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refactor, full run

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based-tachikoma 2025-05-20 20:11:52 -07:00
parent de9dfff221
commit 1ee67de035
12 changed files with 1039 additions and 1127 deletions
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environments/hack0/protein_design_env/configs/binderbench_default.yaml
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@ -1,33 +1,19 @@
# NVIDIA NIM Environment Default Configuration for BinderBench
# Debug Mode - set to true to use mock data instead of actual API calls
debug_protein_design_calls: false
# Retry settings for failed steps
max_retries_per_internal_step: 100 # Increased to allow many retries for tool calls
max_retries_per_internal_step: 100
# API Settings
# nim_api_key is loaded from .env file using NVIDIA_NIM_API_KEY
nim_api_base_url: "https://health.api.nvidia.com/v1"
api_timeout: 600
polling_interval: 10
# Protein Design Settings
output_dir: "environments/hack0/protein_design_env/outputs"
# WandB tracking settings
use_wandb: true
wandb_name: "binderbench"
wandb_project: "atropos" # Will default to this if not specified
include_messages: true # Include messages in WandB logs
wandb_project: "atropos"
include_messages: true
# Dataset configuration
dataset_name: "ronig/protein_binding_sequences"
target_col: "receptor"
binder_col: "peptide"
# Scoring weights for final complex quality
metric_weights:
plddt: 0.3
ptm: 0.3
iptm: 0.4