From c04bccf82c2bf0b40fbfc353f9843cbade00958b Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Thu, 9 Apr 2026 17:43:56 +0000
Subject: [PATCH 1/3] Optimize membership checks inside `balanceTranslator`
 with sets

Converts `x.name not in [y.name for y in ...]` list comprehensions into pre-computed sets before the main loop logic within `balanceTranslator`. This changes the complexity of the membership check from O(N) to O(1), turning the overall operation from O(N*M) to O(N+M).

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 .jules/bolt.md                          | 3 +++
 bionetgen/atomizer/writer/bnglWriter.py | 6 ++++--
 2 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100644 .jules/bolt.md

diff --git a/.jules/bolt.md b/.jules/bolt.md
new file mode 100644
index 0000000..e40c97b
--- /dev/null
+++ b/.jules/bolt.md
@@ -0,0 +1,3 @@
+## 2024-05-19 - Optimize `balanceTranslator` membership testing
+**Learning:** Checking membership inside a loop with a freshly-constructed list comprehension gives an O(N * M) performance impact. Pre-computing a set of keys can reduce it to O(N + M).
+**Action:** When finding a list membership test `x not in [y for y in Y]` inside a loop, elevate the inner list creation out of the loop and convert it to a `set` to reduce time complexity to O(1).
diff --git a/bionetgen/atomizer/writer/bnglWriter.py b/bionetgen/atomizer/writer/bnglWriter.py
index d6a446e..252606a 100644
--- a/bionetgen/atomizer/writer/bnglWriter.py
+++ b/bionetgen/atomizer/writer/bnglWriter.py
@@ -116,16 +116,18 @@ def balanceTranslator(reactant, product, translator):
     for rMolecule in rMolecules:
         for pMolecule in pMolecules:
             if rMolecule.name == pMolecule.name:
+                p_names = {y.name for y in pMolecule.components}
+                r_names = {y.name for y in rMolecule.components}
                 overFlowingComponents = [
                     x
                     for x in rMolecule.components
-                    if x.name not in [y.name for y in pMolecule.components]
+                    if x.name not in p_names
                 ]
                 overFlowingComponents.extend(
                     [
                         x
                         for x in pMolecule.components
-                        if x.name not in [y.name for y in rMolecule.components]
+                        if x.name not in r_names
                     ]
                 )
                 rMolecule.removeComponents(overFlowingComponents)

From 110d65d7816a4bdb5ff07e0e9c752676c39ace3e Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Thu, 9 Apr 2026 18:27:57 +0000
Subject: [PATCH 2/3] Optimize membership checks inside `balanceTranslator`
 with sets

Converts `x.name not in [y.name for y in ...]` list comprehensions into pre-computed sets before the main loop logic within `balanceTranslator`. This changes the complexity of the membership check from O(N) to O(1), turning the overall operation from O(N*M) to O(N+M). This commit also includes formatting fixes by black.

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 bionetgen/atomizer/writer/bnglWriter.py | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/bionetgen/atomizer/writer/bnglWriter.py b/bionetgen/atomizer/writer/bnglWriter.py
index 252606a..8bc50b0 100644
--- a/bionetgen/atomizer/writer/bnglWriter.py
+++ b/bionetgen/atomizer/writer/bnglWriter.py
@@ -119,16 +119,10 @@ def balanceTranslator(reactant, product, translator):
                 p_names = {y.name for y in pMolecule.components}
                 r_names = {y.name for y in rMolecule.components}
                 overFlowingComponents = [
-                    x
-                    for x in rMolecule.components
-                    if x.name not in p_names
+                    x for x in rMolecule.components if x.name not in p_names
                 ]
                 overFlowingComponents.extend(
-                    [
-                        x
-                        for x in pMolecule.components
-                        if x.name not in r_names
-                    ]
+                    [x for x in pMolecule.components if x.name not in r_names]
                 )
                 rMolecule.removeComponents(overFlowingComponents)
                 pMolecule.removeComponents(overFlowingComponents)

From 8664afd050579701ae5e93e30f2e5b8e207c99d8 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Thu, 9 Apr 2026 18:33:14 +0000
Subject: [PATCH 3/3] Optimize membership checks inside `balanceTranslator`
 with sets

Converts `x.name not in [y.name for y in ...]` list comprehensions into pre-computed sets before the main loop logic within `balanceTranslator`. This changes the complexity of the membership check from O(N) to O(1), turning the overall operation from O(N*M) to O(N+M). This commit also includes formatting fixes by black.

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>