Substituent ranking

class scine_molassembler.RankingInformation

Ranking data of substituents around a central vertex

>>> # Model compound with a haptically bonded ethene
>>> compound_smiles = "[Co]1(C#O)(C#O)(C#O)(C#O)(C#O)C=C1"
>>> compound = io.experimental.from_smiles(compound_smiles)
>>> cobalt_index = 0
>>> p = compound.stereopermutators.option(cobalt_index)
>>> is_haptic_site = lambda s: len(s) > 1
>>> any(map(is_haptic_site, p.ranking.sites))
True
>>> # There are no links for this, none of the sites are interconnected
>>> len(p.ranking.links)
0
>>> # All of the sites are ranked equally save for the haptic site
>>> p.ranking.ranked_sites
[[0, 1, 2, 3, 4], [5]]
>>> p.ranking.sites[5] # The constituting atom indices of the haptic site
[11, 12]
>>> p.ranking.site_index_of_atom(12) # Look up atom indices
5
>>> p.ranking.rank_index_of_site(1) # Get ranking position of a site
0

Information on links (graph paths) between sites of a central atom

This captures all cycles that the central atom whose substituents are being ranked and its sites are in.

>>> # Simple example of links between substituents
>>> import scine_utilities as utils
>>> cyclopropane = io.experimental.from_smiles("C1CC1")
>>> p = cyclopropane.stereopermutators.option(0)
>>> # Sites are single-index, non-haptic
>>> site_is_single_index = lambda s: len(s) == 1
>>> all(map(site_is_single_index, p.ranking.sites))
True
>>> # There is a single link between carbon atom sites
>>> is_carbon = lambda a: cyclopropane.graph.element_type(a) == utils.ElementType.C
>>> site_is_carbon = lambda s: len(s) == 1 and is_carbon(s[0])
>>> len(p.ranking.links) == 1
True
>>> single_link = p.ranking.links[0]
>>> site_index_is_carbon = lambda s: site_is_carbon(p.ranking.sites[s])
>>> all(map(site_index_is_carbon, single_link.sites))
True
>>> single_link.cycle_sequence # Atom indices of cycle members
[0, 1, 2]
>>> all(map(is_carbon, single_link.cycle_sequence)) # All carbons
True
__init__(*args, **kwargs)
property cycle_sequence

The in-order atom sequence of the cycle involving the linked sites. The source vertex is always placed at the front of this sequence. The sequence is normalized such that second atom index is less than the last.

property sites

An ordered pair of the site indices that are linked. See the corresponding RankingInformation sites member

__init__(*args, **kwargs)

An ordered list of RankingInformation.Link on all links between binding sites

rank_index_of_site(self: scine_molassembler.RankingInformation, site_index: int) → int

Fetch the position of a site within the site ranking

property ranked_sites

An ordered nested list of indices into the sites member

property ranked_substituents

Sorted substituents grouped by ascending priority

site_index_of_atom(self: scine_molassembler.RankingInformation, atom_index: int) → int

Fetch the site index of an atom index

property sites

An unordered nested list of atom indices that constitute binding sites