Examples¶

Five canonical Packmol workloads ported to Python. Each lives under python/examples/ in the repo and is regression-tested against the equivalent Rust example (same RNG seed → identical final coordinates).

Script	Packmol analogue	What it shows
`pack_water_cube.py`	—	hello-world: 100 waters in a box, frame via `molrs.Frame.from_dict`
`pack_mixture.py`	`mixture.inp`	two species co-packed in one box
`pack_bilayer.py`	`bilayer.inp`	atom-subset restraints for layer-molecule orientation
`pack_interface.py`	`interface.inp`	fixed reference molecule + two solvents
`pack_spherical.py`	`spherical.inp`	nested spheres, double-layer shell
`pack_solvprotein.py`	`solvprotein.inp`	fixed solute solvated by water + ions

All examples require molcrafts-molrs:

pip install molcrafts-molrs

pack_water_cube.py builds its frame in memory with molrs.Frame.from_dict (no PDB file); the others load PDB files via molrs.read_pdb.

Running¶

cd molpack/python
pip install -e .
python examples/pack_water_cube.py       # no PDB file
python examples/pack_mixture.py          # requires molrs

Set MOLPACK_EXAMPLE_PROGRESS=0 to suppress the per-iteration progress log.

Example: mixture¶

The pack_mixture.py example reproduces Packmol's classic mixture.inp:

import molrs
from molpack import InsideBoxRestraint, Molpack, Target

water_frame = molrs.read_pdb("water.pdb")
urea_frame  = molrs.read_pdb("urea.pdb")

box = InsideBoxRestraint([0, 0, 0], [40, 40, 40])

water = Target(water_frame, count=1000).with_name("water").with_restraint(box)
urea  = Target(urea_frame,  count=400).with_name("urea").with_restraint(box)

packer = Molpack().with_tolerance(2.0).with_seed(1_234_567)
result = packer.pack_with_report([water, urea], max_loops=400)
print(f"converged={result.converged}  natoms={result.natoms}")

Example: water cube¶

import molrs
import numpy as np
from molpack import InsideBoxRestraint, Molpack, Target

frame = molrs.Frame.from_dict({
    "blocks": {
        "atoms": {
            "x": np.array([0.00,  0.9572, -0.2400]),
            "y": np.array([0.00,  0.0000,  0.9266]),
            "z": np.zeros(3),
            "element": ["O", "H", "H"],
        }
    }
})

water = Target(frame, count=100).with_name("water").with_restraint(
    InsideBoxRestraint([0, 0, 0], [30, 30, 30])
)
packer = Molpack().with_tolerance(2.0).with_log_level("quiet").with_seed(42)
result = packer.pack_with_report([water], max_loops=200)
print(f"converged={result.converged}  natoms={result.natoms}")