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fix: fixed enzyme optimization with Kcat fitness function #237

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fix: fixed enzyme optimization with Kcat fitness function #237

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yvesnana
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Resolved inconsistencies in core.py and updated the example file to ensure accurate execution of optimization with the KCAT fitness model.

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cla-bot bot commented Apr 24, 2024

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@yvesnana yvesnana assigned yvesnana and unassigned yvesnana Apr 24, 2024
drugilsberg
drugilsberg requested changes Apr 24, 2024
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Fix the build and address comments and then it's good to go.

examples/enzeptional/example_enzeptional.py Outdated
@@ -5,12 +5,16 @@
from gt4sd.configuration import GT4SDConfiguration, sync_algorithm_with_s3


def initialize_environment():
def initialize_environment(model = "feasibility"):
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typing and docstring missing, please add

src/gt4sd/frameworks/enzeptional/core.py Outdated
top_k: int = 2,
selection_ratio: float = 0.5,
perform_crossover: bool = False,
crossover_type: str = "uniform",
minimum_interval_length: int = 8,
pad_intervals: bool = False,
concat_order=["sequence", "substrate", "product"],
scaler_filepath: Optional[str] = None,
fitness_kcat: Optional[bool] = False,
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rename the parameter to something more generic

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cla-bot bot commented Apr 24, 2024

Thank you for your pull request and welcome to our community. We could not parse the GitHub identity of the following contributors: Cloud User.
This is most likely caused by a git client misconfiguration; please make sure to:

  1. check if your git client is configured with an email to sign commits git config --list | grep email
  2. If not, set it up using git config --global user.email [email protected]
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@yvesnana yvesnana closed this Apr 24, 2024
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@yvesnana @drugilsberg