gRNAde MCP Server

""" Shared constants for MCP scripts. These constants are extracted and simplified from repo/geometric-rna-design/src/constants.py to minimize dependencies while maintaining functionality. """ # ============================================================================== # RNA Nucleotide Mappings # ============================================================================== RNA_NUCLEOTIDES = ["A", "G", "C", "U"] LETTER_TO_NUM = {"A": 0, "G": 1, "C": 2, "U": 3} NUM_TO_LETTER = {0: "A", 1: "G", 2: "C", 3: "U"} # ============================================================================== # Secondary Structure Mappings # ============================================================================== DOTBRACKET_TO_NUM = {".": 0, "(": 1, ")": 2} # Bracket pairs for pseudoknot analysis BRACKET_PAIRS = { "(": ")", "[": "]", "{": "}", "<": ">" } # ============================================================================== # Default Values and Thresholds # ============================================================================== FILL_VALUE = 1e-5 DISTANCE_EPS = 1e-5 # Quality thresholds RMSD_THRESHOLD = 2.0 TM_THRESHOLD = 0.45 GDT_THRESHOLD = 0.50 # GC content ranges GC_CONTENT_MIN = 0.2 GC_CONTENT_MAX = 0.8 # Sequence length limits MIN_SEQUENCE_LENGTH = 6 MAX_SEQUENCE_LENGTH = 1000 # ============================================================================== # Model Configuration Defaults # ============================================================================== DEFAULT_MODEL_CONFIG = { "device": "cpu", "checkpoint": "gRNAde_drop3d@0.75_maxlen@500.h5", "ribonanza_model": "ribonanzanet.pt", "ribonanza_ss_model": "ribonanzanet_ss.pt" } # ============================================================================== # File Paths and Extensions # ============================================================================== SUPPORTED_FORMATS = { "sequence": [".fasta", ".fa", ".seq"], "structure": [".pdb"], "data": [".csv", ".tsv", ".json"], "config": [".json", ".yaml", ".yml"] } # ============================================================================== # RNA Chemical Properties # ============================================================================== PURINES = ["A", "G"] PYRIMIDINES = ["C", "U"] # Molecular weights (approximate, in Da) NUCLEOTIDE_WEIGHTS = { "A": 331.2, "G": 347.2, "C": 307.2, "U": 308.2 } # Base pairing rules WATSON_CRICK_PAIRS = { ("A", "U"), ("U", "A"), ("G", "C"), ("C", "G") } WOBBLE_PAIRS = { ("G", "U"), ("U", "G") } ALL_PAIRS = WATSON_CRICK_PAIRS | WOBBLE_PAIRS