struct

Chem::LigandCriteria

Criteria for classifying a molecule (covalent fragment) as a ligand.

Defaults match Schrödinger Maestro LigandParameters / AslLigandSearcher (min/max heavy atoms, ion/AA/NA flags, and the hard excluded-residue list).

TODO: consider a BioLiP/PLIP-style soft filter later (large artifact list; drop only at high copy-count / weak sites) so HEM and true additive-as-substrate cases are not hard-excluded.

Constants

EXCLUDED_DEFAULT = Set {"1PE", "2HT", "2PE", "7PE", "ACT", "ACY", "AKG", "BCT", "BMA", "BME", "BOG", "BU3", "BUD", "CAC", "CIT", "CME", "CO3", "DMS", "DTT", "DTV", "EDO", "EGL", "EPE", "FMT", "FS3", "FS4", "GBL", "GOL", "GSH", "HEC", "HED", "HEM", "IMD", "IOD", "IPA", "MAN", "MES", "MG8", "MLI", "MO6", "MPD", "MYR", "NAG", "NCO", "NH3", "NO3", "OCT", "OGA", "OPG", "P2U", "PG4", "PGE", "PGO", "PHO", "PLP", "PO4", "POP", "PSE", "PSU", "PTL", "SEO", "SGM", "SO4", "SPD", "SPM", "SRT", "SUC", "SUL", "TAM", "TAR", "TFA", "TLA", "TPP", "TRS"}

Maestro-padded CCD names, stripped. Do not mutate.

Constructors

default

Source

new(min_heavy_atoms : Int32 = 5, max_heavy_atoms : Int32 = 100, allow_ion_only : Bool = false, allow_amino_acid_only : Bool = true, allow_nucleic_acid_only : Bool = false, excluded_residue_names : Set(String) = EXCLUDED_DEFAULT, included_residue_names : Set(String) = Set(String).new)

Source