semvec/pypi-packages huggingface dataset:
peppr 0.12.0
It's a package for evaluation of predicted poses, right?
Requires Python: >=3.11

pepp'r
======

    I have a structure prediction model and now I want to know how well it performs in
    reproducing the reference structures.
    But there are so many possible metrics, some for monomers, some for complexes!
    Is there a package that handles this for me?

|

Try

.. image:: https://raw.githubusercontent.com/aivant/peppr/refs/heads/main/docs/static/assets/general/logo.svg
   :alt: pepp'r

|

    It's a Package for Evaluation of Predicted Poses, Right?

|

Yes, indeed!
It allows you to compute a variety of metrics on your structure predictions
for assessing their quality.
It supports

- all *CASP*/*CAPRI* metrics and more
- small molecules to huge protein or nucleic acid complexes
- easy extension with custom metrics
- a command line interface and a Python API

Installation
------------

``peppr`` is available via *PyPI*:

.. code-block:: console

    $ pip install peppr

Usage example
-------------

Using the CLI, you can either compute a single metric for a system...

.. code-block:: console

    $ peppr run dockq reference.cif poses.cif

... or run an entire prediction model evaluation on many systems.

.. code-block:: console

    # Select the metrics you want to compute (here: RMSD and lDDT)
    $ peppr create peppr.pkl monomer-rmsd monomer-lddt

    # Run the evaluation on predicted poses and their corresponding references
    $ peppr evaluate-batch peppr.pkl "systems/*/reference.cif" "systems/*/poses"

    # Select the aggregation method over poses (here: Top-3 and Oracle) and report the results
    $ peppr tabulate peppr.pkl table.csv top3 oracle

Available metrics
-----------------

- RMSD
- TM-score
- lDDT
- lDDT-PLI
- fnat
- iRMSD
- LRMSD
- DockQ

... and more!
sphinx_pytest 0.3.0
Helpful pytest fixtures for sphinx extensions.
Requires Python: >=3.10
Keywords: sphinx, pytest

# sphinx-pytest

[![PyPI][pypi-badge]][pypi-link]

Helpful pytest fixtures for sphinx extensions.

Sphinx is annoying, because the modularity is not great,
meaning that there is no real way just to convert single documents in isolation, etc.

This extension mainly provides some pytest fixtures to "simulate" converting some source text to docutils AST at different stages; before transforms, after transforms, etc.


## Installation

```
pip install sphinx-pytest
```

## Examples

```python
from sphinx_pytest.plugin import CreateDoctree

def test_no_transforms(sphinx_doctree_no_tr: CreateDoctree):
    """Return the doctree, before any transforms have been applied."""
    sphinx_doctree_no_tr.set_conf({"language": "en"})
    result = sphinx_doctree_no_transforms(".. _target:\n\nheader\n------\n")
    assert (
        result.pformat()
        == """\
<document source="<src>/index.rst">
    <target ids="target" names="target">
    <section ids="header" names="header">
        <title>
            header
""".rstrip()
    )
```

```python
def test_with_transforms(sphinx_doctree: CreateDoctree):
    """Return the doctree, after transforms (but not post-transforms)."""
    result = sphinx_doctree(".. _target:\n\nheader\n------\n")
    assert (
        result.pformat()
        == """\
<document source="<src>/index.rst">
    <target refid="target">
    <section ids="header target" names="header target">
        <title>
            header
""".rstrip()
    )
```


[pypi-badge]: https://img.shields.io/pypi/v/sphinx_pytest.svg
[pypi-link]: https://pypi.org/project/sphinx_pytest