Assembly Templates

Assembly templates combine fragment SMILES into full molecules using self-contained PEP 723 scripts executed by uv.

Important

uv must be installed and on PATH. Assembly scripts are self-contained PEP 723 scripts — uv automatically installs their dependencies (e.g. rdkit) on first run.

from lcmd_db import load_dataset

data = load_dataset("fragflp", include=["fragments"])
template = data.assembly_templates["default"]

# Single assembly — returns SMILES, raises on failure
smiles = template.assemble(
    LAr1="c1c(C)c(C)c(C)c(C)c1(C)",
    LAr2="c1c(C)c(C)c(C)c(C)c1(C)",
    LBr1="*cncc1",
    LBr2="*cncc1",
    BB="*c1c2c()cnc()c2c()",
)

# Batch — one subprocess, multiple results
results = template.assemble_batch([
    {"LAr1": "c1ccccc1", "LAr2": "c1ccccc1",
     "LBr1": "*cncc1",   "LBr2": "*cncc1",
     "BB": "*c1c2c()cnc()c2c()"},
])
for r in results:
    print(r.smiles if r.success else r.error)

# Save standalone script for HPC/cluster use
template.save_script("flp_assembler.py")

See also

AssemblyTemplate — full API reference, AssemblyResult — batch result type, Fragments — loading fragment data, Typed Stubs — typed kwargs for assembly functions