Metadata-Version: 2.4
Name: roshambo2
Version: 1.0.0
Summary: 3D molecular shape overlap
License: MIT License
        
        Copyright (c) 2025 molecularinformatics  
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
Project-URL: Homepage, https://github.com/molecularinformatics/roshambo2
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: C++
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: rdkit
Requires-Dist: tqdm
Requires-Dist: h5py
Requires-Dist: psutil
Requires-Dist: flask
Requires-Dist: requests
Requires-Dist: pyyaml
Dynamic: license-file

# ROSHAMBO2

<div align="left" style="padding-bottom: 1em;">
<img width="300px" align="center" src="https://raw.githubusercontent.com/molecularinformatics/roshambo2/main/doc/_img/logo.jpg">
</div>

ROSHAMBO2 is a Python program for molecular shape overlay calculation. It uses the Gaussian description of molecular shape (Grant and Pickup 1995 https://doi.org/10.1021/j100011a016)

MIT License. Copyright (c) 2025

## Install

This software is distributed in source code form. It can be build with pip inside an appropriate conda environment. Please follow the steps below.

1. clone this repo or (extract from tar archive/zip folder).

```
git clone <repo>
```

2. create a conda environment with the provided yaml file

```
cd roshambo2
conda env create -n roshambo2 -f environment.yaml
conda activate roshambo2
```

3. install this package

```
pip install .
```

## Documentation install

To build and view the documentation please go into the `doc` folder.
You will then need to install the extra dependencies to your conda environment:

```
conda install  -c sphinx pydata-sphinx-theme myst-parser
```

You can then build the html docs with:

```
make html
```

And you can view them in your browser:

```
xdg-open build/html/index.html
```

## Requirements

A CMake build system is used to compile the C++ and CUDA code. You will need to have a working C++ and nvcc compiler. Cmake will need to be able to find your CUDA installation.

## Usage

See the examples folder: "examples/README.md"

And the user guide: "USER_GUIDE.md"

## Developers

See the developer guide: "DEV_GUIDE.md"

## Testing

Test can be run using pytest in the test folder. You will need to install `pytest` and `pytorch`.

```
cd test
pytest
```

Note that the PyTorch is used in the testing framework.
(Autograd can compute the overlap gradients which are compared with
the hand-coded ones in the ROSHAMBO2 C++ and CUDA code.)
