NaviCatGA: A flexible Genetic Algorithm Optimizer for the NaviCat project¶

Contents¶

About
Install
Documentation
Examples

About¶

The code runs on pure python and is thus not extremely optimized. However, it is easy to adapt for particular applications. Dependencies are minimal for the base class:

numpy
matplotlib

The library is projected as base class containing the core methods, which are inherited by child classes to define the problem.

Several child solver classes are provided as fairly complete examples, but might need to be adapted or monkeypatched for particular applications.

The child classes and some functionalities have additional dependencies:

The selfies_solver class implementation requires selfies (https://github.com/aspuru-guzik-group/selfies) and rdkit (https://www.rdkit.org/). rdkit may be replaced manually by openbabel python bindings or other chemoinformatic modules.
The smiles_solver class implementation requires rdkit (https://www.rdkit.org/). rdkit may be replaced manually by openbabel python bindings or other chemoinformatic modules.
The xyz_solver class implementation requires AaronTools (https://github.com/QChASM/AaronTools.py).
Wrappers and chemistry modules contain functions that depend on pyscf to solve the electronic structure problem. However, these are provided for exemplary purposes and not a core functionality.
matter-chimera (https://github.com/aspuru-guzik-group/chimera) is recommended for scalarization. Alternatively, a scalarizer object with a scalarize method can be passed to the solver.

Additional features require alive-progress (for progress bars, very useful for CLI usage). However, these are implemented by monkeypatching the base class, and thus no functionality is lost without them.

Install¶

Installation is as simple as:

python setup.py install --record files.txt

This ensures easy uninstall. Just remove all files listed in files.txt using:

rm $(cat files.txt)

Documentation¶

The documentation is available here.

Examples¶

The tests subdirectory contains a copious amount of tests which double as examples.

Module contents:¶

navicatGA.base_solver module¶

navicatGA.cache module¶

navicatGA.chemistry_selfies module¶

navicatGA.chemistry_smiles module¶

navicatGA.chemistry_xyz module¶

navicatGA.exception_messages module¶

navicatGA.exceptions module¶

navicatGA.fitness_functions_float module¶

navicatGA.fitness_functions_selfies module¶

navicatGA.fitness_functions_xyz module¶

navicatGA.float_solver module¶

navicatGA.helpers module¶

navicatGA.logger module¶

navicatGA.progress_bars module¶

navicatGA.quantum_wrappers_selfies module¶

navicatGA.quantum_wrappers_xyz module¶

navicatGA.queue_wrappers_xyz module¶

navicatGA.score_modifiers module¶

navicatGA.selfies_solver module¶

navicatGA.smiles_solver module¶

navicatGA.timeout module¶

navicatGA.wrappers_selfies module¶

navicatGA.wrappers_smiles module¶

navicatGA.wrappers_xyz module¶

navicatGA.xyz_solver module¶

Indices and tables¶

Contents:

NaviCatGA: A flexible Genetic Algorithm Optimizer for the NaviCat project
- Contents
- About
- Install
- Documentation
- Examples
Module contents:
Indices and tables