Examples¶

Five canonical Packmol-equivalent workloads ship in examples/. Each exercises a different combination of restraints, fixed placements, and target counts, and all five are covered by the regression suite (tests/examples_batch.rs).

Workload	Rust example	Python example	Molecules	Restraints	Demonstrates
Mixture	`examples/pack_mixture`	`python/examples/pack_mixture.py`	1000 water + 400 urea	one `inside box` per type	the simplest two-component fill in a cube
Bilayer	`examples/pack_bilayer`	`python/examples/pack_bilayer.py`	water slabs + palmitoil lipids	per-atom `above`/`below plane`	orienting the two leaflets of a membrane
Interface	`examples/pack_interface`	`python/examples/pack_interface.py`	water + chloroform + 1 fixed t3	`inside box` per solvent + one `fixed` molecule	a liquid–liquid interface around a fixed structure
Spherical	`examples/pack_spherical`	`python/examples/pack_spherical.py`	concentric lipid + water shells	per-atom radial `inside`/`outside sphere`	nested shell packing (largest / slowest case)
Solvated protein	`examples/pack_solvprotein`	`python/examples/pack_solvprotein.py`	1 fixed protein + water + Na⁺ + Cl⁻	`inside sphere` solvent around a `fixed` solute	dense solvation that relies on `avoid_overlap`

Run the Rust examples¶

The examples need the io feature so they can read the bundled structure files:

cargo run --release --example pack_mixture     --features io
cargo run --release --example pack_bilayer     --features io
cargo run --release --example pack_interface   --features io
cargo run --release --example pack_spherical   --features io
cargo run --release --example pack_solvprotein --features io

Each directory also contains the matching .inp script (mixture.inp, bilayer-comment.inp, interface.inp, spherical-comment.inp, solvprotein.inp), so the CLI form and the programmatic form can be compared side by side:

cargo run --release --features cli --bin molpack -- examples/pack_mixture/mixture.inp

Optional progress / trajectory dumps are gated behind environment variables:

MOLRS_PACK_EXAMPLE_PROGRESS=1 cargo run --release --example pack_mixture --features io
MOLRS_PACK_EXAMPLE_XYZ=1      cargo run --release --example pack_mixture --features io

Run the Python examples¶

The Python examples mirror the Rust ones and load their structure files through the user's molcrafts-molrs install:

cd python
maturin develop --release
python examples/pack_mixture.py
python examples/pack_bilayer.py
python examples/pack_interface.py
python examples/pack_spherical.py
python examples/pack_solvprotein.py

python/examples/pack_water_cube.py is a minimal standalone starter (single-species cube) for a first look at the Python API.