molcrafts-molpack 0.1.0

Faithful Rust port of Packmol molecular packing (split off from molrs)
Documentation 
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# 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:

```bash
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:

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

Optional progress / trajectory dumps are gated behind environment
variables:

```bash
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:

```bash
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.