semvec/pypi-packages huggingface dataset:
eon-collective-docs-theme 0.0.2.dev0
The theme used to render documentation
Requires Python: >=3.8

# [Eon Collective Documentation theme](https://github.com/janerose-njogu/eon-collective-docs-theme)

The Eon Collective Documentation theme contains all files required to build a Sphinx extension that provides the theme.

> 📘 FYI
> 
> Supports Python >= 3.8


## Assumptions
This guide assumes that you have set up Sphinx in your project. All you need to do is install this theme and include it within your conf.py file.

It is also assumed that you understand Sphinx.

## Installation

```sh
pip install eon-collective-docs-theme
```

## Usage

In your conf.py file of a Sphinx documentation, specify the "Eon Collective Documentation theme" as an extension.

```python
# include the theme in the list of extensions to be loaded
extensions = ['eon_collective_docs_theme', …]

# select the theme
html_theme = 'eon_collective_docs_theme'
```

## Credits

The Eon Collective Documentation theme is based on the [Sphinx Wagtail theme](https://github.com/wagtail/sphinx_wagtail_theme). 

Read more about Sphinx Wagtail theme in their [documentation](https://sphinx-wagtail-theme.readthedocs.io/en/latest/).
tmmpred 0.2.0
Package for predicting Tmm sequences (FMO subfamily with trimethylamine monooxidase activity).
Requires Python: >=3.7

# Tmmpred 

Tmmpred can be used to identify sequences belonging to a subgroup of flavine-containing monooxygenases defined by bacterial trimethylamine monooxygenases (Tmms; [Goris et al. 2020](https://doi.org/10.1128/AEM.02105-20)). The tool is built on a set of manually curated profile HMMs and is implemented in Python using the [PyHMMER module](https://pyhmmer.readthedocs.io/).


## Installation

The Tmmpred can be installed from [PyPI](https://pypi.org/project/tmmpred/):
```
$ pip install tmmpred
```

## Run Tmmpred

Tmmpred installs as a script that can be run from the command line:
```
$ tmmpred -h
usage: tmmpred [-h] [-q] [-d] [-c CUTOFF] [-n] [--html] [-v] sequence_file

Predict Tmm sequences (FMO subfamily with trimethylamine monooxidase activity).

positional arguments:
  sequence_file         FASTA-formated protein sequences.

options:
  -h, --help            show this help message and exit
  -q, --quick           Search with Tmm HMM profile only and use trusted score cutoff: 272.0.
  -d, --deep            Search with Tmm HMM profile using noise score cutoff 40.0 and filter using all FMO-like HMM profiles.
  -c CUTOFF, --cutoff CUTOFF
                        Score cutoff [float, default=40.0 (noise score cutoff)].
  -n, --nofilter        Do not filter using other FMO-like HMM profiles.
  --html                Format results as HTML.
  -v, --verbose         Show details about running tmmpred.
```