Detects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph. More...

#include <MMFF94StretchBendInteractionParameterizer.hpp>

Public Types
typedef std::shared_ptr< MMFF94StretchBendInteractionParameterizer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `MMFF94StretchBendInteractionParameterizer` instances. More...

Public Member Functions
	MMFF94StretchBendInteractionParameterizer ()
	Constructs an `MMFF94StretchBendInteractionParameterizer` instance using the default MMFF94 parameter tables. More...

	MMFF94StretchBendInteractionParameterizer (const Chem::MolecularGraph &molgraph, const MMFF94BondStretchingInteractionList &bs_ia_list, const MMFF94AngleBendingInteractionList &ab_ia_list, MMFF94StretchBendInteractionList &ia_list, bool strict)
	Constructs the parameterizer and processes the molecular graph molgraph. More...

void	setFilterFunction (const InteractionFilterFunction3 &func)
	Sets the filter function used to skip atom triplets during parameterization. More...

void	setAtomTypeFunction (const MMFF94NumericAtomTypeFunction &func)
	Sets the function used to look up the MMFF94 numeric atom type of an atom. More...

void	setStretchBendParameterTable (const MMFF94StretchBendParameterTable::SharedPointer &table)
	Sets the primary table providing stretch-bend type-specific stretch-bend parameters. More...

void	setDefaultStretchBendParameterTable (const MMFF94DefaultStretchBendParameterTable::SharedPointer &table)
	Sets the fallback table providing periodic-table-row-based default stretch-bend parameters. More...

void	setAtomTypePropertyTable (const MMFF94AtomTypePropertyTable::SharedPointer &table)
	Sets the table providing MMFF94 numeric atom type property data (used to look up the periodic table row of an atom for the default-parameter fallback). More...

void	parameterize (const Chem::MolecularGraph &molgraph, const MMFF94BondStretchingInteractionList &bs_ia_list, const MMFF94AngleBendingInteractionList &ab_ia_list, MMFF94StretchBendInteractionList &ia_list, bool strict)
	Perceives the MMFF94 stretch-bend interactions for molgraph and outputs the corresponding parameter data into ia_list. More...

Detailed Description

Detects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph.

Stretch-bend interactions couple the bending of an i-j-k bond angle to the stretching of the two participating bonds i-j and j-k. For every non-filtered atom triplet the parameterizer derives the stretch-bend type index from the bond type indices and angle type index of the already-parameterized bond-stretching and angle-bending interactions, looks up the matching stretch-bend force constants (falling back to the periodic-table-row-based default parameter table when no exact entry is available) and appends an MMFF94StretchBendInteraction instance to the output list.

See also: [MMFF94]

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<MMFF94StretchBendInteractionParameterizer> CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94StretchBendInteractionParameterizer instances.

Constructor & Destructor Documentation

◆ MMFF94StretchBendInteractionParameterizer() [1/2]

CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::MMFF94StretchBendInteractionParameterizer ( )

Constructs an MMFF94StretchBendInteractionParameterizer instance using the default MMFF94 parameter tables.

◆ MMFF94StretchBendInteractionParameterizer() [2/2]

CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::MMFF94StretchBendInteractionParameterizer	(	const Chem::MolecularGraph &	molgraph,
		const MMFF94BondStretchingInteractionList &	bs_ia_list,
		const MMFF94AngleBendingInteractionList &	ab_ia_list,
		MMFF94StretchBendInteractionList &	ia_list,
		bool	strict
	)

Constructs the parameterizer and processes the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to parameterize the stretch-bend interactions.
bs_ia_list	The list of already-parameterized MMFF94 bond-stretching interactions (provides per-bond type indices and reference lengths).
ab_ia_list	The list of already-parameterized MMFF94 angle-bending interactions (provides per-angle type indices and reference angles).
ia_list	Output list receiving the generated MMFF94StretchBendInteraction instances.
strict	If `true`, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

Member Function Documentation

◆ setFilterFunction()

void CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::setFilterFunction ( const InteractionFilterFunction3 & func )

Sets the filter function used to skip atom triplets during parameterization.

Parameters

func	The new three-atom filter function (when it returns `false`, the triplet is skipped).

◆ setAtomTypeFunction()

void CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::setAtomTypeFunction ( const MMFF94NumericAtomTypeFunction & func )

Sets the function used to look up the MMFF94 numeric atom type of an atom.

Parameters

func	The new numeric atom type lookup function.

◆ setStretchBendParameterTable()

void CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::setStretchBendParameterTable ( const MMFF94StretchBendParameterTable::SharedPointer & table )

Sets the primary table providing stretch-bend type-specific stretch-bend parameters.

Parameters

table The new stretch-bend parameter table.

◆ setDefaultStretchBendParameterTable()

void CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::setDefaultStretchBendParameterTable ( const MMFF94DefaultStretchBendParameterTable::SharedPointer & table )

Sets the fallback table providing periodic-table-row-based default stretch-bend parameters.

Parameters

table The new default stretch-bend parameter table.

◆ setAtomTypePropertyTable()

void CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::setAtomTypePropertyTable ( const MMFF94AtomTypePropertyTable::SharedPointer & table )

Sets the table providing MMFF94 numeric atom type property data (used to look up the periodic table row of an atom for the default-parameter fallback).

Parameters

table The new atom type property table.

◆ parameterize()

void CDPL::ForceField::MMFF94StretchBendInteractionParameterizer::parameterize	(	const Chem::MolecularGraph &	molgraph,
		const MMFF94BondStretchingInteractionList &	bs_ia_list,
		const MMFF94AngleBendingInteractionList &	ab_ia_list,
		MMFF94StretchBendInteractionList &	ia_list,
		bool	strict
	)

Perceives the MMFF94 stretch-bend interactions for molgraph and outputs the corresponding parameter data into ia_list.

Parameters

molgraph	The molecular graph for which to parameterize the stretch-bend interactions.
bs_ia_list	The list of already-parameterized MMFF94 bond-stretching interactions (provides per-bond type indices and reference lengths).
ab_ia_list	The list of already-parameterized MMFF94 angle-bending interactions (provides per-angle type indices and reference angles).
ia_list	Output list receiving the generated MMFF94StretchBendInteraction instances.
strict	If `true`, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

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

MMFF94StretchBendInteractionParameterizer.hpp

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ MMFF94StretchBendInteractionParameterizer() [1/2]

◆ MMFF94StretchBendInteractionParameterizer() [2/2]

Member Function Documentation

◆ setFilterFunction()

◆ setAtomTypeFunction()

◆ setStretchBendParameterTable()

◆ setDefaultStretchBendParameterTable()

◆ setAtomTypePropertyTable()

◆ parameterize()