbolicToNumericAtomTypeMap::SharedPointer & map )

Sets the symbolic-to-numeric atom-type map used to convert symbolic types to numeric ones.

Parameters

map	The new symbolic-to-numeric atom-type map.

◆ setAromaticAtomTypeDefinitionTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setAromaticAtomTypeDefinitionTable ( const MMFF94AromaticAtomTypeDefinitionTable::SharedPointer & table )

Sets the aromatic-atom-type definition table used to override types of aromatic atoms.

Parameters

table The new aromatic-atom-type definition table.

◆ setAtomTypePropertyTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setAtomTypePropertyTable ( const MMFF94AtomTypePropertyTable::SharedPointer & table )

Sets the atom-type property table used to resolve per-numeric-type properties.

Parameters

table The new atom-type property table.

◆ setFormalAtomChargeDefinitionTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setFormalAtomChargeDefinitionTable ( const MMFF94FormalAtomChargeDefinitionTable::SharedPointer & table )

Sets the formal-atomic-charge definition table used during charge assignment.

Parameters

table The new formal-atomic-charge definition table.

◆ setBondChargeIncrementTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setBondChargeIncrementTable ( const MMFF94BondChargeIncrementTable::SharedPointer & table )

Sets the bond charge-increment table used during partial-charge calculation.

Parameters

table The new bond-charge-increment table.

◆ setPartialBondChargeIncrementTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setPartialBondChargeIncrementTable ( const MMFF94PartialBondChargeIncrementTable::SharedPointer & table )

Sets the partial bond charge-increment table used during partial-charge calculation.

Parameters

table The new partial-bond-charge-increment table.

◆ setPrimaryToParameterAtomTypeMap()

void CDPL::ForceField::MMFF94InteractionParameterizer::setPrimaryToParameterAtomTypeMap ( const MMFF94PrimaryToParameterAtomTypeMap::SharedPointer & map )

Sets the primary-to-parameter atom-type map used by the parameter look-ups.

Parameters

map	The new primary-to-parameter atom-type map.

◆ setAngleBendingParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setAngleBendingParameterTable ( const MMFF94AngleBendingParameterTable::SharedPointer & table )

Sets the angle-bending parameter table to use.

Parameters

table The new angle-bending parameter table.

◆ setBondStretchingParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setBondStretchingParameterTable ( const MMFF94BondStretchingParameterTable::SharedPointer & table )

Sets the bond-stretching parameter table to use.

Parameters

table The new bond-stretching parameter table.

◆ setBondStretchingRuleParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setBondStretchingRuleParameterTable ( const MMFF94BondStretchingRuleParameterTable::SharedPointer & table )

Sets the bond-stretching rule parameter table used as a fallback when no explicit bond-stretching entry is available.

Parameters

table The new bond-stretching rule parameter table.

◆ setStretchBendParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setStretchBendParameterTable ( const MMFF94StretchBendParameterTable::SharedPointer & table )

Sets the stretch-bend parameter table to use.

Parameters

table The new stretch-bend parameter table.

◆ setDefaultStretchBendParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setDefaultStretchBendParameterTable ( const MMFF94DefaultStretchBendParameterTable::SharedPointer & table )

Sets the default stretch-bend parameter table used as a periodic-row fallback.

Parameters

table The new default stretch-bend parameter table.

◆ setOutOfPlaneBendingParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setOutOfPlaneBendingParameterTable ( const MMFF94OutOfPlaneBendingParameterTable::SharedPointer & table )

Sets the out-of-plane bending parameter table to use.

Parameters

table The new out-of-plane bending parameter table.

◆ setTorsionParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setTorsionParameterTable ( const MMFF94TorsionParameterTable::SharedPointer & table )

Sets the torsion parameter table to use.

Parameters

table The new torsion parameter table.

◆ setVanDerWaalsParameterTable()

void CDPL::ForceField::MMFF94InteractionParameterizer::setVanDerWaalsParameterTable ( const MMFF94VanDerWaalsParameterTable::SharedPointer & table )

Sets the van-der-Waals parameter table to use.

Parameters

table The new van-der-Waals parameter table.

◆ setDielectricConstant()

void CDPL::ForceField::MMFF94InteractionParameterizer::setDielectricConstant ( double de_const )

Sets the dielectric constant used by the electrostatic interaction parameterizer.

Parameters

de_const The new dielectric constant.

◆ setDistanceExponent()

void CDPL::ForceField::MMFF94InteractionParameterizer::setDistanceExponent ( double dist_expo )

Sets the distance exponent used by the electrostatic interaction parameterizer.

Parameters

dist_expo The new distance exponent.

◆ setParameterSet()

void CDPL::ForceField::MMFF94InteractionParameterizer::setParameterSet ( unsigned int param_set )

Switches the active MMFF94 parameter-set variant and reinstalls the matching default tables.

Parameters

param_set The new parameter-set variant (see namespace ForceField::MMFF94ParameterSet).

◆ operator=()

MMFF94InteractionParameterizer& CDPL::ForceField::MMFF94InteractionParameterizer::operator= ( const MMFF94InteractionParameterizer & parameterizer )

Copies the state of parameterizer.

Parameters

parameterizer The parameterizer to copy.

Returns: A reference to itself.

◆ parameterize()

void CDPL::ForceField::MMFF94InteractionParameterizer::parameterize	(	const Chem::MolecularGraph &	molgraph,
		MMFF94InteractionData &	ia_data,
		unsigned int	ia_types = `InteractionType::ALL`,
		bool	strict = `true`
	)

Parameterizes the MMFF94 force field interactions for molgraph and stores them in ia_data.

Parameters

molgraph	The molecular graph to parameterize.
ia_data	The output container receiving the perceived interactions.
ia_types	A bitmask of ForceField::InteractionType flags selecting which interaction types are parameterized.
strict	If `true`, the parameterization fails when any required parameter is missing; otherwise fallback strategies (rule-based parameters, default values) are used.

The documentation for this class was generated from the following file:

MMFF94InteractionParameterizer.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ MMFF94InteractionParameterizer() [1/2]

◆ MMFF94InteractionParameterizer() [2/2]

Member Function Documentation

◆ setBondStretchingFilterFunction()

◆ setAngleBendingFilterFunction()

◆ setStretchBendFilterFunction()

◆ setOutOfPlaneBendingFilterFunction()

◆ setTorsionFilterFunction()

◆ setElectrostaticFilterFunction()

◆ setVanDerWaalsFilterFunction()

◆ clearFilterFunctions()

◆ setSymbolicAtomTypePatternTable()

◆ setHeavyToHydrogenAtomTypeMap()

◆ setSymbolicToNumericAtomTypeMap()

◆ setAromaticAtomTypeDefinitionTable()

◆ setAtomTypePropertyTable()

◆ setFormalAtomChargeDefinitionTable()

◆ setBondChargeIncrementTable()

◆ setPartialBondChargeIncrementTable()

◆ setPrimaryToParameterAtomTypeMap()

◆ setAngleBendingParameterTable()

◆ setBondStretchingParameterTable()

◆ setBondStretchingRuleParameterTable()

◆ setStretchBendParameterTable()

◆ setDefaultStretchBendParameterTable()

◆ setOutOfPlaneBendingParameterTable()

◆ setTorsionParameterTable()

◆ setVanDerWaalsParameterTable()

◆ setDielectricConstant()

◆ setDistanceExponent()

◆ setParameterSet()

◆ operator=()

◆ parameterize()