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Merge top #249

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Merge top #249

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345ac51
draft merge method
May 5, 2022
353e815
merge method+tests
fgrunewald Jul 8, 2022
b50f138
fix bugs in tests and merge top
fgrunewald Aug 3, 2022
4094a64
add test for merge error
fgrunewald Aug 3, 2022
9acfa6a
bug fix when error is raised due to conficting types and test for it
fgrunewald Aug 3, 2022
51def84
add test for unsafe merge method
fgrunewald Aug 3, 2022
f2d6a29
Update polyply/src/topology.py
fgrunewald Aug 17, 2022
a0ada0a
Update polyply/src/topology.py
fgrunewald Aug 17, 2022
9c39221
Update polyply/src/topology.py
fgrunewald Aug 17, 2022
08c1f13
Update polyply/src/topology.py
fgrunewald Aug 17, 2022
f0e2f1f
Update polyply/src/topology.py
fgrunewald Aug 17, 2022
c2b2130
Merge branch 'master' into merge_top
fgrunewald Aug 17, 2022
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15 changes: 7 additions & 8 deletions polyply/src/topology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,7 @@ def __init__(self, force_field, name=None):
self.defines = {}
self.atom_types = {}
self.nonbond_params = {}
self.volumes = {}
# list attributes
self.description = []
self.persistences = []
Expand All @@ -243,12 +244,12 @@ def __init__(self, force_field, name=None):
def merge(self, other_top, check_duplicates=True):
"""
Merge two topologies updating their attribute dictionaries.
If check_dublicates is True attribute value combinations
already existent in self will be overwritten by those in
If `check_duplicates` is True attribute value combinations
that already exist will be overwritten by those in
the to be merged topology. An error will raise otherwise if
there are any conflicting dublicate entries.
there are any conflicting duplicate entries.

Note distance restraints are not checked for possibly
Note distance restraints are not checked for possible
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Something went wrong here

conflicting definitions.

Parameters
Expand All @@ -260,16 +261,14 @@ def merge(self, other_top, check_duplicates=True):
check for conflicting attribute value pairs

"""
for attribute in ["defaults", "defines", "atom_types", "nonbond_params"]:
for attribute in ["defaults", "defines", "atom_types", "nonbond_params", "volumes"]:
self_dict = getattr(self, attribute)
if check_duplicates:
for key, value in getattr(other_top, attribute).items():
if key in self_dict and self_dict[key] != value:
msg = f"Conflicting entry in {attribute} with key {key}"
raise MergeError(msg)
self_dict[key] = value
else:
getattr(self, attribute).update(getattr(other_top, attribute))
getattr(self, attribute).update(getattr(other_top, attribute))

self.description += other_top.description
self.persistences += other_top.persistences
Expand Down