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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Detects and parameterizes the MMFF94 torsion interactions of a molecular graph. More...
#include <MMFF94TorsionInteractionParameterizer.hpp>
Public Types | |
| typedef std::shared_ptr< MMFF94TorsionInteractionParameterizer > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94TorsionInteractionParameterizer instances. More... | |
Public Member Functions | |
| MMFF94TorsionInteractionParameterizer () | |
Constructs an MMFF94TorsionInteractionParameterizer instance using the default MMFF94 parameter tables. More... | |
| MMFF94TorsionInteractionParameterizer (const Chem::MolecularGraph &molgraph, MMFF94TorsionInteractionList &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 | setBondTypeIndexFunction (const MMFF94BondTypeIndexFunction &func) |
| Sets the function used to look up the MMFF94 bond type index of a bond. More... | |
| void | setAromaticRingSetFunction (const MMFF94RingSetFunction &func) |
| Sets the function used to obtain the set of MMFF94 aromatic rings of the input molecular graph. More... | |
| void | setTorsionParameterTable (const MMFF94TorsionParameterTable::SharedPointer &table) |
| Sets the primary table providing torsion type-specific \( V_1/V_2/V_3 \) parameters. More... | |
| void | setAtomTypePropertyTable (const MMFF94AtomTypePropertyTable::SharedPointer &table) |
| Sets the table providing MMFF94 numeric atom type property data (used by the empirical fallback). 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, MMFF94TorsionInteractionList &ia_list, bool strict) |
| Perceives the MMFF94 torsion interactions for molgraph and outputs the corresponding parameter data into ia_list. More... | |
Detects and parameterizes the MMFF94 torsion interactions of a molecular graph.
For every non-filtered atom quadruplet (i-j-k-l) consisting of a central bond j-k and one neighbor each on j and k the parameterizer looks up the matching MMFF94 torsion type-specific parameters \( V_1, V_2, V_3 \) from the supplied parameter table, falling back to the primary-to-parameter atom type map for atoms with no exact parameter entry, and emits an MMFF94TorsionInteraction instance.
| typedef std::shared_ptr<MMFF94TorsionInteractionParameterizer> CDPL::ForceField::MMFF94TorsionInteractionParameterizer::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94TorsionInteractionParameterizer instances.
| CDPL::ForceField::MMFF94TorsionInteractionParameterizer::MMFF94TorsionInteractionParameterizer | ( | ) |
Constructs an MMFF94TorsionInteractionParameterizer instance using the default MMFF94 parameter tables.
| CDPL::ForceField::MMFF94TorsionInteractionParameterizer::MMFF94TorsionInteractionParameterizer | ( | const Chem::MolecularGraph & | molgraph, |
| MMFF94TorsionInteractionList & | ia_list, | ||
| bool | strict | ||
| ) |
Constructs the parameterizer and processes the molecular graph molgraph.
| molgraph | The molecular graph for which to parameterize the torsion interactions. |
| ia_list | Output list receiving the generated MMFF94TorsionInteraction instances. |
| strict | If true, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setFilterFunction | ( | const InteractionFilterFunction4 & | func | ) |
Sets the filter function used to skip atom quadruplets during parameterization.
| func | The new four-atom filter function (when it returns false, the quadruplet is skipped). |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setAtomTypeFunction | ( | const MMFF94NumericAtomTypeFunction & | func | ) |
Sets the function used to look up the MMFF94 numeric atom type of an atom.
| func | The new numeric atom type lookup function. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setBondTypeIndexFunction | ( | const MMFF94BondTypeIndexFunction & | func | ) |
Sets the function used to look up the MMFF94 bond type index of a bond.
| func | The new bond type index lookup function. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setAromaticRingSetFunction | ( | const MMFF94RingSetFunction & | func | ) |
Sets the function used to obtain the set of MMFF94 aromatic rings of the input molecular graph.
| func | The new aromatic ring set retrievaly function. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setTorsionParameterTable | ( | const MMFF94TorsionParameterTable::SharedPointer & | table | ) |
Sets the primary table providing torsion type-specific \( V_1/V_2/V_3 \) parameters.
| table | The new torsion parameter table. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setAtomTypePropertyTable | ( | const MMFF94AtomTypePropertyTable::SharedPointer & | table | ) |
Sets the table providing MMFF94 numeric atom type property data (used by the empirical fallback).
| table | The new atom type property table. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::setParameterAtomTypeMap | ( | const MMFF94PrimaryToParameterAtomTypeMap::SharedPointer & | map | ) |
Sets the map used to translate primary atom types into their corresponding parameter atom types.
| map | The new primary-to-parameter atom type map. |
| void CDPL::ForceField::MMFF94TorsionInteractionParameterizer::parameterize | ( | const Chem::MolecularGraph & | molgraph, |
| MMFF94TorsionInteractionList & | ia_list, | ||
| bool | strict | ||
| ) |
Perceives the MMFF94 torsion interactions for molgraph and outputs the corresponding parameter data into ia_list.
| molgraph | The molecular graph for which to parameterize the torsion interactions. |
| ia_list | Output list receiving the generated MMFF94TorsionInteraction instances. |
| strict | If true, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used. |
1.9.1