diff --git a/README.md b/README.md index fa81f99d..67762590 100644 --- a/README.md +++ b/README.md @@ -267,22 +267,22 @@ Extension List | Extension | Description | Status | |-----------|-------------|--------| -| GlobalChem Entities | GlobalChem has internal DNA/RNA/Protein/Molecule objects with all common attributes associated and conversion to SMILES | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| ForceField Molecules | GlobalChem can parse, manipulate, and write CGenFF and GaFF2 files as objects | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| PDF Generation and Parsing | GlobalChem can generate SMILES to PDF and convert the PDF to SMILES | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | +| GlobalChem Entities | GlobalChem has internal DNA/RNA/Protein/Molecule objects with all common attributes associated and conversion to SMILES | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/entities/globalchem-molecule) | +| ForceField Molecules | GlobalChem can parse, manipulate, and write CGenFF and GaFF2 files as objects | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/entities/cgenffmolecule) | +| PDF Generation and Parsing | GlobalChem can generate SMILES to PDF and convert the PDF to SMILES | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/cheminformatics/pdf-parsing) | | SMILES Validation | GlobalChem has connection to PySMILES, DeepSMILES, PartialSmiles, SELFIES, MolVS for validation of SMILES sets | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| SMILES Protonation States | GlobalChem can take a set of compounds and predict the protonation states of a SMILES string over a range of pH | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Open Source Database Monitoring | GlobalChem uses Uptime-Cheminformatics to Keep Track of Open Source Chemical Data | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Networkx Software Adapter | GlobalChem Network can be converted into NetworkX Graph Objects | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| SMARTS Pattern Validation | GlobalChem uses the MiniFrag Database to test SMARTS strings accuracy for functional group selection | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Principal Component Analysis | GlobalChem can readily interpret SMILES, fingerprint, cluster and apply PCA analysis user can tweak parameters | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Drug Design Filters | GlobalChem can filter compounds based on Common Drug Design Filtering Rules | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Deep Layer Scatter Analysis | To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Sunbursting Radial Analysis | GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| Graphing Templates | GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| CGenFF Dissimilarity Score | GlobalChem can offer the difference between two molecules based on their Atom Types | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| OneHot Encoding | GlobalChem has it's own one hot encoder and decoder based on the common lists for Machine Learning | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | -| SMARTS Pattern Identifier | GlobalChem connects to the SMARTS Plus and can offer visualization into different SMARTS components | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://img.shields.io/badge/status-maintained-green) | +| SMILES Protonation States | GlobalChem can take a set of compounds and predict the protonation states of a SMILES string over a range of pH | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/cheminformatics/dimorphitedl-protonation-states-over-range-of-ph) | +| Open Source Database Monitoring | GlobalChem uses Uptime-Cheminformatics to Keep Track of Open Source Chemical Data | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/development-operations/open-source-database-monitor) | +| Networkx Software Adapter | GlobalChem Network can be converted into NetworkX Graph Objects | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/interoperability/networkx-adapter) | +| SMARTS Pattern Identifier | GlobalChem uses the MiniFrag Database to test SMARTS strings accuracy for functional group selection | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/cheminformatics/smarts-pattern-identifier) | +| Principal Component Analysis | GlobalChem can readily interpret SMILES, fingerprint, cluster and apply PCA analysis user can tweak parameters | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/machine-learning/principal-component-analysis) | +| Drug Design Filters | GlobalChem can filter compounds based on Common Drug Design Filtering Rules | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/cheminformatics/drug-design-filters) | +| Deep Layer Scatter Analysis | To visualize relations between sets of molecules, GlobalChem offers a parallel coordinate diagram generation | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/machine-learning/deep-layer-scatter) | +| Sunbursting Radial Analysis | GlobalChem offers a sunbursting mechanism to allow uses to observe how sets of compounds relate to the common set | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/machine-learning/sunbursting) | +| Graphing Templates | GlobalChem offers graphing templates to aid in faster data analysis, currently the only offer is Plotly | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/graphing-templates/plotly-template) | +| CGenFF Dissimilarity Score | GlobalChem can offer the difference between two molecules based on their Atom Types | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/forcefields/cgenff-dissimilarity-score) | +| OneHot Encoding | GlobalChem has it's own one hot encoder and decoder based on the common lists for Machine Learning | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/machine-learning/one-hot-encoding) | +| SMARTS Pattern Visualizer | GlobalChem connects to the SMARTS Plus and can offer visualization into different SMARTS components | [![Downloads](https://img.shields.io/badge/status-maintained-green)](https://sulstice.gitbook.io/globalchem-your-chemical-graph-network/cheminformatics/smarts-pattern-visualizing) | Open Source Software Compliance ===============================