Skip to content

Fix SBML import #116

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
tebuck wants to merge 7 commits into
base: master
Choose a base branch
from
Draft

Fix SBML import #116

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
b0fc7a2
Merge pull request #1 from mcellteam/master
tebuck Aug 8, 2019
9dfe034
Merge pull request #2 from mcellteam/master
tebuck Jul 12, 2020
dc5d074
Check for extension at end of filename during BNGL and SBML import
tebuck Jul 12, 2020
8329315
Do not replace existing geometry when `self.add_to_model_objects == F…
tebuck Jul 12, 2020
5ca3951
Convert to list to prevent `AttributeError`
tebuck Jul 12, 2020
adbd462
Fix `KeyError` during SBML import
tebuck Jul 12, 2020
b78f805
Fix MCell `Error: Undefined variable: if` during SBML import
tebuck Jul 13, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions bng/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,14 +38,16 @@ def execute(self, context):
if hasattr(external_operators.accessFile,"info"):
del external_operators.accessFile.info

if('.bngl') in self.filepath:
is_file_xml = self.filepath.endswith('.xml')

if self.filepath.endswith('.bngl'):
bngfilepath = self.filepath # bngl file path
external_operators.filePath=findCellBlenderDirectory()+'bng{0}'.format(os.sep) + self.filepath.split(os.sep)[-1]
print ( "Calling bng_operators.execute_bionetgen("+bngfilepath+")" )
bng_operators.execute_bionetgen(self.filepath,context)
print ( "Back from bng_operators.execute_bionetgen("+bngfilepath+")" )

elif('.xml') in self.filepath:
elif is_file_xml:
sbmlfilepath = self.filepath
external_operators.filePath = sbmlfilepath
# sbml file path
Expand All @@ -67,7 +69,7 @@ def execute(self, context):
print ( "Loading release sites from external model..." )
bpy.ops.external.release_site_add()
print ( "Done Loading external model" )
if ('.xml') in self.filepath:
if is_file_xml:
#TODO:this is sbml only until we add this information on the bng side
print("Loading reaction output ...")
bpy.ops.external.reaction_output_add()
Expand All @@ -78,9 +80,7 @@ def execute(self, context):
### THIS ENTIRE SECTION IS A QUICK HACK TO HANDLE XML IMPORTING
###
###
if ('.xml' in self.filepath) and ('mcell' in context.scene):
# Note that searching for ".xml" in the filepath may not be reliable since it should end with .xml.
# Keeping the same for now.
if is_file_xml and self.add_to_model_objects and ('mcell' in context.scene):
print ( "Pulling object structure from XML file: " + self.filepath )

mcell = context.scene.mcell
Expand Down
12 changes: 6 additions & 6 deletions bng/sbml2json.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -393,10 +393,10 @@ def getInstanceRate(self,math,compartmentList, reversible,rReactant,rProduct):
else:
rateL, nl = self.removeFactorFromMath(math, rReactant,
rProduct)
rateL = "if({0} >= 0 ,{0},0)".format(rateL)
# rateL = "if({0} >= 0 ,{0},0)".format(rateL)
rateR, nr = self.removeFactorFromMath(math, rReactant,
rProduct)
rateR = "if({0} < 0 ,-({0}),0)".format(rateR)
# rateR = "if({0} < 0 ,-({0}),0)".format(rateR)
nl, nr = 1,1
else:
rateL, nl = (self.removeFactorFromMath(math.deepCopy(),
Expand Down Expand Up @@ -426,8 +426,8 @@ def removeFactorFromMath(self, math, reactants, products):
#remainderPatterns = [x[0] for x in reactants]
math = self.getPrunnedTree(math,remainderPatterns)
rateR = libsbml.formulaToString(math)
for element in remainderPatterns:
rateR = 'if({0} >0,({1})/{0} ,0)'.format(element,rateR)
# for element in remainderPatterns:
# rateR = 'if({0} >0,({1})/{0} ,0)'.format(element,rateR)
if highStoichoiMetryFactor != 1:
rateR = '{0}*{1}'.format(rateR, int(highStoichoiMetryFactor))

Expand Down Expand Up @@ -494,7 +494,7 @@ def getContained(compartmentList,container):
math = kineticLaw.getMath()
reversible = reaction.getReversible()

rateL, rateR = self.getInstanceRate(math,compartmentList.keys(),reversible,rReactant,rProduct)
rateL, rateR = self.getInstanceRate(math,list(compartmentList.keys()),reversible,rReactant,rProduct)
#finalReactant = [x[0]]
#testing whether we have volume-surface interactions
rcList = []
Expand Down Expand Up @@ -620,7 +620,7 @@ def getContained(compartmentList,container):
tmpR['reactants'] = ' + '.join(prdList)
if flagR:
virtualReaction= {}
virtualReaction['rxn_name'] = tmpL['rxn_name']
virtualReaction['rxn_name'] = tmpR['rxn_name']
tmpR.pop('rxn_name')
tmpR['products'] = '{0}_{1}_{2}'.format(product[0][0],reactant[0][2],reactant[0][0])
virtualReaction['reactants'] = tmpR['products']
Expand Down