Merge branch 'master' of https://github.com/Sulstice/global-chem

Sulstice · Apr 11, 2022 · 9867baa · 9867baa
2 parents 026514e + 13df842
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diff --git a/README.md b/README.md
@@ -27,9 +27,19 @@ Overview
 
 #### GlobalChemExtensions
 
-| Release | Licensing | Stats | Demo | 
-| ------- | --------- | ----- | ---- |
-| [![PyPI version](https://badge.fury.io/py/global-chem-extensions.svg)](https://badge.fury.io/py/global-chem-extensions) | [![License: MPL 2.0](https://img.shields.io/badge/License-MPL%202.0-brightgreen.svg)](https://opensource.org/licenses/MPL-2.0) | [![Downloads](https://pepy.tech/badge/global-chem-extensions)](https://pepy.tech/project/global-chem-extensions) | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1gGx4mOmkXP8voGelHwCt8Eq4Xq8Lj5_k?usp=sharing) |
+| Release   | Licensing | Stats |
+| --------- | --------- | ----- |
+| [![PyPI version](https://badge.fury.io/py/global-chem-extensions.svg)](https://badge.fury.io/py/global-chem-extensions) | [![License: MPL 2.0](https://img.shields.io/badge/License-MPL%202.0-brightgreen.svg)](https://opensource.org/licenses/MPL-2.0) | [![Downloads](https://pepy.tech/badge/global-chem-extensions)](https://pepy.tech/project/global-chem-extensions) |
+
+Different extensions demos can be found below, or head to the navigate the "all" to check out the full feature suite. 
+
+| Extension | Demo |
+| --------- | ---- |
+| extensions | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1OrskD75wWaxLIk-wZXC4_5_vl98UNlu8?usp=sharing)
+| bioinformatics | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1dDB922p-CZC5ADZcI6YgBFGGhq_j4HDr?usp=sharing)
+| validation | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1OrskD75wWaxLIk-wZXC4_5_vl98UNlu8?usp=sharing)
+| machine_learning | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1SPAxEL5PTOZM5ob4-Zv41eVHZ0V02uYe?usp=sharing)
+| pdf | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1qJPEmPhUKlbbcoBR3nkD8L-BJoRKAIzq?usp=sharing)
 
 Installation 
 ============
@@ -285,10 +295,10 @@ Extension List
 | Networkx Software Adapter       | GlobalChem Network can be converted into NetworkX Graph Objects                                                         | extensions       |
 | SMARTS Pattern Validation       | GlobalChem uses the MiniFrag Database to test SMARTS strings accuracy for functional group selection                    | extensions       |
 | Principal Component Analysis    | GlobalChem can readily interpret SMILES, fingerprint, cluster and apply PCA analysis user can tweak parameters          | machine_learning |
-| Drug Design Filters             | GlobalChem can filter compounds based on Common Drug Design Filtering Rules                                             | extensions       |
-| Deep Layer Scatter Analysis     | To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation            | plotting         |
-| Sunbursting Radial Analysis     | GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set       | plotting         |
-| Graphing Templates              | GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly                 | plotting         |
+| Drug Design Filters             | GlobalChem can filter compounds based on Common Drug Design Filtering Rules                                            | extensions       |
+| Deep Layer Scatter Analysis     | To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation            | machine_learning | 
+| Sunbursting Radial Analysis     | GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set      | machine_learning |
+| Graphing Templates              | GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly               | machine_learning |
 | CGenFF Dissimilarity Score      | GlobalChem can offer the difference between two molecules based on their Atom Types                                     | extensions       |
 | OneHot Encoding                 | GlobalChem has it's own one hot encoder and decoder based on the common lists for Machine Learning                      | extensions       |
 | SMARTS Pattern Identifier       | GlobalChem connects to the SMARTS Plus and can offer visualization into different SMARTS components                     | extensions       |

diff --git a/global_chem/setup.py b/global_chem/setup.py
@@ -46,15 +46,13 @@
         'bioinformatics': ['global-chem-extensions[bioinformatics]'],
         'machine_learning': ['global-chem-extensions[machine_learning]'],
         'pdf': ['global-chem-extensions[pdf]'],
-        'plotting': ['global-chem-extensions[plotting]'],
         'all': [
             'global-chem-extensions',
             'global-chem-extensions[web_server]',
             'global-chem-extensions[validation]',
             'global-chem-extensions[bioinformatics]',
             'global-chem-extensions[machine_learning]',
             'global-chem-extensions[pdf]',
-            'global-chem-extensions[plotting]'
         ]
     },
     zip_safe=False,

diff --git a/global_chem_extensions/setup.py b/global_chem_extensions/setup.py
@@ -46,9 +46,8 @@
     extras_require={
         'validation': ['partialsmiles', 'pysmiles', 'deepsmiles', 'selfies', 'molvs'],
         'web_server': ['flask'],
-        'plotting': ['plotly', 'bokeh', 'kaleido'],
         'bioinformatics': ['biopython', 'dna_features_viewer'],
-        'machine_learning': ['sklearn'],
+        'machine_learning': ['sklearn', 'plotly', 'bokeh', 'kaleido'],
         'pdf': ['molpdf']
     },
     long_description=long_description,