Chemical Data Processing Library C++ API - Version 1.1.1
Public Types | Public Member Functions | List of all members
CDPL::ForceField::MMFF94ChargeCalculator Class Reference

#include <MMFF94ChargeCalculator.hpp>

Public Types

typedef std::shared_ptr< MMFF94ChargeCalculatorSharedPointer
 

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::DArraygetFormalCharges () const
 

Member Typedef Documentation

◆ 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
molgraphThe molecular graph for which to calculate partial atomic charges.
chargesThe output array storing the calculated partial charges.
strictIf true, strict parameterization will be peformed that might fail.

◆ getFormalCharges()

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

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