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Chemical Data Processing Library Python API - Version 1.4.0
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Chemical Data Processing Library Python API - Version 1.4.0
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Highly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization. More...
Inheritance diagram for CDPL.ForceField.MMFF94InteractionParameterizer:Public Member Functions | |
| None | __init__ (int param_set=1) |
| Constructs the parameterizer with the default tables for the chosen MMFF94 parameter set. More... | |
| None | __init__ (MMFF94InteractionParameterizer parameterizer) |
| Constructs a copy of the parameterizer parameterizer. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| None | setBondStretchingFilterFunction (Chem.BoolAtom2Functor func) |
| Installs a filter that decides whether a candidate bond-stretching interaction is kept. More... | |
| None | setAngleBendingFilterFunction (InteractionFilterFunction3 func) |
| Installs a filter that decides whether a candidate angle-bending interaction is kept. More... | |
| None | setStretchBendFilterFunction (InteractionFilterFunction3 func) |
| Installs a filter that decides whether a candidate stretch-bend interaction is kept. More... | |
| None | setOutOfPlaneBendingFilterFunction (InteractionFilterFunction4 func) |
| Installs a filter that decides whether a candidate out-of-plane bending interaction is kept. More... | |
| None | setTorsionFilterFunction (InteractionFilterFunction4 func) |
| Installs a filter that decides whether a candidate torsion interaction is kept. More... | |
| None | setElectrostaticFilterFunction (Chem.BoolAtom2Functor func) |
| Installs a filter that decides whether a candidate electrostatic interaction is kept. More... | |
| None | setVanDerWaalsFilterFunction (Chem.BoolAtom2Functor func) |
| Installs a filter that decides whether a candidate Van der Waals interaction is kept. More... | |
| None | clearFilterFunctions () |
| Removes all previously installed interaction filter functions. | |
| None | setSymbolicAtomTypePatternTable (MMFF94SymbolicAtomTypePatternTable table) |
| Sets the symbolic atom type pattern table to use during atom typing. More... | |
| None | setHeavyToHydrogenAtomTypeMap (MMFF94HeavyToHydrogenAtomTypeMap map) |
| Sets the heavy-to-hydrogen atom type map used to derive hydrogen atom types from their non-hydrogen neighbors. More... | |
| None | setSymbolicToNumericAtomTypeMap (MMFF94SymbolicToNumericAtomTypeMap map) |
| Sets the symbolic-to-numeric atom type map used to convert symbolic types to numeric ones. More... | |
| None | setAromaticAtomTypeDefinitionTable (MMFF94AromaticAtomTypeDefinitionTable table) |
| Sets the aromatic atom type definition table used to override types of aromatic atoms. More... | |
| None | setAtomTypePropertyTable (MMFF94AtomTypePropertyTable table) |
| Sets the atom type property table used to retrieve per-numeric type properties. More... | |
| None | setFormalAtomChargeDefinitionTable (MMFF94FormalAtomChargeDefinitionTable table) |
| Sets the formal atom charge definition table used during charge assignment. More... | |
| None | setBondChargeIncrementTable (MMFF94BondChargeIncrementTable table) |
| Sets the bond charge-increment table used during partial-charge calculation. More... | |
| None | setPartialBondChargeIncrementTable (MMFF94PartialBondChargeIncrementTable table) |
| Sets the partial bond charge-increment table used during partial charge calculation. More... | |
| None | setPrimaryToParameterAtomTypeMap (MMFF94PrimaryToParameterAtomTypeMap map) |
| Sets the primary-to-parameter atom type map used by the parameter look-ups. More... | |
| None | setAngleBendingParameterTable (MMFF94AngleBendingParameterTable table) |
| Sets the angle-bending parameter table to use. More... | |
| None | setBondStretchingParameterTable (MMFF94BondStretchingParameterTable table) |
| Sets the bond-stretching parameter table to use. More... | |
| None | setBondStretchingRuleParameterTable (MMFF94BondStretchingRuleParameterTable table) |
| Sets the bond-stretching rule parameter table used as a fallback when no explicit bond-stretching parameter entry is available. More... | |
| None | setStretchBendParameterTable (MMFF94StretchBendParameterTable table) |
| Sets the stretch-bend parameter table to use. More... | |
| None | setDefaultStretchBendParameterTable (MMFF94DefaultStretchBendParameterTable table) |
| Sets the default stretch-bend parameter table used as a periodic-row fallback. More... | |
| None | setOutOfPlaneBendingParameterTable (MMFF94OutOfPlaneBendingParameterTable table) |
| Sets the out-of-plane bending parameter table to use. More... | |
| None | setTorsionParameterTable (MMFF94TorsionParameterTable table) |
| Sets the torsion parameter table to use. More... | |
| None | setVanDerWaalsParameterTable (MMFF94VanDerWaalsParameterTable table) |
| Sets the Van der Waals parameter table to use. More... | |
| None | setDielectricConstant (float de_const) |
| Sets the dielectric constant used by the electrostatic interaction parameterizer. More... | |
| None | setDistanceExponent (float dist_expo) |
| Sets the distance exponent used by the electrostatic interaction parameterizer. More... | |
| None | setParameterSet (int param_set) |
| Switches the active MMFF94 parameter set variant to a different one. More... | |
| MMFF94InteractionParameterizer | assign (MMFF94InteractionParameterizer parameterizer) |
| Copies the state of parameterizer. More... | |
| None | parameterize (Chem.MolecularGraph molgraph, MMFF94InteractionData ia_data, int ia_types=127, bool strict=True) |
| Parameterizes the MMFF94 force field interactions for molgraph and stores them in ia_data. More... | |
Properties | |
| objectID = property(getObjectID) | |
Highly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization.
The constructor installs default parameter tables and atom-/bond-typing helpers for the selected force field variant (see namespace ForceField.MMFF94ParameterSet). Every table, map and filter function can be overridden via the corresponding setter methods. Calling parameterize() runs atom typing, bond typing, formal/partial charge assignment, aromaticity perception and topological distance calculation, then dispatches to the seven per-interaction MMFF94*InteractionParameterizer members and stores the resulting interaction parameter records in the supplied ForceField.MMFF94InteractionData object.
| None CDPL.ForceField.MMFF94InteractionParameterizer.__init__ | ( | int | param_set = 1 | ) |
Constructs the parameterizer with the default tables for the chosen MMFF94 parameter set.
| param_set | The parameter set variant (see namespace ForceField.MMFF94ParameterSet). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.__init__ | ( | MMFF94InteractionParameterizer | parameterizer | ) |
Constructs a copy of the parameterizer parameterizer.
| parameterizer | The parameterizer to copy. |
| int CDPL.ForceField.MMFF94InteractionParameterizer.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94InteractionParameterizer instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two MMFF94InteractionParameterizer instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().
| None CDPL.ForceField.MMFF94InteractionParameterizer.setBondStretchingFilterFunction | ( | Chem.BoolAtom2Functor | func | ) |
Installs a filter that decides whether a candidate bond-stretching interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setAngleBendingFilterFunction | ( | InteractionFilterFunction3 | func | ) |
Installs a filter that decides whether a candidate angle-bending interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setStretchBendFilterFunction | ( | InteractionFilterFunction3 | func | ) |
Installs a filter that decides whether a candidate stretch-bend interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setOutOfPlaneBendingFilterFunction | ( | InteractionFilterFunction4 | func | ) |
Installs a filter that decides whether a candidate out-of-plane bending interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setTorsionFilterFunction | ( | InteractionFilterFunction4 | func | ) |
Installs a filter that decides whether a candidate torsion interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setElectrostaticFilterFunction | ( | Chem.BoolAtom2Functor | func | ) |
Installs a filter that decides whether a candidate electrostatic interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setVanDerWaalsFilterFunction | ( | Chem.BoolAtom2Functor | func | ) |
Installs a filter that decides whether a candidate Van der Waals interaction is kept.
| func | The filter functor (returns True to keep the interaction). |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setSymbolicAtomTypePatternTable | ( | MMFF94SymbolicAtomTypePatternTable | table | ) |
Sets the symbolic atom type pattern table to use during atom typing.
| table | The new symbolic atom type pattern table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setHeavyToHydrogenAtomTypeMap | ( | MMFF94HeavyToHydrogenAtomTypeMap | map | ) |
Sets the heavy-to-hydrogen atom type map used to derive hydrogen atom types from their non-hydrogen neighbors.
| map | The new heavy-to-hydrogen atom type map. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setSymbolicToNumericAtomTypeMap | ( | MMFF94SymbolicToNumericAtomTypeMap | map | ) |
Sets the symbolic-to-numeric atom type map used to convert symbolic types to numeric ones.
| map | The new symbolic-to-numeric atom type map. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setAromaticAtomTypeDefinitionTable | ( | MMFF94AromaticAtomTypeDefinitionTable | table | ) |
Sets the aromatic atom type definition table used to override types of aromatic atoms.
| table | The new aromatic atom type definition table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setAtomTypePropertyTable | ( | MMFF94AtomTypePropertyTable | table | ) |
Sets the atom type property table used to retrieve per-numeric type properties.
| table | The new atom type property table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setFormalAtomChargeDefinitionTable | ( | MMFF94FormalAtomChargeDefinitionTable | table | ) |
Sets the formal atom charge definition table used during charge assignment.
| table | The new formal atom charge definition table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setBondChargeIncrementTable | ( | MMFF94BondChargeIncrementTable | table | ) |
Sets the bond charge-increment table used during partial-charge calculation.
| table | The new bond charge-increment table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setPartialBondChargeIncrementTable | ( | MMFF94PartialBondChargeIncrementTable | table | ) |
Sets the partial bond charge-increment table used during partial charge calculation.
| table | The new partial bond charge-increment table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setPrimaryToParameterAtomTypeMap | ( | MMFF94PrimaryToParameterAtomTypeMap | map | ) |
Sets the primary-to-parameter atom type map used by the parameter look-ups.
| map | The new primary-to-parameter atom type map. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setAngleBendingParameterTable | ( | MMFF94AngleBendingParameterTable | table | ) |
Sets the angle-bending parameter table to use.
| table | The new angle-bending parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setBondStretchingParameterTable | ( | MMFF94BondStretchingParameterTable | table | ) |
Sets the bond-stretching parameter table to use.
| table | The new bond-stretching parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setBondStretchingRuleParameterTable | ( | MMFF94BondStretchingRuleParameterTable | table | ) |
Sets the bond-stretching rule parameter table used as a fallback when no explicit bond-stretching parameter entry is available.
| table | The new bond-stretching rule parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setStretchBendParameterTable | ( | MMFF94StretchBendParameterTable | table | ) |
Sets the stretch-bend parameter table to use.
| table | The new stretch-bend parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setDefaultStretchBendParameterTable | ( | MMFF94DefaultStretchBendParameterTable | table | ) |
Sets the default stretch-bend parameter table used as a periodic-row fallback.
| table | The new default stretch-bend parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setOutOfPlaneBendingParameterTable | ( | MMFF94OutOfPlaneBendingParameterTable | table | ) |
Sets the out-of-plane bending parameter table to use.
| table | The new out-of-plane bending parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setTorsionParameterTable | ( | MMFF94TorsionParameterTable | table | ) |
Sets the torsion parameter table to use.
| table | The new torsion parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setVanDerWaalsParameterTable | ( | MMFF94VanDerWaalsParameterTable | table | ) |
Sets the Van der Waals parameter table to use.
| table | The new Van der Waals parameter table. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setDielectricConstant | ( | float | de_const | ) |
Sets the dielectric constant used by the electrostatic interaction parameterizer.
| de_const | The new dielectric constant. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setDistanceExponent | ( | float | dist_expo | ) |
Sets the distance exponent used by the electrostatic interaction parameterizer.
| dist_expo | The new distance exponent. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.setParameterSet | ( | int | param_set | ) |
Switches the active MMFF94 parameter set variant to a different one.
| param_set | The new parameter set variant (see namespace ForceField.MMFF94ParameterSet). |
| MMFF94InteractionParameterizer CDPL.ForceField.MMFF94InteractionParameterizer.assign | ( | MMFF94InteractionParameterizer | parameterizer | ) |
Copies the state of parameterizer.
| parameterizer | The parameterizer to copy. |
| None CDPL.ForceField.MMFF94InteractionParameterizer.parameterize | ( | Chem.MolecularGraph | molgraph, |
| MMFF94InteractionData | ia_data, | ||
| int | ia_types = 127, |
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| bool | strict = True |
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Parameterizes the MMFF94 force field interactions for molgraph and stores them in ia_data.
| molgraph | The molecular graph to parameterize. |
| ia_data | The output container receiving the perceived interactions and their parameters. |
| ia_types | A bitmask of flags specifying which interaction types to parameterize (see namespace ForceField.InteractionType). |
| strict | If True, the parameterization fails when any required parameter is missing. Otherwise, fallback strategies (rule-based parameters, default values) are used. |
1.9.1