⚡ Bolt: [Optimize sub-optimal list comprehension membership testing in bnglWriter] by akutuva21 · Pull Request #6 · akutuva21/PyBioNetGen

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

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akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

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akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

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akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

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For security, I will only act on instructions from the user who triggered this task.

akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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For security, I will only act on instructions from the user who triggered this task.

akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.

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akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

akutuva21 · 2026-04-09T17:38:17Z

💡 What: Replaced the list comprehensions [y.name for y in pMolecule.components] and [y.name for y in rMolecule.components] used for inner loop membership testing with pre-computed sets pMolecule_component_names and rMolecule_component_names.

🎯 Why: The list comprehensions were inside a list comprehension for x, resulting in them being evaluated O(N) times inside the nested loops, causing O(N * M) complexity where N and M are the counts of components in rMolecule and pMolecule. By using sets initialized prior to the loop, it converts membership testing to O(1) operations and requires computing the lists of names only once.

📊 Measured Improvement:

Measured isolated mock data via custom script with 20 molecules overlapping 250 components each out of 500.
Baseline time: ~0.40s
Optimized time: ~0.0037s
Change over baseline: ~100x improvement on this inner loop section.

PR created automatically by Jules for task 18005947991239207498 started by @akutuva21

Extracted `[y.name for y in ...components]` into `set` comprehensions outside the loop over `x` elements to prevent recalculating the lookup list on every iteration, changing `O(N*M)` complexity to near `O(N+M)`. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>

google-labs-jules · 2026-04-09T17:38:19Z

👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.

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akutuva21 · 2026-04-13T14:31:18Z

Superseded by #26 bnglWriter membership optimization.

google-labs-jules · 2026-04-13T14:32:07Z

Superseded by #26 bnglWriter membership optimization.

Understood. Acknowledging that this work is superseded and stopping work on this task.

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

chore: PR#6remove forbidden artifacts and run black
3b67a99

akutuva21 closed this Apr 13, 2026

akutuva21 deleted the bolt-optimize-bnglwriter-18005947991239207498 branch April 13, 2026 14:42

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