Exhaustive crosslinked gel¶

Script: examples/topology/07_gel_exhaustive.py

Statistical network: grow strands, mark backbone carbons, replicate, then pair every allowed inter-chain site within a cutoff.

build_linear → mark_backbone_crosslink_sites → Replicas.grid
  → GraphAssembler(XLINK).assemble(..., ExhaustiveSelector)

from molpy.builder.assembly import ExhaustiveSelector, GraphAssembler, Replicas
from eo_kit import XLINK, eo_builder, mark_backbone_crosslink_sites
import molpy as mp

strand = eo_builder().build_linear("EO", 8)
mark_backbone_crosslink_sites(strand, step=2)
melt = Replicas(strand).grid(2, spacing=6.0, jitter=0.4, seed=3)

gel = GraphAssembler(mp.Reaction(XLINK)).assemble(
    melt,
    ExhaustiveSelector(cutoff=6.0, exclude_same_molecule=True),
)

exclude_same_molecule=True uses bond connectivity (not only mol_id) so intra-chain pairs are skipped while chains remain separate components.

cd examples && python topology/07_gel_exhaustive.py

Exhaustive crosslinked gel¶

See also¶