Parameter Database#

Use tmol.database.ParameterDatabase to load the chemical and scoring parameters used to construct poses and score functions.

Chemical and scoring parameter databases used by TMol.

class tmol.database.AtomType(name: str, element: str, is_acceptor: bool = False, is_donor: bool = False, is_hydroxyl: bool = False, is_polarh: bool = False, acceptor_hybridization: AcceptorHybridization | None = None)[source]#

Bases: object

Chemical atom-type properties used by scoring terms.

class tmol.database.ChemicalDatabase(element_types: Tuple[Element, ...], atom_types: Tuple[AtomType, ...], residues: Tuple[RawResidueType, ...], variants: Tuple[VariantType, ...])[source]#

Bases: object

Immutable collection of chemical types, residues, and patches.

classmethod from_file(path: str | PathLike[str]) → ChemicalDatabase[source]#

Load a chemical database from a directory containing YAML data.

classmethod get_default() → ChemicalDatabase[source]#

Load and return default parameter database.

class tmol.database.ParameterDatabase(scoring: ScoringDatabase, chemical: PatchedChemicalDatabase)[source]#

Bases: object

Immutable chemical and scoring parameter container used by tmol.

The process-global accessor get_default() returns a shared read-only instance. To add ligand or custom residue data, use inject_residue_params() which returns a new database.

classmethod get_default() → ParameterDatabase[source]#

Return the process-global cached parameter database (read-only).

classmethod from_file(path: str) → ParameterDatabase[source]#

Load chemical and scoring parameters rooted at path.

create_stable_subset(desired_names: list[str], desired_variants: list[str]) → ParameterDatabase[source]#

Create a ParameterDatabase representing a subset of the RefinedResidueTypes in this PD’s PatchedChemicalDatabase from a list of RRT names and patched with the given variants (identified by their display names) where the order in which RRTs will appear in the subset will be stable over time (as long as this source PCD is only accumulating new RRTs over time and not losing the RRTs that it starts with).

class tmol.database.PatchedChemicalDatabase(element_types: Tuple[Element, ...], atom_types: Tuple[AtomType, ...], residues: Tuple[RawResidueType, ...], variants: Tuple[VariantType, ...])[source]#

Bases: object

Chemical database containing residue types after variant application.

class tmol.database.RawResidueType(name: str, base_name: str, name3: str, io_equiv_class: str, atoms: Tuple[Atom, ...], atom_aliases: Tuple[AtomAlias, ...], bonds: Tuple[tuple, ...], connections: Tuple[Connection, ...], torsions: Tuple[Torsion, ...], icoors: Tuple[Icoor, ...], properties: ChemicalProperties, chi_samples: Tuple[ChiSamples, ...], default_jump_connection_atom: str, hydrogens_regenerated: bool = False, is_ligand_fragment: bool = False, one_letter_code: str | None = None)[source]#

Bases: object

Unpatched residue definition loaded from the chemical database.

atom_name(index: int) → str[source]#

Return the name of the atom at index.

class tmol.database.ScoringDatabase(cartbonded: CartBondedDatabase, genbonded: GenBondedDatabase, disulfide: DisulfideDatabase, na_torsion: NaTorsionDatabase, dun: DunbrackRotamerLibrary, elec: ElecDatabase, hbond: HBondDatabase, ljlk: LJLKDatabase, omega_bbdep: OmegaBBDepDatabase, rama: RamaDatabase, ref: RefDatabase)[source]#

Bases: object

Immutable parameters for all standard TMol energy terms.

classmethod from_file(path: str | PathLike[str] = '/home/runner/work/tmol/tmol/tmol/database/scoring') → ScoringDatabase[source]#

Load all scoring-term databases rooted at path.

tmol.database.inject_residue_params(param_db: ParameterDatabase, residue_types: list[RawResidueType], atom_types: list[AtomType] | None = None, partial_charges: Mapping[str, dict[str, float]] | None = None, cartbonded_params: Mapping[str, CartRes] | None = None) → ParameterDatabase[source]#

Return a new ParameterDatabase with additional residue type data.

This is the primary API for extending a database with ligand or custom residue types. The input param_db is not modified.

Parameters:

  • param_db – Base database to extend.

  • residue_types – New RawResidueType entries to add.

  • atom_types – Optional new AtomType entries (deduplicated by name).

  • partial_charges – Per-residue charge dicts {res_name: {atom: charge}}.

  • cartbonded_params – Per-residue CartRes {res_name: CartRes}.

Returns:

A new frozen ParameterDatabase with the additional data.