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

class molpher.algorithms.bidirectional.pathfinder.BidirectionalPathFinder(settings)[source]

Bases: object

Parameters:settings (Settings) – search 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.

__call__()[source]

Execute the search and return the path.

Returns:a list of SMILES strings representing the found path (defaults to an empty list)
__dict__ = mappingproxy({'__call__': <function BidirectionalPathFinder.__call__ at 0x7f28391d22f0>, '__dict__': <attribute '__dict__' of 'BidirectionalPathFinder' objects>, '__module__': 'molpher.algorithms.bidirectional.pathfinder', '__doc__': '\n :param settings: search settings\n :type settings: `Settings`\n\n Implements a search where two trees are used to explore against each other.\n After every iteration the targets of the trees are updated so that the closest molecule\n from one tree becomes a target in the other.\n\n This search might be quicker and the morphs on the resulting paths are more balanced\n in terms of similarity to both source and the target.\n ', '__init__': <function BidirectionalPathFinder.__init__ at 0x7f28391d2268>, '__weakref__': <attribute '__weakref__' of 'BidirectionalPathFinder' objects>})
__init__(settings)[source]
__module__ = 'molpher.algorithms.bidirectional.pathfinder'
__weakref__

list of weak references to the object (if defined)

path = None

a list of SMILES strings representing the found path (defaults to an empty list)

source_target = None

ExplorationTree from source to target

source_target_min = None

FindClosest holding the current minimum in the ‘source to target’ tree.

target_source = None

ExplorationTree from target to source

target_source_min = None

FindClosest holding the current minimum in the ‘target to source’ tree.

verbose = None

True if verbose output was requested

1.1.1.2.1.2.3. molpher.algorithms.bidirectional.run module

molpher.algorithms.bidirectional.run.run(settings, paths_to_find=1)[source]

Run the search.

Parameters:
  • settings – Settings instance
  • paths_to_find – number of paths to find with the algorithm
Returns:

a path as a list of SMILES strings

1.1.1.2.1.2.4. Module contents