scine_chemoton.reaction_rules.polarization_rules

Classes

PaulingElectronegativityRule([min_difference])	Polarization rule for the Pauli electronegativity scale.
PolarizationBaseRule(*args, **kwargs)	A rule that assigns polarizations (+, -, or +-) to each atom based on given molecules
PolarizationFunctionalGroupRule(...)
PolarizationRuleAndArray([rules])	An array of logically 'and' connected rules.
PolarizationRuleSet(kwargs)	A dictionary holding elements as keys and a respective PolarizationRule for it.

class scine_chemoton.reaction_rules.polarization_rules.PaulingElectronegativityRule(min_difference=0.4)

Polarization rule for the Pauli electronegativity scale.

Attributes:

min_differencefloat

The minimum difference in electronegativities to assign a polarization. Default: 0.4 (avoids polarization of C–H bonds)

property name: str

string_from_rule(molecules, idx_map, elements, atom_index)

Return ‘+’ if the atom is electron poor, ‘-’ if it is electron rich, some combination thereof if the atom is neighbouring elements with significantly higher and lower electronegativity, and ‘’ if it is neighbouring neither.

Return type:

str

class scine_chemoton.reaction_rules.polarization_rules.PolarizationBaseRule(*args, **kwargs)

A rule that assigns polarizations (+, -, or +-) to each atom based on given molecules

property name: str

abstract string_from_rule(molecules, idx_map, elements, atom_index)

Method to be implemented for each rule, giving back a polarization character for atom_index in multiple molecules

Return type:

str

Parameters:

moleculesList[masm.Molecule]

A list of molassembler molecules representing the total system

idx_mapList[Tuple[int, int]]

An index map generated by molassembler that allows to map the atom_index to the atom in the molecules

elementsList[str]

A list of all elements

atom_indexint

The index we want the polarization of

Returns:

polarization_charstr

Either ‘+’, ‘-’, or ‘+-’

class scine_chemoton.reaction_rules.polarization_rules.PolarizationFunctionalGroupRule(polarization_char, distance_rule)

property name: str

string_from_rule(molecules, idx_map, elements, atom_index)

Method to be implemented for each rule, giving back a polarization character for atom_index in multiple molecules

Return type:

str

Parameters:

moleculesList[masm.Molecule]

A list of molassembler molecules representing the total system

idx_mapList[Tuple[int, int]]

An index map generated by molassembler that allows to map the atom_index to the atom in the molecules

elementsList[str]

A list of all elements

atom_indexint

The index we want the polarization of

Returns:

polarization_charstr

Either ‘+’, ‘-’, or ‘+-’

class scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleAndArray(rules=None)

An array of logically ‘and’ connected rules.

Parameters:

rulesOptional[List[PolarizationBaseRule]]

A list of Polarization rules that all may add a character.

property name: str

string_from_rule(*args, **kwargs)

Method to be implemented for each rule, giving back a polarization character for atom_index in multiple molecules

Return type:

str

Parameters:

moleculesList[masm.Molecule]

A list of molassembler molecules representing the total system

idx_mapList[Tuple[int, int]]

An index map generated by molassembler that allows to map the atom_index to the atom in the molecules

elementsList[str]

A list of all elements

atom_indexint

The index we want the polarization of

Returns:

polarization_charstr

Either ‘+’, ‘-’, or ‘+-’

class scine_chemoton.reaction_rules.polarization_rules.PolarizationRuleSet(kwargs)

A dictionary holding elements as keys and a respective PolarizationRule for it. All keys are checked for valid element types. Lists as values are automatically transformed to an PolarizationRuleAndArray.

clear() → None.  Remove all items from D.

copy()

classmethod fromkeys(iterable, value=None)

get(k[, d]) → D[k] if k in D, else d.  d defaults to None.

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

pop(k[, d]) → v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised.

popitem() → (k, v), remove and return some (key, value) pair

as a 2-tuple; but raise KeyError if D is empty.

setdefault(k[, d]) → D.get(k,d), also set D[k]=d if k not in D

update([E, ]**F) → None.  Update D from mapping/iterable E and F.

If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v

values() → an object providing a view on D's values