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fix bug with duplicate library reactions #1676

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merged 2 commits into from
Aug 9, 2019
Merged

fix bug with duplicate library reactions #1676

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e29a4a6
fix bug with duplicate library reactions
mjohnson541 Aug 8, 2019
ac6162f
skip parsing template and library reaction if the library isn't autog…
mjohnson541 Aug 8, 2019
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5 changes: 3 additions & 2 deletions rmgpy/data/kinetics/library.py
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Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ def getLibraryReactions(self):
"""
rxns = []
for entry in self.entries.values():
if entry._longDesc and 'Originally from reaction library: ' in entry._longDesc:
if self.autoGenerated and entry._longDesc and 'Originally from reaction library: ' in entry._longDesc:
lib = [line for line in entry._longDesc.split('\n') if 'Originally from reaction library: ' in line]
lib = lib[0].replace('Originally from reaction library: ','')
lib = lib.replace('\n','')
Expand All @@ -245,7 +245,8 @@ def getLibraryReactions(self):
duplicate=entry.item.duplicate, reversible=entry.item.reversible,
allow_pdep_route=entry.item.allow_pdep_route,
elementary_high_p=entry.item.elementary_high_p)
elif entry._longDesc and 'rate rule' in entry._longDesc: #template reaction
rxn.family = self.label #the library the reaction was loaded from (opposed to originally from)
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elif self.autoGenerated and entry._longDesc and 'rate rule' in entry._longDesc: #template reaction
c = entry._longDesc.split('\n')
family_comments = [i for i in c if 'family: ' in i]
familyname = family_comments[0].replace('family: ','')
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