plinder.core.structure.ccd_template

CCD component templates: missing-atom detection and opt-in completion.

class plinder.core.structure.ccd_template.ComponentTemplate(heavy, elements, leaving, bonds)

Bases: NamedTuple

heavy: tuple[str, ...]

Alias for field number 0

elements: dict[str, str]

Alias for field number 1

leaving: frozenset[str]

Alias for field number 2

bonds: tuple[tuple[str, str, int], ...]

Alias for field number 3

plinder.core.structure.ccd_template.ccd_component_template(comp_id: str) → ComponentTemplate | None

Heavy atoms, elements, leaving atoms and bonds of a CCD component.

plinder.core.structure.ccd_template.ccd_heavy_atom_names(comp_id: str) → tuple[frozenset[str], frozenset[str]] | None

Heavy atom names and leaving-group atom names of a CCD component.

plinder.core.structure.ccd_template.departed_leaving_atoms(template: ComponentTemplate, linked_atom_names: Collection[str]) → frozenset[str]

Leaving atoms whose anchor atom is bonded outside the residue, i.e. gone on linkage.

plinder.core.structure.ccd_template.linked_atoms_by_residue(atoms: AtomArray, starts: ndarray) → dict[int, set[str]]

Residue start index -> names of its atoms bonded to another residue.

starts are residue starts with the exclusive stop appended.

plinder.core.structure.ccd_template.unresolved_atoms_from_template(comp_id: str, resolved_atom_names: Iterable[str], linked_atom_names: Collection[str] | None = None) → list[str] | None

CCD heavy atoms absent from resolved_atom_names.

Leaving atoms whose anchor is in linked_atom_names (atoms bonded outside the residue) departed on linkage and are not missing; with linked_atom_names=None every leaving atom is excluded. None when comp_id is not in the CCD.

plinder.core.structure.ccd_template.add_missing_atoms(atoms: AtomArray, *, mask_annotation: str = 'is_unresolved') → AtomArray

Append CCD heavy atoms missing from each residue, with NaN coordinates.

A residue is completed only when its CCD template is known and every resolved heavy atom name is a template name; hydrogens are never added, leaving atoms only for a non-polymer residue not bonded through their anchor (never when atoms has no bonds), and fully unresolved residues are not created. Added atoms copy their residue’s annotations, take element from the CCD, get occupancy/b_factor/charge 0 where present, and mask_annotation True (deposited atoms get False). Existing bonds are kept and the template bonds of added atoms appended. The input is not modified.