ConfSeq

ConfSeq decoding uses an input SMILES string and a ConfSeq string to recover a 3D molecule. COSMolKit exposes two template backends:

distance_geometry

Reference backend. It uses the RDKit-derived distance-geometry path and is the default.

fast_geometry

Lightweight backend. It only replaces the initial coordinate source; after that, it runs the same ConfSeq token decode as distance_geometry. It is opt-in and may raise ValueError for unsupported FastGeometry cases.

Decode one tokenized corpus record with the reference backend. The spaces are part of the ConfSeq token stream, not cosmetic formatting: tokens such as <112> | and bracketed atoms must remain separated. The ConfSeq string contains both the molecular topology and recovered numeric angle/dihedral tokens, so normal callers pass only this one string.

import cosmolkit

confseq = (
    "N C <112> | ( = O ) <84> C <111> | <-45> n 1 c c ( <21> N <123> | "
    "<173> C <116> | ( = O ) <120> c 2 c c c c c 2 <112> C <112> | <-66> "
    "N 2 <-172> C ( = O ) <-2> C <0> N <3> C <174> 2 = O ) c n 1"
)

mol = cosmolkit.confseq.decode(
    confseq,
    optimize_with_uff=False,
    template_backend="distance_geometry",
)

print(mol.num_atoms())
print(mol.coordinates_3d().shape)

Decode the same record with FastGeometry:

fast = cosmolkit.confseq.decode(
    confseq,
    optimize_with_uff=False,
    template_backend="fast_geometry",
)

print(fast.num_conformers())

Batch decoding accepts the same backend option:

confseq_1 = (
    "N C <113> | ( = O ) <-54> C <113> | <44> n 1 c c ( <-132> N <128> | "
    "<-9> C <115> | ( = O ) <-118> c 2 c c c c c 2 <-95> C <116> | <117> "
    "N 2 <176> C ( = O ) <6> C <-8> N <11> C <-176> 2 = O ) c n 1"
)

mols = cosmolkit.confseq.decode_batch(
    [confseq, confseq_1],
    errors="keep",
    n_jobs=8,
    optimize_with_uff=False,
    template_backend="distance_geometry",
)

print([mol is not None for mol in mols])

Use template_backend="distance_geometry" when measuring ConfSeq reference behavior or comparing FastGeometry output. Use template_backend="fast_geometry" only when testing the fast initialization path explicitly.