updated Readme file

README.md

@@ -4,52 +4,61 @@
 
 This repository is maintained by the [KNIME Team Rakete](mailto:team-rakete@knime.com).
 
-It provides a template for creating KNIME Python extensions.
+It provides a template for creating a KNIME Python extension that integrates [RDKit](https://rdkit.org/docs/index.html) functionality. 
 
 ## Contents
 
-This repository contains a template KNIME Python Extensions.
+This repository contains a template KNIME Python Extension that integrates RDKit functionality.
+It contains one simple example node that counts the number of carbons in molecules provided in an input table.
+Note that this tutorial only works with KNIME AP version 5.6 or higher. 
 The code is organized as follows:
 
 ```
 .
 ├── icons
-│   │── icon.png
+│   └── icon.png
 ├── src
+│   └── __init.py__
 │   └── extension.py
 ├── demos
-│   └── Example_with_Python_node.knwf
+│   └── demo-chemistry-python-adapter.knwf
+├── tests
+│   ├── test
+│   └── conftest.py
+│   └── test_extension.py
 ├── knime.yml
 ├── pixi.toml
 ├── config.yml
 │── LICENSE.TXT
 └── README.md
 ```
 
-## Instructions
+## General Instructions
 
-You can find instructions on how to work with our code or develop python extensions for KNIME Analytics Platform in the KNIME documentation:
+You can find general instructions on how to work with our code or develop python extensions for KNIME Analytics Platform in the KNIME documentation:
 * [KNIME Python Extension](https://docs.knime.com/latest/pure_python_node_extensions_guide/index.html)
 
-## Minimal Instructions to create a KNIME Python extension
+## Create a KNIME Python extension using RDKit based on this repository
 ### Prerequisites:
 * [KNIME Analytics Platform](https://www.knime.com/downloads/overview)
 * [git](https://git-scm.com/downloads)
 * [pixi](https://pixi.sh/latest/)
 
+
 ### Instructions:
-1. **Clone** this repository or use it as a **template** (click on the green "Use this template" button):
-2. **Edit** `knime.yml` -  provide your metadata, license, ...
-3. _(Optional)_ Modify the `src/extension.py` file to implement your own logic.
+1. **Clone** this repository or use it as a **template** (click on the green "Use this template" button).
+2. **Edit** `knime.yml` to provide your metadata, license, etc. The last two lines of this file indicate that the extension created with this repository depends on the KNIME Base Chemistry Types & Nodes and the RDKit extensions. 
+3. **Modify** the `src/extension.py` file or **add** further files to implement your own logic. Note that every py file equivalent to one node needs to be imported in the init.py file.
 4. _(Optional)_ Add python packages to the environment with the following command, or by manually editing the `pixi.toml` file:
     ```bash
     pixi add <package_name>
     ```
+    If you leave the `pixi.toml` file unchanged, the Python environment that you will create in the next step will have the RDKit package installed per default. 
 5. **Install** the python environment:
     ```bash
     pixi install
     ```
-6. **Test** the extension in the KNIME Analytics Platform with the extension in debug mode by adding the following line to the knime.ini file (adjust <path_to_this_repository> in the config.yml):    
+6. **Test** the extension in the KNIME Analytics Platform with the extension in debug mode by adding the following line to the `knime.ini` file (adjust <path_to_this_repository> in the `config.yml`):    
     ```
     -Dknime.python.extension.config=<path/to/your/config.yml>
     ```
@@ -71,6 +80,19 @@ You can find instructions on how to work with our code or develop python extensi
 
 For detailed instructions on how to create a KNIME Python extension, please refer to the [KNIME Python Extension documentation](https://docs.knime.com/latest/pure_python_node_extensions_guide/index.html).
 
+
+### Background information:
+From KNIME AP version 5.6 on, the KNIME Base Chemistry Types & Nodes extension is shipped with extended adapator functionality between Python and Java. 
+
+It also provides two functions designed to simplify the work of node developers:
+
+`to_rdkit_series`: convert a pandas series of KNIME chemistry types to a series of RDKit Mol objects
+
+`is_molecule`: True if the column holds any supported chemistry type
+
+The adaptor file can be found in the following location of the KNIME AP installation /plugins/org.knime.chem.types_<version>/python/src/org/knime/types/chemistry.py. 
+
+
 ## Join the Community
 
 * [KNIME Forum](https://forum.knime.com)