Source code for gmso.core.subtopology

"""A topology within a topology."""
import warnings

from boltons.setutils import IndexedSet

from gmso.core.atom import Atom
from gmso.core.topology import Topology

[docs]class SubTopology(object): """A sub-topology i.e. topology within a topology. This class provides a hierarchical topological representation to the topology as it imperative with many chemical structures to have separation of layers/ boundaries. A sub-topology can be added to a gmso.Topology object which will be the parent of the sub-topology. Parameters ---------- name : str, optional, default='Sub-Topology' Name of the sub-topology parent : gmso.Topology, optional, default=None The parent topology of this SubTopology Attributes ---------- sites : IndexedSet of gmso.Site objects Collection of sites within this sub-topology n_sites : int Number of sites withing this sub-topology """ def __init__(self, name="Sub-Topology", parent=None): if name is not None: self._name = str(name) if parent is None: self._parent = parent else: self._parent = _validate_parent(parent) self._sites = IndexedSet() @property def name(self): """Return the name of the sub-topology.""" return self._name @name.setter def name(self, name): """Set the name of the sub-topology.""" self._name = str(name) @property def sites(self): """Return the sites associated with the sub-topology.""" return self._sites @property def n_sites(self): """Return the number of sites associated with the sub-topology.""" return len(self.sites) @property def parent(self): """Return the parent of the sub-topology.""" return self._parent @parent.setter def parent(self, parent): """Set the parent of the sub-topology.""" warnings.warn( "Setting a parent is potentially dangerous. Consider using " "Topology.add_subtopology instead" ) if parent is None: raise NotImplementedError( "Setting parents to None is not yet supported" ) self._parent = _validate_parent(parent)
[docs] def add_site(self, site, update_types=True): """Add a site to this sub-topology. This method adds a site to the sub-topology. If the sub-topology has a parent, the site will also be added to the parent topology. If the update_types parameter is set to true (default behavior), this method will also check if there is an gmso.AtomType associated with the site and it to the sub-topology's AtomTypes collection. Parameters ---------- site : gmso.Atom The site to be added to this sub-topology update_types : (bool), default=True If true, add this site's atom type to the sub-topology's set of AtomTypes Raises ------ TypeError If the parameter site is not of type topology.Site """ site = _validate_site_addability(site) if site in self.sites: warnings.warn("Redundantly adding Site {}".format(site)) self._sites.add(site) if self.parent: self.parent.add_site(site, update_types=update_types)
def __repr__(self): """Return a formatted representation of the sub-topology.""" return ( f"<SubTopology {},\n " f"{self.n_sites} sites,\n " f"id: {id(self)}>" ) def __str__(self): """Return a string representation of the sub-topology.""" return ( f"<SubTopology {}, " f"{self.n_sites} sites, " f"id: {id(self)}>" )
[docs] def json_dict(self): """Return a json serializable dictionary of this subtopology.""" subtop_dict = {"name":, "atoms": []} for site in self._sites: subtop_dict["atoms"].append(self.parent.get_index(site)) return subtop_dict
def _validate_parent(parent): """Ensure the parent is a topology.""" if isinstance(parent, Topology): return parent else: raise TypeError("Argument {} is not type Topology".format(parent)) def _validate_site_addability(site): """Ensure a site is a site and not already a part of a top/subtop.""" if not isinstance(site, Atom): raise TypeError("Argument {} is not a Site. See gmso/core/") # TODO: Some sort of a check on site.parent return site