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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 bond-stretching interactions of a molecular graph. More...
#include <MMFF94BondStretchingInteractionParameterizer.hpp>
Public Types | |
| typedef std::shared_ptr< MMFF94BondStretchingInteractionParameterizer > | SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94BondStretchingInteractionParameterizer instances. More... | |
Public Member Functions | |
| MMFF94BondStretchingInteractionParameterizer () | |
Constructs an MMFF94BondStretchingInteractionParameterizer instance using the default MMFF94 parameter tables. More... | |
| MMFF94BondStretchingInteractionParameterizer (const Chem::MolecularGraph &molgraph, MMFF94BondStretchingInteractionList &ia_list, bool strict) | |
| Constructs the parameterizer and processes the molecular graph molgraph. More... | |
| void | setFilterFunction (const InteractionFilterFunction2 &func) |
| Sets the filter function used to skip bonds 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 table providing bond type-specific bond-stretching parameters. More... | |
| void | setBondStretchingRuleParameterTable (const MMFF94BondStretchingRuleParameterTable::SharedPointer &table) |
| Sets the fallback table providing rule-based bond-stretching 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 | parameterize (const Chem::MolecularGraph &molgraph, MMFF94BondStretchingInteractionList &ia_list, bool strict) |
| Perceives the MMFF94 bond-stretching interactions for molgraph and outputs the corresponding parameter data into ia_list. More... | |
| void | getParameters (const Chem::MolecularGraph &molgraph, const Chem::Bond &bond, unsigned int &bond_type_idx, double &force_const, double &ref_length, bool strict) const |
| Looks up the MMFF94 bond-stretching parameters for a single bond. More... | |
Detects and parameterizes the MMFF94 bond-stretching interactions of a molecular graph.
For every non-filtered bond the parameterizer looks up the matching MMFF94 bond type-specific parameters from the supplied tables (falling back to the rule-based table when no exact match is available) and appends an MMFF94BondStretchingInteraction instance to the output list.
| typedef std::shared_ptr<MMFF94BondStretchingInteractionParameterizer> CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer::SharedPointer |
A reference-counted smart pointer [SHPTR] for dynamically allocated MMFF94BondStretchingInteractionParameterizer instances.
| CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer::MMFF94BondStretchingInteractionParameterizer | ( | ) |
Constructs an MMFF94BondStretchingInteractionParameterizer instance using the default MMFF94 parameter tables.
| CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer::MMFF94BondStretchingInteractionParameterizer | ( | const Chem::MolecularGraph & | molgraph, |
| MMFF94BondStretchingInteractionList & | ia_list, | ||
| bool | strict | ||
| ) |
Constructs the parameterizer and processes the molecular graph molgraph.
| molgraph | The molecular graph for which to parameterize the bond-stretching interactions. |
| ia_list | Output list receiving the generated MMFF94BondStretchingInteraction 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::MMFF94BondStretchingInteractionParameterizer::setFilterFunction | ( | const InteractionFilterFunction2 & | func | ) |
Sets the filter function used to skip bonds during parameterization.
| func | The new filter function (when it returns false for a bond pair, the bond is skipped). |
| void CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer::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::MMFF94BondStretchingInteractionParameterizer::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::MMFF94BondStretchingInteractionParameterizer::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::MMFF94BondStretchingInteractionParameterizer::setBondStretchingParameterTable | ( | const MMFF94BondStretchingParameterTable::SharedPointer & | table | ) |
Sets the primary table providing bond type-specific bond-stretching parameters.
| table | The new bond-stretching parameter table. |
| void CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer::setBondStretchingRuleParameterTable | ( | const MMFF94BondStretchingRuleParameterTable::SharedPointer & | table | ) |
Sets the fallback table providing rule-based bond-stretching parameters.
| table | The new bond-stretching rule parameter table. |
| void CDPL::ForceField::MMFF94BondStretchingInteractionParameterizer::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::MMFF94BondStretchingInteractionParameterizer::parameterize | ( | const Chem::MolecularGraph & | molgraph, |
| MMFF94BondStretchingInteractionList & | ia_list, | ||
| bool | strict | ||
| ) |
Perceives the MMFF94 bond-stretching interactions for molgraph and outputs the corresponding parameter data into ia_list.
| molgraph | The molecular graph for which to parameterize the bond-stretching interactions. |
| ia_list | Output list receiving the generated MMFF94BondStretchingInteraction 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::MMFF94BondStretchingInteractionParameterizer::getParameters | ( | const Chem::MolecularGraph & | molgraph, |
| const Chem::Bond & | bond, | ||
| unsigned int & | bond_type_idx, | ||
| double & | force_const, | ||
| double & | ref_length, | ||
| bool | strict | ||
| ) | const |
Looks up the MMFF94 bond-stretching parameters for a single bond.
| molgraph | The molecular graph the bond belongs to. |
| bond | The bond whose parameters are queried. |
| bond_type_idx | Output variable receiving the MMFF94 bond type index. |
| force_const | Output variable receiving the bond-stretching force constant. |
| ref_length | Output variable receiving the reference bond length \( r_0 \). |
| strict | If true, missing parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used. |
1.9.1