# Documentation example data

`water_mp2.out` is copied from cclib's ORCA regression data and is distributed
under the BSD 3-Clause License in `LICENSE.cclib`. MolOP keeps the file as a
small, reproducible input for the quick start and documentation smoke tests.

Upstream fixture in this repository:

```text
tests/test_files/orca/output_files/cclib/basicORCA6.0/water_mp2.out
```

The documentation examples parse this file; they do not execute ORCA or any
other quantum-chemistry program.

`mn_complex_sp.log` is copied from MolOP's existing Gaussian 16 parser regression
fixture:

```text
tests/test_files/g16log/MnCO3C6H6PMe3-mod2-sp-smd-DSDPBEP86d3.log
```

It is a 32-atom, charge-1 manganese-complex single-point calculation used to
demonstrate coordinate-derived graph reconstruction. The documentation parses
the checked-in output; it does not execute Gaussian.

The SVG files in this directory are generated by:

```text
uv run python scripts/generate_doc_images.py
```

`mn_complex_graph_reconstruction.svg` compares the raw coordinate-only graph,
RDKit distance connectivity, and MolGR reconstruction for `mn_complex_sp.log`.
`ts_imaginary_mode.svg` and `ts_endpoints_difference.svg` are generated from the
real MolOP results for:

```text
tests/test_files/g16log/000000000000_000016928457_00_conf_01_ts.107c60f3cfcb.log
```

The script uses `ts_vibration(...)`, `possible_pre_post_ts(...)`, and
`to_diff_rdmol()` directly, then renders with MolOP's default `rdkit-dof`
drawer. It does not edit SVG paths or notebook outputs by hand.

`ts_endpoints_additional_sampling.svg` compares the standard and additional-sampling
endpoint representations generated from:

```text
tests/test_files/g16log/R6-BOX_2-COO_Me_w-Cl_C_new_type-a_conf-1_TS_Opt.log
```

`ts_endpoint_additional_sampling.log` is the same checked-in Gaussian 16 fixture,
copied here so the endpoint-comparison Notebook can read a self-contained
documentation input through `AutoParser`.

The image is generated by calling `possible_pre_post_ts(show_3D=True)` followed
by `additional_pre_post_ts(...)`; it is a static visual companion for the transition-
state tutorial and the endpoint-comparison Notebook.