plinder.core.structure.inputs

Structure input files for search and evaluation workflows.

plinder.core.structure.inputs.find_structure_files(path: Path) → list[Path]

List PDB/mmCIF files in a folder, or select a single coordinate file.

class plinder.core.structure.inputs.StructureInput(coordinates: str | Path, ligand_sdfs: Sequence[str | Path] | None = None, reference_id: str | None = None)

Bases: object

A complete structure, or a receptor with separate ligand poses.

coordinates is a PDB or mmCIF file, optionally gzip-compressed. ligand_sdfs=None identifies a complete structure. A supplied sequence identifies separate ligand poses, one molecule per SDF, in the receptor’s coordinate frame. An empty sequence represents zero predicted ligand poses.

Examples

StructureInput("complex.cif") StructureInput("receptor.pdb", ligand_sdfs=["pose.sdf"])

coordinates: str | Path

ligand_sdfs: Sequence[str | Path] | None = None

reference_id: str | None = None

classmethod from_path(coordinates: str | Path) → StructureInput

Pair coordinates with model.sdf or model.ligands/*.sdf.

With no matching SDF or ligand folder, use the complete-structure form. Matching uses the coordinate basename, including for compressed files.

plinder.core.structure.inputs.read_structure_table(source: str | Path | DataFrame, *, require_reference: bool = False) → dict[str, StructureInput]

Read CSV/TSV/Parquet inputs, grouped by input_id.

Required columns are input_id and structure_path. ligand_path holds one SDF or a folder of SDFs; repeat the input row for multiple ligands. Evaluation also requires reference_id. Relative file paths are resolved from the table’s directory (the working directory for a DataFrame).

plinder.core.structure.inputs.read_ligand_sdf(path: str | Path) → Mol

Read one supplied pose, preserving its coordinates and bond information.

plinder.core.structure.inputs.read_input_structure(path: str | Path) → tuple[struc.AtomArray, pdbx.CIFBlock | None]

Read the first coordinate model and its mmCIF metadata where available.

plinder.core.structure.inputs.write_search_structure(structure: StructureInput, destination: Path, *, include_ligands: bool) → Path

Write a search mmCIF with the supplied SDF chemistry and pose coordinates.

PDB receptors contribute amino-acid residues, including modified amino acids. Other PDB components are omitted; ligand poses can be supplied as SDFs.