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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 bond-stretching interactions of a molecular graph. More...
Inheritance diagram for CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer:Public Member Functions | |
| None | __init__ () |
Constructs an MMFF94BondStretchingInteractionParameterizer instance using the default MMFF94 parameter tables. | |
| None | __init__ (MMFF94BondStretchingInteractionParameterizer parameterizer) |
Initializes a copy of the MMFF94BondStretchingInteractionParameterizer instance parameterizer. More... | |
| None | __init__ (Chem.MolecularGraph molgraph, MMFF94BondStretchingInteractionList 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 (Chem.BoolAtom2Functor func) |
| Sets the filter function used to skip bonds during parameterization. More... | |
| None | setAtomTypeFunction (MMFF94NumericAtomTypeFunction func) |
| Sets the function used to look up the MMFF94 numeric atom type of an atom. More... | |
| None | setBondTypeIndexFunction (MMFF94BondTypeIndexFunction func) |
| Sets the function used to look up the MMFF94 bond type index of a bond. More... | |
| None | setAromaticRingSetFunction (MMFF94RingSetFunction func) |
| Sets the function used to obtain the set of MMFF94 aromatic rings of the input molecular graph. More... | |
| None | setBondStretchingParameterTable (MMFF94BondStretchingParameterTable table) |
| Sets the primary table providing bond type-specific bond-stretching parameters. More... | |
| None | setBondStretchingRuleParameterTable (MMFF94BondStretchingRuleParameterTable table) |
| Sets the fallback table providing rule-based bond-stretching parameters. More... | |
| None | setAtomTypePropertyTable (MMFF94AtomTypePropertyTable table) |
| Sets the table providing MMFF94 numeric atom type property data (used by the empirical fallback). More... | |
| MMFF94BondStretchingInteractionParameterizer | assign (MMFF94BondStretchingInteractionParameterizer parameterizer) |
Replaces the current state of self with a copy of the state of the MMFF94BondStretchingInteractionParameterizer instance parameterizer. More... | |
| None | parameterize (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... | |
Properties | |
| objectID = property(getObjectID) | |
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.
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.__init__ | ( | MMFF94BondStretchingInteractionParameterizer | parameterizer | ) |
Initializes a copy of the MMFF94BondStretchingInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94BondStretchingInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.__init__ | ( | 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. |
| int CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.getObjectID | ( | ) |
Returns the numeric identifier (ID) of the wrapped C++ class instance.
Different Python MMFF94BondStretchingInteractionParameterizer 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 MMFF94BondStretchingInteractionParameterizer 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.MMFF94BondStretchingInteractionParameterizer.setFilterFunction | ( | Chem.BoolAtom2Functor | 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). |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.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.MMFF94BondStretchingInteractionParameterizer.setBondTypeIndexFunction | ( | 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. |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.setAromaticRingSetFunction | ( | 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. |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.setBondStretchingParameterTable | ( | MMFF94BondStretchingParameterTable | table | ) |
Sets the primary table providing bond type-specific bond-stretching parameters.
| table | The new bond-stretching parameter table. |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.setBondStretchingRuleParameterTable | ( | MMFF94BondStretchingRuleParameterTable | table | ) |
Sets the fallback table providing rule-based bond-stretching parameters.
| table | The new bond-stretching rule parameter table. |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.setAtomTypePropertyTable | ( | MMFF94AtomTypePropertyTable | table | ) |
Sets the table providing MMFF94 numeric atom type property data (used by the empirical fallback).
| table | The new atom type property table. |
| MMFF94BondStretchingInteractionParameterizer CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.assign | ( | MMFF94BondStretchingInteractionParameterizer | parameterizer | ) |
Replaces the current state of self with a copy of the state of the MMFF94BondStretchingInteractionParameterizer instance parameterizer.
| parameterizer | The MMFF94BondStretchingInteractionParameterizer instance to copy. |
| None CDPL.ForceField.MMFF94BondStretchingInteractionParameterizer.parameterize | ( | 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. |
1.9.1