Source code for gmso.core.subtopology

import warnings

from boltons.setutils import IndexedSet

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

[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 self._name @name.setter def name(self, name): self._name = str(name) @property def sites(self): return self._sites @property def n_sites(self): return len(self.sites) @property def parent(self): return self._parent @parent.setter def parent(self, parent): 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 f"<SubTopology {},\n " \ f"{self.n_sites} sites,\n " \ f"id: {id(self)}>" def __str__(self): return f"<SubTopology {}, " \ f"{self.n_sites} sites, " \ f"id: {id(self)}>"
def _validate_parent(parent): 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