Metadata-Version: 2.1
Name: cg-flatland
Version: 0.0.1
Summary: Easier development of polymer structure prediction tools.
Home-page: https://github.com/cayleygroup/flatland
Author: The Cayley Group
Author-email: contact@cayleygroup.org
License: UNKNOWN
Description: # Flatland
        
        #### Easier development of polymer structure prediction tools
        
        The development and debugging of modern neural network approaches for protein structure prediction has the potential to be a somewhat complicated task. Here we provide a framework, Flatland, for simulating training datasets of the form used by current state-of-the-art systems. The central task performed is to evolve a population of polymer sequences, predict their folded structure, produce distance matrix and bond angle tensors, and calculate spectra of per-polymer compound or other polymer interaction likelihoods (emulating protein-protein and compound-protein interaction datasets). This framework intentionally performs such simulations in a highly simplified manner that does not accurately model the real biological processes. Relatedly, it provides the means to simplify the problem to an arbitrary extent - including permitting the reduction from three to two dimensions, reducing the amino acid alphabet from twenty-one to three, and simplifying characteristics of the evolutionary optimization. We provide the framework together with a collection of starting-point notebooks for training neural network models to learn from such data by way of an open source repository to kick-start the development efforts of those interested in contributing to solving this vitally important problem.
        
        ## Installation
        
        You can install the last released version of Flatland via pip
        
        ```bash
        
        pip install cg-flatland
        
        ```
        
        Or install the most recent development version of Flatland using git
        
        ```bash
        
        git clone https://github.com/cayley-group/flatland
        pip install -e flatland
        
        ```
        
        ## Demonstrations
        
        We're putting together various demonstration notebooks which you'll be able to access via the following:
        
        * [Data Generation](https://colab.research.google.com/github/cayley-group/flatland/blob/master/nb/data-generation.ipynb)
        * [Structure Solver Example](https://colab.research.google.com/github/cayley-group/flatland/blob/master/nb/structure-solver.ipynb)
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
