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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 angle-bending interactions of a molecular graph. More...
#include <MMFF94AngleBendingInteractionParameterizer.hpp>
Public Types | |
| typedef std::shared_ptr< MMFF94AngleBendingInteractionParameterizer > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94AngleBendingInteractionParameterizer instances. More... | |
Public Member Functions | |
| MMFF94AngleBendingInteractionParameterizer () | |
Constructs an MMFF94AngleBendingInteractionParameterizer instance using the default MMFF94 parameter tables. More... | |
| MMFF94AngleBendingInteractionParameterizer (const Chem::MolecularGraph &molgraph, MMFF94AngleBendingInteractionList &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 | 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 | setBondStretchingParameterTable (const MMFF94BondStretchingParameterTable::SharedPointer &table) |
| Sets the primary bond-stretching parameter table (used to retrieve reference bond lengths in the empirical rule fallback). More... | |
| void | setBondStretchingRuleParameterTable (const MMFF94BondStretchingRuleParameterTable::SharedPointer &table) |
| Sets the fallback bond-stretching rule parameter table (used in the empirical rule fallback). More... | |
| void | setAngleBendingParameterTable (const MMFF94AngleBendingParameterTable::SharedPointer &table) |
| Sets the primary table providing angle type-specific angle-bending parameters. More... | |
| void | setAtomTypePropertyTable (const MMFF94AtomTypePropertyTable::SharedPointer &table) |
| Sets the table providing MMFF94 numeric atom type property data (used by the empirical rule 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, MMFF94AngleBendingInteractionList &ia_list, bool strict) |
| Perceives the MMFF94 angle-bending interactions for molgraph and outputs the corresponding parameter data into ia_list. More... | |
Detects and parameterizes the MMFF94 angle-bending interactions of a molecular graph.
For every non-filtered atom triplet (i-j-k) consisting of a central atom j and two of its neighbors the parameterizer determines the MMFF94 angle type index (0-8, accounting for ring membership and double bond character), looks up the matching MMFF94 angle-bending parameters, falls back to the empirical rule when no exact entry is found and emits an MMFF94AngleBendingInteraction instance.
| typedef std::shared_ptr<MMFF94AngleBendingInteractionParameterizer> CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94AngleBendingInteractionParameterizer instances.
| CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::MMFF94AngleBendingInteractionParameterizer | ( | ) |
Constructs an MMFF94AngleBendingInteractionParameterizer instance using the default MMFF94 parameter tables.
| CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::MMFF94AngleBendingInteractionParameterizer | ( | const Chem::MolecularGraph & | molgraph, |
| MMFF94AngleBendingInteractionList & | ia_list, | ||
| bool | strict | ||
| ) |
Constructs the parameterizer and processes the molecular graph molgraph.
| molgraph | The molecular graph for which to parameterize the angle-bending interactions. |
| ia_list | Output list receiving the generated MMFF94AngleBendingInteraction 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::MMFF94AngleBendingInteractionParameterizer::setFilterFunction | ( | const InteractionFilterFunction3 & | func | ) |
Sets the filter function used to skip atom triplets during parameterization.
| func | The new three-atom filter function (when it returns false, the triplet is skipped). |
| void CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::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::MMFF94AngleBendingInteractionParameterizer::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::MMFF94AngleBendingInteractionParameterizer::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 retrieval function. |
| void CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setBondStretchingParameterTable | ( | const MMFF94BondStretchingParameterTable::SharedPointer & | table | ) |
Sets the primary bond-stretching parameter table (used to retrieve reference bond lengths in the empirical rule fallback).
| table | The new bond-stretching parameter table. |
| void CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setBondStretchingRuleParameterTable | ( | const MMFF94BondStretchingRuleParameterTable::SharedPointer & | table | ) |
Sets the fallback bond-stretching rule parameter table (used in the empirical rule fallback).
| table | The new bond-stretching rule parameter table. |
| void CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setAngleBendingParameterTable | ( | const MMFF94AngleBendingParameterTable::SharedPointer & | table | ) |
Sets the primary table providing angle type-specific angle-bending parameters.
| table | The new angle-bending parameter table. |
| void CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::setAtomTypePropertyTable | ( | const MMFF94AtomTypePropertyTable::SharedPointer & | table | ) |
Sets the table providing MMFF94 numeric atom type property data (used by the empirical rule fallback).
| table | The new atom type property table. |
| void CDPL::ForceField::MMFF94AngleBendingInteractionParameterizer::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::MMFF94AngleBendingInteractionParameterizer::parameterize | ( | const Chem::MolecularGraph & | molgraph, |
| MMFF94AngleBendingInteractionList & | ia_list, | ||
| bool | strict | ||
| ) |
Perceives the MMFF94 angle-bending interactions for molgraph and outputs the corresponding parameter data into ia_list.
| molgraph | The molecular graph for which to parameterize the angle-bending interactions. |
| ia_list | Output list receiving the generated MMFF94AngleBendingInteraction 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