1.1.1.2. molpher.algorithms package

The algorithms package contains implementations of complete exploration algorithms. Each algorithm is implemented within its own subpackage. All subpackages contain a run module that contains the run() function which can be used to set up and initiate a search (or multiple searches).

1.1.1.2.1. Subpackages

• 1.1.1.2.1.1. molpher.algorithms.antidecoys package
  • 1.1.1.2.1.1.1. Submodules
  • 1.1.1.2.1.1.2. molpher.algorithms.antidecoys.custom_opers module
  • 1.1.1.2.1.1.3. molpher.algorithms.antidecoys.pathfinder module
  • 1.1.1.2.1.1.4. molpher.algorithms.antidecoys.run module
  • 1.1.1.2.1.1.5. molpher.algorithms.antidecoys.settings module
  • 1.1.1.2.1.1.6. molpher.algorithms.antidecoys.utils module
  • 1.1.1.2.1.1.7. Module contents
• 1.1.1.2.1.2. molpher.algorithms.bidirectional package
  • 1.1.1.2.1.2.1. Submodules
  • 1.1.1.2.1.2.2. molpher.algorithms.bidirectional.pathfinder module
  • 1.1.1.2.1.2.3. molpher.algorithms.bidirectional.run module
  • 1.1.1.2.1.2.4. Module contents
• 1.1.1.2.1.3. molpher.algorithms.classic package
  • 1.1.1.2.1.3.1. Submodules
  • 1.1.1.2.1.3.2. molpher.algorithms.classic.pathfinder module
  • 1.1.1.2.1.3.3. molpher.algorithms.classic.run module
  • 1.1.1.2.1.3.4. Module contents

1.1.1.2.2. Submodules

1.1.1.2.3. molpher.algorithms.functions module

General utility functions for the algorithms.

molpher.algorithms.functions.find_path(tree, end_mol=None)

Backtracks the tree starting from end_mol and returns a list of SMILES strings representing the path from the root of the tree to end_mol.

Parameters

• tree (instance of ExplorationTree) – a tree to backtrack through

• end_mol (str) – SMILES of the last molecule in the requested path (target molecule by default)

Returns

list of SMILES of molecules on the path

Return type

list of str

molpher.algorithms.functions.timeit(func)

Executes func and returns its runtime.

Parameters

func (any callable) – function to time

Returns

runtime of func

Return type

float

1.1.1.2.4. molpher.algorithms.operations module

Custom operations and callbacks shared between algorithms.

class molpher.algorithms.operations.FindClosest

Bases: object

Callback that will search for a molecule closest to the target and saves it as a copy to the self.closest

See also

TraverseOper, traverse()

closest

MolpherMol instance (copy of the closest molecule) after the callback was executed, initialized to None

1.1.1.2.5. molpher.algorithms.settings module

class molpher.algorithms.settings.Settings(source, target, storage_dir, max_threads=None, max_iters=100, tree_params=None, verbose=False, filters=63)

Bases: object

Holds basic settings and parameters shared among the exploration algorithms.

max_iters

maximum number of iterations to spend on a search

max_threads

maximum number of threads to use in computations (uses all available CPUs by default)

source

SMILES string of the source molecule

storage_dir

path to a directory where results will be stored

target

SMILES string of the target molecule

tree_params

parameters of the exploration tree; either a dictionary like in params or an instance of ExplorationData

verbose

some algorithms can support verbose output

1.1.1.2.6. Module contents