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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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Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph. More...
Inheritance diagram for CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer:Public Member Functions | |
| None | __init__ () |
Constructs an MMFF94OutOfPlaneBendingInteractionParameterizer instance using the default MMFF94 parameter tables. | |
| None | __init__ (MMFF94OutOfPlaneBendingInteractionParameterizer parameterizer) |
Initializes a copy of the MMFF94OutOfPlaneBendingInteractionParameterizer instance parameterizer. More... | |
| None | __init__ (Chem.MolecularGraph molgraph, MMFF94OutOfPlaneBendingInteractionList ia_list, bool strict) |
| Constructs the parameterizer and processes the molecular graph molgraph. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| None | setFilterFunction (InteractionFilterFunction4 func) |
| Sets the filter function used to skip atom quadruplets during parameterization. More... | |
| None | setAtomTypeFunction (MMFF94NumericAtomTypeFunction func) |
| Sets the function used to look up the MMFF94 numeric atom type of an atom. More... | |
| None | setOutOfPlaneBendingParameterTable (MMFF94OutOfPlaneBendingParameterTable table) |
| Sets the table providing the out-of-plane bending force constants. More... | |
| None | setAtomTypePropertyTable (MMFF94AtomTypePropertyTable table) |
| Sets the table providing MMFF94 numeric atom type property data (used to identify trigonal centers). More... | |
| None | setParameterAtomTypeMap (MMFF94PrimaryToParameterAtomTypeMap map) |
| Sets the map used to translate primary atom types into their corresponding parameter atom types. More... | |
| MMFF94OutOfPlaneBendingInteractionParameterizer | assign (MMFF94OutOfPlaneBendingInteractionParameterizer parameterizer) |
Replaces the current state of self with a copy of the state of the MMFF94OutOfPlaneBendingInteractionParameterizer instance parameterizer. More... | |
| None | parameterize (Chem.MolecularGraph molgraph, MMFF94OutOfPlaneBendingInteractionList ia_list, bool strict) |
| Perceives the MMFF94 out-of-plane bending interactions for molgraph and outputs the corresponding parameter data into ia_list. More... | |
Properties | |
| objectID = property(getObjectID) | |
Detects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph.
For every atom j with exactly three neighbors that is a trigonal center (per the MMFF94 atom type properties) the parameterizer generates three out-of-plane parameter sets - one for each permutation of the three neighbors as the out-of-plane atom l with the remaining two as in-plane terminal atoms. The required out-of-plane force constants are taken from the parameter table, falling back through the primary-to-parameter atom type map when no exact entry is available.
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.__init__ | ( | MMFF94OutOfPlaneBendingInteractionParameterizer | parameterizer | ) |
Initializes a copy of the MMFF94OutOfPlaneBendingInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94OutOfPlaneBendingInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.__init__ | ( | Chem.MolecularGraph | molgraph, |
| MMFF94OutOfPlaneBendingInteractionList | ia_list, | ||
| bool | strict | ||
| ) |
Constructs the parameterizer and processes the molecular graph molgraph.
| molgraph | The molecular graph for which to parameterize the out-of-plane bending interactions. |
| ia_list | Output list receiving the generated MMFF94OutOfPlaneBendingInteraction instances. |
| strict | If True, missing/ambiguous parameters cause a parameterization failure. Otherwise, in case of parameterization problems, suitable fallback parameters will be used. |
| int CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94OutOfPlaneBendingInteractionParameterizer 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 MMFF94OutOfPlaneBendingInteractionParameterizer 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.MMFF94OutOfPlaneBendingInteractionParameterizer.setFilterFunction | ( | 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). |
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.setAtomTypeFunction | ( | 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. |
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.setOutOfPlaneBendingParameterTable | ( | MMFF94OutOfPlaneBendingParameterTable | table | ) |
Sets the table providing the out-of-plane bending force constants.
| table | The new out-of-plane bending parameter table. |
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.setAtomTypePropertyTable | ( | MMFF94AtomTypePropertyTable | table | ) |
Sets the table providing MMFF94 numeric atom type property data (used to identify trigonal centers).
| table | The new atom type property table. |
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.setParameterAtomTypeMap | ( | MMFF94PrimaryToParameterAtomTypeMap | 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. |
| MMFF94OutOfPlaneBendingInteractionParameterizer CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.assign | ( | MMFF94OutOfPlaneBendingInteractionParameterizer | parameterizer | ) |
Replaces the current state of self with a copy of the state of the MMFF94OutOfPlaneBendingInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94OutOfPlaneBendingInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94OutOfPlaneBendingInteractionParameterizer.parameterize | ( | Chem.MolecularGraph | molgraph, |
| MMFF94OutOfPlaneBendingInteractionList | ia_list, | ||
| bool | strict | ||
| ) |
Perceives the MMFF94 out-of-plane bending interactions for molgraph and outputs the corresponding parameter data into ia_list.
| molgraph | The molecular graph for which to parameterize the out-of-plane bending interactions. |
| ia_list | Output list receiving the generated MMFF94OutOfPlaneBendingInteraction 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