CDPL::ForceField::MMFF94ChargeCalculator Class Reference

#include <MMFF94ChargeCalculator.hpp>

Public Types
typedef std::shared_ptr< MMFF94ChargeCalculator >	SharedPointer

Public Member Functions
	MMFF94ChargeCalculator ()
	MMFF94ChargeCalculator (const Chem::MolecularGraph &molgraph, Util::DArray &charges, bool strict)
void	setBondChargeIncrementTable (const MMFF94BondChargeIncrementTable::SharedPointer &table)
void	setPartialBondChargeIncrementTable (const MMFF94PartialBondChargeIncrementTable::SharedPointer &table)
void	setAtomTypePropertyTable (const MMFF94AtomTypePropertyTable::SharedPointer &table)
void	setFormalChargeDefinitionTable (const MMFF94FormalAtomChargeDefinitionTable::SharedPointer &table)
void	setAromaticRingSetFunction (const MMFF94RingSetFunction &func)
void	setNumericAtomTypeFunction (const MMFF94NumericAtomTypeFunction &func)
void	setSymbolicAtomTypeFunction (const MMFF94SymbolicAtomTypeFunction &func)
void	setBondTypeIndexFunction (const MMFF94BondTypeIndexFunction &func)
void	calculate (const Chem::MolecularGraph &molgraph, Util::DArray &charges, bool strict)
	Calculates MMFF94 partial charges for the atoms of a molecular graph. More...
const Util::DArray &	getFormalCharges () const

Member Typedef Documentation

SharedPointer

typedef std::shared_ptr<MMFF94ChargeCalculator> CDPL::ForceField::MMFF94ChargeCalculator::SharedPointer

Constructor & Destructor Documentation

MMFF94ChargeCalculator() [1/2]

CDPL::ForceField::MMFF94ChargeCalculator::MMFF94ChargeCalculator

(

)

MMFF94ChargeCalculator() [2/2]

CDPL::ForceField::MMFF94ChargeCalculator::MMFF94ChargeCalculator	(	const Chem::MolecularGraph &	molgraph,
		Util::DArray &	charges,
		bool	strict
	)

Member Function Documentation

setBondChargeIncrementTable()

void CDPL::ForceField::MMFF94ChargeCalculator::setBondChargeIncrementTable

(

const MMFF94BondChargeIncrementTable::SharedPointer &

table

)

setPartialBondChargeIncrementTable()

void CDPL::ForceField::MMFF94ChargeCalculator::setPartialBondChargeIncrementTable

(

const MMFF94PartialBondChargeIncrementTable::SharedPointer &

table

)

setAtomTypePropertyTable()

void CDPL::ForceField::MMFF94ChargeCalculator::setAtomTypePropertyTable

(

const MMFF94AtomTypePropertyTable::SharedPointer &

table

)

setFormalChargeDefinitionTable()

void CDPL::ForceField::MMFF94ChargeCalculator::setFormalChargeDefinitionTable

(

const MMFF94FormalAtomChargeDefinitionTable::SharedPointer &

table

)

setAromaticRingSetFunction()

void CDPL::ForceField::MMFF94ChargeCalculator::setAromaticRingSetFunction

(

const MMFF94RingSetFunction &

func

)

setNumericAtomTypeFunction()

void CDPL::ForceField::MMFF94ChargeCalculator::setNumericAtomTypeFunction

(

const MMFF94NumericAtomTypeFunction &

func

)

setSymbolicAtomTypeFunction()

void CDPL::ForceField::MMFF94ChargeCalculator::setSymbolicAtomTypeFunction

(

const MMFF94SymbolicAtomTypeFunction &

func

)

setBondTypeIndexFunction()

void CDPL::ForceField::MMFF94ChargeCalculator::setBondTypeIndexFunction

(

const MMFF94BondTypeIndexFunction &

func

)

calculate()

void CDPL::ForceField::MMFF94ChargeCalculator::calculate	(	const Chem::MolecularGraph &	molgraph,
		Util::DArray &	charges,
		bool	strict
	)

Calculates MMFF94 partial charges for the atoms of a molecular graph.

The partial atomic charges are constructed from initial full or fractional formal atomic charges \( q_I^0 \) (usually zero, but, e.g., +1/3 for guanidinium nitrogens) by adding contributions from bond charge increments \( w_{KI} \) which describe the polarity of the bonds to atom i from attached atoms k. Thus, \( w_{KI} \) is the contribution to the total charge on atom i of atom type I accumulated from, and at the expense of, its bonded neighbor k of atom type K. Specifically, MMFF computes \( q_i \) as

\( q_i = (1 - M_I \: u_I) \:q_I^0 + \sum (u_K \: q_K^0) + \sum w_{KI} \)

where \( w_{KI} = -w_{IK} \) and where the sums on the right hand side run over the \( M_I = crd(I) \) atoms k of MMFF atom type K directly attached to atom i ( \( crd(I) \) comes from "MMFFPROP.PAR"). In this equation, \( q_I^0 \) and \( q_K^0 \) are the formal charges assigned in the atom typing procedure (usually, by subroutine XTYPE), and the sum of the first two terms gives the "effective" fractional formal atomic charge residing on atom i. This approach allows a formal atomic charge initially affixed by the atom-typing procedure (e.g., \( q_I^0 \)) to be shared in a prescribed manner with the neighbors bonded to the atom in question. For example, for the series PO4(-3), HPO4(-2), H2PO4-, H3P04, it allows allows the partial charges on the terminal oxygens (each represented by the same numerical atom type, "32") to vary in a way which properly reflects the partial charges obtained from fits to the 6-31G* electrostatic potential. In particular, the difference between the resultant charges \( q_i \) calculated for the single terminal oxygen in H3PO4 and for the four equivalent terminal oxygens in PO4(-3) comes to -0.375, half (because \( u_{32} = -0.5 \)) the difference of -0.75 in the \( q_K^0 \) charges (i.e., 0.00 and -0.75, respectively) and reasonably in accord with the difference of -0.42 found by fitting the electrostatic potential.

Parameters

molgraph	The molecular graph for which to calculate partial atomic charges.
charges	The output array storing the calculated partial charges.
strict	If true, strict parameterization will be peformed that might fail.

getFormalCharges()

const Util::DArray& CDPL::ForceField::MMFF94ChargeCalculator::getFormalCharges

(

)

const

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

• MMFF94ChargeCalculator.hpp