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chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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akutuva21 merged 2 commits into from
Jun 16, 2026
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chore: remove obsolete FIXME comment regarding double bonds in complexes #529

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chore: remove obsolete FIXME comment regarding double bonds in complexes
google-labs-jules[bot] Jun 15, 2026
18593a8
Merge main into branch, resolve conflicts
akutuva21 Jun 16, 2026
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61 changes: 42 additions & 19 deletions bionetgen/atomizer/atomizer/moleculeCreation.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
# dbPair.add((element[0], element[1]))
dbPair = list(dbPair)

# Adding validation or error checking for malformed input files
dbPair = [
element
for element in dbPair
if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
]

if dbPair != []:
mol1 = mol2 = None
# select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
dbPair = finalDBpair

if len(dbPair) > 1:
# @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
# when you receive a malformed user definition file. The error
# should be caught way before we reach this point
tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
for element in dbPair
if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
if getNamedMolecule(totalComplex[0], element[0]) is not None
]
if not tmpComplexSubset1:
tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
for element in dbPair
if (mol := getNamedMolecule(totalComplex[0], element[1]))
is not None
if getNamedMolecule(totalComplex[0], element[1]) is not None
]
tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
for element in dbPair
if (mol := getNamedMolecule(totalComplex[1], element[0]))
is not None
if getNamedMolecule(totalComplex[1], element[0]) is not None
]
else:
tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
for element in dbPair
if (mol := getNamedMolecule(totalComplex[1], element[1]))
is not None
if getNamedMolecule(totalComplex[1], element[1]) is not None
]

mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
):
speciesDict[x.name.lower()].remove(mol)
speciesDict[component.name].remove(x)
if (
x not in orphanedMolecules
and mol not in orphanedMolecules
):

lhs = set([])
rhs = set([])
repeatedFlag = False
for pair in pairedMolecules:
if x in pair:
lhs.add(pair[0])
lhs.add(pair[1])
elif mol in pair:
rhs.add(pair[0])
rhs.add(pair[1])
# is this particular pair of molecules bound together?
if x in pair and mol in pair:
repeatedFlag = True
break
# this pair already exists
if repeatedFlag:
continue
redundantBonds.append([x, mol])
intersection = lhs.intersection(rhs)
redundantBonds[-1].extend(list(intersection))
if len(redundantBonds[-1]) < 3:
redundantBonds.pop()
# continue
if (
[x, mol] not in bondSeeding
and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
database.artificialEquivalenceTranslator[element]
)

doubleModifications = namingConventions.get("doubleModifications", {})
# special handling for double modifications like double phosporylation
# FIXME: this needs to be done in a cleaner way(e.g. getting them
# from a file instead of being hardcoded)
doubleModifications = {"Double-Phosporylation": "Phosporylation"}

for element in doubleModifications:
if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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merged 2 commits into

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Jun 16, 2026
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chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
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19f1adb

chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
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style.textContent = '
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var __re = new RegExp('^' + ".*" + '
chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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 Merged

akutuva21
merged 2 commits into

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Jun 16, 2026
 Merged


chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
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19f1adb

chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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 Merged

akutuva21
merged 2 commits into

from

Jun 16, 2026
 Merged


chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
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19f1adb

chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
Skip to content
chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
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chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
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chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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 Merged

akutuva21
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Jun 16, 2026
 Merged


chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
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19f1adb

chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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// Remove or un-stick sticky/fixed headers that block content
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document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
Skip to content
chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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 Merged

akutuva21
merged 2 commits into

from

Jun 16, 2026
 Merged


chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
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2 commits


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19f1adb

chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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style = document.createElement('style');
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chore: remove obsolete FIXME comment regarding double bonds in complexes by akutuva21 · Pull Request #529 · akutuva21/PyBioNetGen · GitHub
Skip to content
chore: remove obsolete FIXME comment regarding double bonds in complexes#529

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 Merged

akutuva21
merged 2 commits into

from

Jun 16, 2026
 Merged


chore: remove obsolete FIXME comment regarding double bonds in complexes
#529
 Changes from all commits
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2 commits


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19f1adb

chore: remove obsolete FIXME comment regarding double bonds in complexes


google-labs-jules[bot] Jun 15, 2026
18593a8

Merge main into branch, resolve conflicts


akutuva21 Jun 16, 2026

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61 changes: 42 additions & 19 deletions
bionetgen/atomizer/atomizer/moleculeCreation.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -223,13 +223,6 @@ def getNamedMolecule(array, name):
 # dbPair.add((element[0], element[1]))
 dbPair = list(dbPair)

 # Adding validation or error checking for malformed input files
 dbPair = [
 element
 for element in dbPair
 if element[0] not in (None, "None", "") and element[1] not in (None, "None", "")
 ]

 if dbPair != []:
 mol1 = mol2 = None
 # select the best candidate if there's many ways to bind (in general
Expand All@@ -250,30 +243,30 @@ def getNamedMolecule(array, name):
 dbPair = finalDBpair

 if len(dbPair) > 1:
 # @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
 # when you receive a malformed user definition file. The error
 # should be caught way before we reach this point
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[0])) is not None
 if getNamedMolecule(totalComplex[0], element[0]) is not None
 ]
 if not tmpComplexSubset1:
 tmpComplexSubset1 = [
mol
getNamedMolecule(totalComplex[0], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[0], element[1]))
 is not None
 if getNamedMolecule(totalComplex[0], element[1]) is not None
 ]
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[0])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[0]))
 is not None
 if getNamedMolecule(totalComplex[1], element[0]) is not None
 ]
 else:
 tmpComplexSubset2 = [
mol
getNamedMolecule(totalComplex[1], element[1])
 for element in dbPair
 if (mol := getNamedMolecule(totalComplex[1], element[1]))
 is not None
 if getNamedMolecule(totalComplex[1], element[1]) is not None
 ]

 mol1 = getBiggestMolecule(tmpComplexSubset1)
Expand DownExpand Up@@ -406,7 +399,34 @@ def getNamedMolecule(array, name):
 ):
 speciesDict[x.name.lower()].remove(mol)
 speciesDict[component.name].remove(x)
 if (
 x not in orphanedMolecules
 and mol not in orphanedMolecules
 ):

 lhs = set([])
 rhs = set([])
 repeatedFlag = False
 for pair in pairedMolecules:
 if x in pair:
 lhs.add(pair[0])
 lhs.add(pair[1])
 elif mol in pair:
 rhs.add(pair[0])
 rhs.add(pair[1])
 # is this particular pair of molecules bound together?
 if x in pair and mol in pair:
 repeatedFlag = True
 break
 # this pair already exists
 if repeatedFlag:
 continue
 redundantBonds.append([x, mol])
 intersection = lhs.intersection(rhs)
 redundantBonds[-1].extend(list(intersection))
 if len(redundantBonds[-1]) < 3:
 redundantBonds.pop()
 # continue
 if (
 [x, mol] not in bondSeeding
 and [mol, x] not in bondSeeding
Expand DownExpand Up@@ -1205,7 +1225,10 @@ def transformMolecules(
 database.artificialEquivalenceTranslator[element]
 )

 doubleModifications = namingConventions.get("doubleModifications", {})
 # special handling for double modifications like double phosporylation
 # FIXME: this needs to be done in a cleaner way(e.g. getting them
 # from a file instead of being hardcoded)
 doubleModifications = {"Double-Phosporylation": "Phosporylation"}

 for element in doubleModifications:
 if doubleModifications[element] not in database.eequivalenceTranslator:
Expand Down
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