CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer Class Reference

Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph. More...

#include <MMFF94OutOfPlaneBendingInteractionParameterizer.hpp>

Public Types
typedef std::shared_ptr< MMFF94OutOfPlaneBendingInteractionParameterizer >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94OutOfPlaneBendingInteractionParameterizer instances. More...

Public Member Functions
	MMFF94OutOfPlaneBendingInteractionParameterizer ()
	Constructs an MMFF94OutOfPlaneBendingInteractionParameterizer instance using the default MMFF94 parameter tables. More...
	MMFF94OutOfPlaneBendingInteractionParameterizer (const Chem::MolecularGraph &molgraph, MMFF94OutOfPlaneBendingInteractionList &ia_list, bool strict)
	Constructs the parameterizer and processes the molecular graph molgraph. More...
void	setFilterFunction (const InteractionFilterFunction4 &func)
	Sets the filter function used to skip atom quadruplets 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	setOutOfPlaneBendingParameterTable (const MMFF94OutOfPlaneBendingParameterTable::SharedPointer &table)
	Sets the table providing the out-of-plane bending force constants. More...
void	setAtomTypePropertyTable (const MMFF94AtomTypePropertyTable::SharedPointer &table)
	Sets the table providing MMFF94 numeric atom type property data (used to identify trigonal centers). More...
void	setParameterAtomTypeMap (const MMFF94PrimaryToParameterAtomTypeMap::SharedPointer &map)
	Sets the map used to translate primary atom types into their corresponding parameter atom types. More...
void	parameterize (const Chem::MolecularGraph &molgraph, MMFF94OutOfPlaneBendingInteractionList &ia_list, bool strict)
	Perceives the MMFF94 out-of-plane bending interactions for molgraph and outputs the corresponding parameter data into ia_list. More...

Detailed Description

Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph.

For every atom j with exactly three neighbors that is a trigonal center (per the MMFF94 atom type properties) the parameterizer generates three out-of-plane parameter sets - one for each permutation of the three neighbors as the out-of-plane atom l with the remaining two as in-plane terminal atoms. The required out-of-plane force constants are taken from the parameter table, falling back through the primary-to-parameter atom type map when no exact entry is available.

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<MMFF94OutOfPlaneBendingInteractionParameterizer> CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94OutOfPlaneBendingInteractionParameterizer instances.

Constructor & Destructor Documentation

MMFF94OutOfPlaneBendingInteractionParameterizer() [1/2]

CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::MMFF94OutOfPlaneBendingInteractionParameterizer

(

)

Constructs an MMFF94OutOfPlaneBendingInteractionParameterizer instance using the default MMFF94 parameter tables.

MMFF94OutOfPlaneBendingInteractionParameterizer() [2/2]

CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::MMFF94OutOfPlaneBendingInteractionParameterizer	(	const Chem::MolecularGraph &	molgraph,
		MMFF94OutOfPlaneBendingInteractionList &	ia_list,
		bool	strict
	)

Constructs the parameterizer and processes the molecular graph molgraph.

Parameters

molgraph	The molecular graph for which to parameterize the out-of-plane bending interactions.
ia_list	Output list receiving the generated MMFF94OutOfPlaneBendingInteraction 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::MMFF94OutOfPlaneBendingInteractionParameterizer::setFilterFunction

(

const InteractionFilterFunction4 &

func

)

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

Parameters

func	The new four-atom filter function (when it returns false, the quadruplet is skipped).

setAtomTypeFunction()

void CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::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.

setOutOfPlaneBendingParameterTable()

void CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::setOutOfPlaneBendingParameterTable

(

const MMFF94OutOfPlaneBendingParameterTable::SharedPointer &

table

)

Sets the table providing the out-of-plane bending force constants.

Parameters

table

The new out-of-plane bending parameter table.

setAtomTypePropertyTable()

void CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::setAtomTypePropertyTable

(

const MMFF94AtomTypePropertyTable::SharedPointer &

table

)

Sets the table providing MMFF94 numeric atom type property data (used to identify trigonal centers).

Parameters

table

The new atom type property table.

setParameterAtomTypeMap()

void CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::setParameterAtomTypeMap

(

const MMFF94PrimaryToParameterAtomTypeMap::SharedPointer &

map

)

Sets the map used to translate primary atom types into their corresponding parameter atom types.

Parameters

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

parameterize()

void CDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizer::parameterize	(	const Chem::MolecularGraph &	molgraph,
		MMFF94OutOfPlaneBendingInteractionList &	ia_list,
		bool	strict
	)

Perceives the MMFF94 out-of-plane bending interactions for molgraph and outputs the corresponding parameter data into ia_list.

Parameters

molgraph	The molecular graph for which to parameterize the out-of-plane bending interactions.
ia_list	Output list receiving the generated MMFF94OutOfPlaneBendingInteraction instances.
strict	If true, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used.

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

• MMFF94OutOfPlaneBendingInteractionParameterizer.hpp