Source code for molpher.algorithms.bidirectional.pathfinder

from molpher.algorithms.functions import find_path, timeit
from molpher.algorithms.operations import FindClosest
from molpher.core.ExplorationTree import ExplorationTree as ETree
from molpher.core.operations import *

[docs]class BidirectionalPathFinder: """ :param settings: search settings :type settings: `Settings` Implements a search where two trees are used to explore against each other. After every iteration the targets of the trees are updated so that the closest molecule from one tree becomes a target in the other. This search might be quicker and the morphs on the resulting paths are more balanced in terms of similarity to both source and the target. """
[docs] def __init__(self, settings): self.verbose = settings.verbose """`True` if verbose output was requested""" self.source_target = ETree.create(source=settings.source, target=settings.target) """:class:`~molpher.core.ExplorationTree.ExplorationTree` from source to target""" self.target_source = ETree.create(source=settings.target, target=settings.source) """:class:`~molpher.core.ExplorationTree.ExplorationTree` from target to source""" if settings.tree_params: self.source_target.params = settings.tree_params self.target_source.params = settings.tree_params self.source_target.thread_count = settings.max_threads self.target_source.thread_count = settings.max_threads self.source_target_min = FindClosest() """`FindClosest` holding the current minimum in the 'source to target' tree.""" self.target_source_min = FindClosest() """`FindClosest` holding the current minimum in the 'target to source' tree.""" self._iteration = [ GenerateMorphsOper() , SortMorphsOper() , FilterMorphsOper() , ExtendTreeOper() , PruneTreeOper() ] self.path = [] """a list of SMILES strings representing the found path (defaults to an empty `list`)"""
[docs] def __call__(self): """ Execute the search and return the path. :return: a list of SMILES strings representing the found path (defaults to an empty `list`) """ counter = 0 connecting_molecule = None while True: counter+=1 print('Iteration {0}:'.format(counter)) for oper in self._iteration: if self.verbose: print('Execution times ({0}):'.format(type(oper).__name__)) source_target_time = timeit(lambda : self.source_target.runOperation(oper)) print('\tsource -> target: {0}'.format(source_target_time)) target_source_time = timeit(lambda : self.target_source.runOperation(oper)) print('\ttarget -> source: {0}'.format(target_source_time)) print('\ttotal time: {0}'.format(source_target_time + target_source_time)) else: self.source_target.runOperation(oper) self.target_source.runOperation(oper) if self.verbose: print('Traversal times:') source_target_time = timeit(lambda : self.source_target.traverse(self.source_target_min)) print('\tsource -> target: {0}'.format(source_target_time)) target_source_time = timeit(lambda : self.target_source.traverse(self.target_source_min)) print('\ttarget -> source: {0}'.format(target_source_time)) print('\ttotal execution time: {0}'.format(source_target_time + target_source_time)) print('Current Targets:') print('\tsource to target:', self.source_target.params['target']) print('\ttarget to source:', self.target_source.params['target']) else: self.source_target.traverse(self.source_target_min) self.target_source.traverse(self.target_source_min) print('Current Minima:') print('\tsource to target:', self.source_target_min.closest.getSMILES(), self.source_target_min.closest.getDistToTarget()) print('\ttarget to source:', self.target_source_min.closest.getSMILES(), self.target_source_min.closest.getDistToTarget()) self.source_target.params = { 'target' : self.target_source_min.closest.getSMILES() } self.target_source_min = FindClosest() self.target_source.params = { 'target' : self.source_target_min.closest.getSMILES() } self.target_source_min = FindClosest() if self.verbose: print('New Targets:') print('\tsource to target:', self.source_target.params['target']) print('\ttarget to source:', self.target_source.params['target']) if self.source_target.path_found: connecting_molecule = self.source_target.params['target'] if self.verbose: print('Path Found in tree going from source to target') print('Connecting molecule:', connecting_molecule) assert self.source_target.hasMol(connecting_molecule) assert self.target_source.hasMol(connecting_molecule) break if self.target_source.path_found: connecting_molecule = self.target_source.params['target'] if self.verbose: print('Path Found in tree going from target to source') print('Connecting molecule:', connecting_molecule) assert self.target_source.hasMol(connecting_molecule) assert self.source_target.hasMol(connecting_molecule) break source_target_path = find_path(self.source_target, connecting_molecule) target_source_path = find_path(self.target_source, connecting_molecule) assert source_target_path.pop(-1) == connecting_molecule target_source_path.reverse() source_target_path.extend(target_source_path) self.path = source_target_path print('Path:', self.path) return self.path