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Use list to store compound.children #1121

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May 31, 2023
Merged

Use list to store compound.children #1121

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5 changes: 2 additions & 3 deletions mbuild/coarse_graining.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@

from mbuild.compound import Compound, clone
from mbuild.exceptions import MBuildError
from mbuild.utils.orderedset import OrderedSet

__all__ = ["coarse_grain"]

Expand Down Expand Up @@ -95,7 +94,7 @@ def _clone(self, clone_of=None, root_container=None):
if self.children is None:
newone.children = None
else:
newone.children = OrderedSet()
newone.children = list()
# Parent should be None initially.
newone.parent = None
newone.labels = OrderedDict()
Expand All @@ -106,7 +105,7 @@ def _clone(self, clone_of=None, root_container=None):
if self.children:
for child in self.children:
newchild = child._clone(clone_of, root_container)
newone.children.add(newchild)
newone.children.append(newchild)
newchild.parent = newone

# Copy labels, except bonds with atoms outside the hierarchy.
Expand Down
13 changes: 6 additions & 7 deletions mbuild/compound.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@
from mbuild.utils.exceptions import RemovedFuncError
from mbuild.utils.io import import_, run_from_ipython
from mbuild.utils.jsutils import overwrite_nglview_default
from mbuild.utils.orderedset import OrderedSet


def clone(existing_compound, clone_of=None, root_container=None):
Expand Down Expand Up @@ -117,7 +116,7 @@ class Compound(object):
----------
bond_graph : mb.BondGraph
Graph-like object that stores bond information for this Compound
children : OrderedSet
children : list
Contains all children (other Compounds).
labels : OrderedDict
Labels to Compound/Atom mappings. These do not necessarily need not be
Expand Down Expand Up @@ -174,7 +173,7 @@ def __init__(
self._pos = np.zeros(3)

self.parent = None
self.children = OrderedSet()
self.children = list()
self.labels = OrderedDict()
self.referrers = set()

Expand Down Expand Up @@ -920,7 +919,7 @@ def add(

# Create children and labels on the first add operation
if self.children is None:
self.children = OrderedSet()
self.children = list()
if self.labels is None:
self.labels = OrderedDict()

Expand All @@ -931,7 +930,7 @@ def add(
new_child, new_child.parent
)
)
self.children.add(new_child)
self.children.append(new_child)
new_child.parent = self

if new_child.bond_graph is not None and not isinstance(self, Port):
Expand Down Expand Up @@ -3500,7 +3499,7 @@ def _clone(self, clone_of=None, root_container=None):
if self.children is None:
newone.children = None
else:
newone.children = OrderedSet()
newone.children = list()
# Parent should be None initially.
newone.parent = None
newone.labels = OrderedDict()
Expand All @@ -3511,7 +3510,7 @@ def _clone(self, clone_of=None, root_container=None):
if self.children:
for child in self.children:
newchild = child._clone(clone_of, root_container)
newone.children.add(newchild)
newone.children.append(newchild)
newchild.parent = newone

# Copy labels, except bonds with atoms outside the hierarchy.
Expand Down