https://github.com/simonboothroyd/graffan

Gradient based analysis of force field optimizations.
https://github.com/simonboothroyd/graffan

Last synced: 20 days ago
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Gradient based analysis of force field optimizations.

• Host: GitHub
• URL: https://github.com/simonboothroyd/graffan
• Owner: SimonBoothroyd
• License: mit
• Created: 2021-02-09T14:32:47.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-01-13T22:01:24.000Z (almost 2 years ago)
• Last Synced: 2023-03-05T22:12:35.443Z (over 1 year ago)
• Language: Python
• Size: 47.9 KB
• Stars: 3
• Watchers: 2
• Forks: 2
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

        
# Gradient Based Force Field Analysis (GraFFan)

[![tests](https://github.com/SimonBoothroyd/graffan/workflows/CI/badge.svg?branch=main)](https://github.com/SimonBoothroyd/graffan/actions?query=workflow%3ACI)

[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/SimonBoothroyd/graffan.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/SimonBoothroyd/graffan/context:python)

[![codecov](https://codecov.io/gh/SimonBoothroyd/graffan/branch/main/graph/badge.svg?token=Aa8STE8WBZ)](https://codecov.io/gh/SimonBoothroyd/graffan)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

This framework aims to offer a set of common utilities for analyzing the outputs of force field optimization (performed 

by [ForceBalance](https://github.com/leeping/forcebalance)), with a focus on providing tools for inspecting the many 

contributions to the gradient of the objective function. 

## Installation

The package and its dependencies can be installed using the `conda` package manager:

```shell

conda env create --name graffan --file devtools/conda-envs/test_env.yaml

python setup.py develop

```

If any targets require MOL2 or GZipped SDF (`*.sdf.gz`) molecule files then you will also need to install the OpenEye

toolkit as the `openff-toolkit` package does not currently support loading these formats through RDKit. The OpenEye 

toolkits can be installed by first activating the `graffan` conda environment created above, and then running:

```shell

conda install -c openeye openeye-toolkits

```

## Getting Started

The framework offers two CLI utilities which encapsulate most of this frameworks features: `graffan analyse` and 

`graffan visualise FILENAME`.

The `graffan analyse` command should be run in the root directory of a force balance optimization and will analyze the 

outputs of each fitting target used in the optimization. Namely, it will create a new `iteration_0000.json` file (or 

similar depending on whether the `--iteration X` flag was used) which contains the contributions of each target to the 

total gradient of the objective function with respect to the force field parameters which were refit.

The `graffan visualise iteration_0000.json` command will then open up of GUI in a webbrowser allowing the extracted 

gradients to be viewed in higher detail.

## Copyright

Copyright (c) 2020, Simon Boothroyd