navicatGA.xyz_solver

Attributes

logger

Classes

XYZGenAlgSolver

Shared base for solvers whose chromosome genes are drawn from a

Module Contents

class navicatGA.xyz_solver.XYZGenAlgSolver(starting_population: list = [[None]], starting_random: bool = False, alphabet_list: list = None, chromosome_to_xyz=random_merge_xyz(), multi_alphabet: bool = False, equivalences: Sequence = None, max_counter: int = 10, n_genes: int = 1, fitness_function=None, excluded_genes: Sequence = None, **base_kwargs)

Bases: navicatGA.alphabet_solver.AlphabetGenAlgSolver

Shared base for solvers whose chromosome genes are drawn from a per-gene alphabet (SMILES fragments, SELFIES tokens, XYZ fragments).

Factors out the alphabet/equivalences setup, population init/refill, crossover-point sampling, and mutation logic that SmilesGenAlgSolver/SelfiesGenAlgSolver/XYZGenAlgSolver used to each reimplement independently. Subclasses still own create_offspring (crossover behaviour genuinely differs between them) and write_population (different depiction backend per representation).

Example child solver class for the GA. This child solver class is an example meant for a particular purpose, which also shows how to use the GA with xyz coordinate fragments using AaronTools.py. It might require heavy modification for other particular usages. Only the parameters specific for this child class are covered here.

Parameters: :param starting_population: list containing the starting AaronTools.py interpretable elements for all chromosomes; overridden by starting_random=True :type starting_population: list :param starting_random: whether to initialize all chromosomes with random elements from alphabet; overrides starting_selfies :type starting_random: bool :param alphabet_list: list containing the alphabets for the individual genes; or a single alphabet for all; can be a path directing to a directory containing xyz files. None (default) reads the AaronTools substituent library. :type alphabet_list: list :param chromosome_to_xyz: object that can take a chromosome and generate an AaronTools.py geometry object :type chromosome_to_xyz: object :param multi_alphabet: whether alphabet_list contains a single alphabet or a list of n_genes alphabet :type multi_alphabet: bool :param equivalences: list of integers that set the equivalent genes of a chromosome; see examples for clarification :type equivalences: list :param max_counter: maximum number of times a wrong structure will try to be corrected before skipping :type max_counter: int :param base_kwargs: any GenAlgSolver parameter (max_gen, pop_size, mutation_rate, …); see GenAlgSolver for the full list and defaults

create_offspring(first_parent, sec_parent, crossover_pt, offspring_number)

Creates an offspring from 2 parents.

write_population(basename='chromosome')

Print xyz for all the population at the current state.

max_counter = 10

starting_population = [[None]]

starting_random = False

navicatGA.xyz_solver.logger