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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 stretch-bend interactions of a molecular graph. More...
Inheritance diagram for CDPL.ForceField.MMFF94StretchBendInteractionParameterizer:Public Member Functions | |
| None | __init__ () |
Constructs an MMFF94StretchBendInteractionParameterizer instance using the default MMFF94 parameter tables. | |
| None | __init__ (MMFF94StretchBendInteractionParameterizer parameterizer) |
Initializes a copy of the MMFF94StretchBendInteractionParameterizer instance parameterizer. More... | |
| None | __init__ (Chem.MolecularGraph molgraph, MMFF94BondStretchingInteractionList bs_ia_list, MMFF94AngleBendingInteractionList ab_ia_list, MMFF94StretchBendInteractionList 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 (InteractionFilterFunction3 func) |
| Sets the filter function used to skip atom triplets during parameterization. More... | |
| None | setAtomTypeFunction (MMFF94NumericAtomTypeFunction func) |
| Sets the function used to look up the MMFF94 numeric atom type of an atom. More... | |
| None | setStretchBendParameterTable (MMFF94StretchBendParameterTable table) |
| Sets the primary table providing stretch-bend type-specific stretch-bend parameters. More... | |
| None | setDefaultStretchBendParameterTable (MMFF94DefaultStretchBendParameterTable table) |
| Sets the fallback table providing periodic-table-row-based default stretch-bend parameters. More... | |
| None | setAtomTypePropertyTable (MMFF94AtomTypePropertyTable table) |
| Sets the table providing MMFF94 numeric atom type property data (used to look up the periodic table row of an atom for the default-parameter fallback). More... | |
| MMFF94StretchBendInteractionParameterizer | assign (MMFF94StretchBendInteractionParameterizer parameterizer) |
Replaces the current state of self with a copy of the state of the MMFF94StretchBendInteractionParameterizer instance parameterizer. More... | |
| None | parameterize (Chem.MolecularGraph molgraph, MMFF94BondStretchingInteractionList bs_ia_list, MMFF94AngleBendingInteractionList ab_ia_list, MMFF94StretchBendInteractionList ia_list, bool strict) |
| Perceives the MMFF94 stretch-bend interactions for molgraph and outputs the corresponding parameter data into ia_list. More... | |
Properties | |
| objectID = property(getObjectID) | |
Detects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph.
Stretch-bend interactions couple the bending of an i-j-k bond angle to the stretching of the two participating bonds i-j and j-k. For every non-filtered atom triplet the parameterizer derives the stretch-bend type index from the bond type indices and angle type index of the already-parameterized bond-stretching and angle-bending interactions, looks up the matching stretch-bend force constants (falling back to the periodic-table-row-based default parameter table when no exact entry is available) and appends an MMFF94StretchBendInteraction instance to the output list.
| None CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.__init__ | ( | MMFF94StretchBendInteractionParameterizer | parameterizer | ) |
Initializes a copy of the MMFF94StretchBendInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94StretchBendInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.__init__ | ( | Chem.MolecularGraph | molgraph, |
| MMFF94BondStretchingInteractionList | bs_ia_list, | ||
| MMFF94AngleBendingInteractionList | ab_ia_list, | ||
| MMFF94StretchBendInteractionList | ia_list, | ||
| bool | strict | ||
| ) |
Constructs the parameterizer and processes the molecular graph molgraph.
| molgraph | The molecular graph for which to parameterize the stretch-bend interactions. |
| bs_ia_list | The list of already-parameterized MMFF94 bond-stretching interactions (provides per-bond type indices and reference lengths). |
| ab_ia_list | The list of already-parameterized MMFF94 angle-bending interactions (provides per-angle type indices and reference angles). |
| ia_list | Output list receiving the generated MMFF94StretchBendInteraction 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.MMFF94StretchBendInteractionParameterizer.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94StretchBendInteractionParameterizer 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 MMFF94StretchBendInteractionParameterizer 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.MMFF94StretchBendInteractionParameterizer.setFilterFunction | ( | 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). |
| None CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.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.MMFF94StretchBendInteractionParameterizer.setStretchBendParameterTable | ( | MMFF94StretchBendParameterTable | table | ) |
Sets the primary table providing stretch-bend type-specific stretch-bend parameters.
| table | The new stretch-bend parameter table. |
| None CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.setDefaultStretchBendParameterTable | ( | MMFF94DefaultStretchBendParameterTable | table | ) |
Sets the fallback table providing periodic-table-row-based default stretch-bend parameters.
| table | The new default stretch-bend parameter table. |
| None CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.setAtomTypePropertyTable | ( | MMFF94AtomTypePropertyTable | table | ) |
Sets the table providing MMFF94 numeric atom type property data (used to look up the periodic table row of an atom for the default-parameter fallback).
| table | The new atom type property table. |
| MMFF94StretchBendInteractionParameterizer CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.assign | ( | MMFF94StretchBendInteractionParameterizer | parameterizer | ) |
Replaces the current state of self with a copy of the state of the MMFF94StretchBendInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94StretchBendInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94StretchBendInteractionParameterizer.parameterize | ( | Chem.MolecularGraph | molgraph, |
| MMFF94BondStretchingInteractionList | bs_ia_list, | ||
| MMFF94AngleBendingInteractionList | ab_ia_list, | ||
| MMFF94StretchBendInteractionList | ia_list, | ||
| bool | strict | ||
| ) |
Perceives the MMFF94 stretch-bend interactions for molgraph and outputs the corresponding parameter data into ia_list.
| molgraph | The molecular graph for which to parameterize the stretch-bend interactions. |
| bs_ia_list | The list of already-parameterized MMFF94 bond-stretching interactions (provides per-bond type indices and reference lengths). |
| ab_ia_list | The list of already-parameterized MMFF94 angle-bending interactions (provides per-angle type indices and reference angles). |
| ia_list | Output list receiving the generated MMFF94StretchBendInteraction 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