Access system files with PlinderSystem

PlinderSystem provides the files and coordinate views for one ligand system. See Structures and reconstruction for their provenance and storage.

from plinder.core import PlinderSystem

plinder_system = PlinderSystem(system_id="4agi__1__1.C__1.W")

/home/runner/micromamba/envs/plinder/lib/python3.12/site-packages/vcs_versioning/_backends/_git.py:709: UserWarning: "/home/runner/work/plinder/plinder" is shallow and may cause errors
  pre_parse(wd)

Ligand

canonical_ligand_sdfs contains the asymmetric-unit SDF for each ligand. ligand_sdfs writes copies in the reconstructed biological-assembly coordinates.

plinder_system.canonical_ligand_sdfs, plinder_system.ligand_sdfs

({'1.W': '/home/runner/.local/share/plinder/2026-09/ligand_archives/4agi/ligand_files/W.sdf'},
 {'1.W': '/home/runner/.local/share/plinder/2026-09/reconstructed_systems/4agi__1__1.C__1.W/ligand_files/1.W.sdf'})

Use smiles for the corresponding SMILES strings.

plinder_system.smiles

{'1.W': 'C[Se][C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O'}

Receptor

receptor_cif returns the path to an mmCIF containing the system’s receptor chains.

plinder_system.receptor_cif

'/home/runner/.local/share/plinder/2026-09/reconstructed_systems/4agi__1__1.C__1.W/receptor.cif'

system_cif includes the selected receptor and ligand chains. Both structure views are written as self-contained PDBx/mmCIF files.

plinder_system.system_cif

'/home/runner/.local/share/plinder/2026-09/reconstructed_systems/4agi__1__1.C__1.W/system.cif'

sequences_fasta returns the receptor FASTA path, while sequences returns the protein sequences by chain.

plinder_system.sequences_fasta, plinder_system.sequences

('/home/runner/.local/share/plinder/2026-09/reconstructed_systems/4agi__1__1.C__1.W/sequences.fasta',
 {'1.C': 'MSTPGAQQVLFRTGIAAVNSTNHLRVYFQDVYGSIRESLYEGSWANGTEKNVIGNAKLGSPVAATSKELKHIRVYTLTEGNTLQEFAYDSGTGWYNGGLGGAKFQVAPYSXIAAVFLAGTDALQLRIYAQKPDNTIQEYMWNGDGWKEGTNLGGALPGTGIGATSFRYTDYNGPSIRIWFQTDDLKLVQRAYDPHKGWYPDLVTIFDRAPPRTAIAATSFGAGNSSIYMRIYFVNSDNTIWQVCWDHGKGYHDKGTITPVIQGSEVAIISWGSFANNGPDLRLYFQNGTYISAVSEWVWNRAHGSQLGRSALPPA'})

Linked apo chains

linked_apo_structures returns the ranked apo links for a holo ligand system.

linked_system = PlinderSystem(system_id="10be__1__1.C__1.A_1.B")
link_info = linked_system.linked_apo_structures

link_info[
    [
        "linked_structure_id",
        "source_entry_id",
        "source_chain_instance",
        "rank",
        "source_resolution",
        "min_pocket_fident",
        "min_protein_fident_qcov_weighted_sum",
    ]
]

	linked_structure_id	source_entry_id	source_chain_instance	rank	source_resolution	min_pocket_fident	min_protein_fident_qcov_weighted_sum
0	6n4o_A	6n4o	1.A	1	2.899	100	99
1	9rwz_A	9rwz	1.A	2	3.100	100	98
2	6nit_A	6nit	1.A	3	3.800	100	98
3	6nit_B	6nit	1.B	4	3.800	100	98
4	9cmp_C	9cmp	1.C	5	3.300	100	98

reconstruct_linked_apo() selects rank 1 by default or accepts a linked_structure_id.

if link_info.empty:
    print("No linked apo chain is available for this system.")
else:
    apo_cif = linked_system.reconstruct_linked_apo(overwrite=True)
    selected_cif = linked_system.reconstruct_linked_apo(
        linked_structure_id=link_info.iloc[0]["linked_structure_id"],
        overwrite=True,
    )
    print(apo_cif, selected_cif)

/home/runner/.local/share/plinder/2026-09/reconstructed_systems/10be__1__1.C__1.A_1.B/linked_apo/6n4o_A.cif /home/runner/.local/share/plinder/2026-09/reconstructed_systems/10be__1__1.C__1.A_1.B/linked_apo/6n4o_A.cif