MolPort KNIME Node

Looking for an easy way to improve your workflow?

Open source KNIME interface can be tailored and constructed for your complex workflow. MolPort KNIME nodes can simplify your chemical data mining process. The intuitive drag-and-drop interface of the KNIME platform makes it easy to use the MolPort node in your existing workflow. With our node you can integrate MolPort services with your in-house developed software or off the shelf tools. MolPort node will help you quickly gather real-time commercially available compound data directly from our database.

MolPort nodes allow the user to get the following information from MolPort database:

Search result – FOUND / NOT FOUND

MolPortID – MolPort unique identifier for each Molecule

Canonical SMILES – chemical structure of Molecule in the form of SMILES string

Unverified amount – maximum amount of compound that is available for purchase

Verified amount – maximum amount of compound that is available for purchase which was confirmed by supplier as current stock amount.

Unverified amount always more or equal than Verified amount!

Link – a link to molecular page on MolPort with information about molecule and all information form compound suppliers.

The input of the MolPort nodes is a string containing SMILES or MolPort ID.

To use MolPort nodes you need a User name and Password. If you are using our API or webservers through Excel, you may use the same credential. Otherwise follow API page to get a new credential.

Currently we have a two different KNIME nodes:

Chemical Search Node

Performs different chemical search types and returns one or many molecules per request; based on chemical structure in SMILES format as an input.

This node is currently in the stage of beta testing and available upon request. Find out more on KNIME Chemical Search node page.


MolPort Chemical Search KNIME Node
Picture 1. MolPort Chemical Search KNIME Node

Simple Search Node

Performs exact molecule search based on MolPort ID or chemical structure in SMILES format. This node returns only one Molecule per request.


MolPort Simple Search KNIME Node
Picture 2. MolPort Simple Search KNIME Node


The input of the MolPort node is a string containing SMILES format of chemical compounds (one compound per row). You can get the list of compounds from a text file using the FileReader node as shown above and in the example workflow. If you want to use SMILES format from your existing workflow you need to convert SMILES into a string. We suggest you use the String Replacer node without any specific settings.


Picture 3. Input data


Alternatively, you may use MolPort ID list as input.

You can use the output of the MolPort node for further processing, or redirect it to the FileWriter node. In the example, we use CSV writer to create a file with structures. Use first node port (Output port 0) for Matched values. Here is an example of found molecule output:


Picture 4. Found output data

In case of no matches, the output for such molecules will be redirected to the second node port (Ouput port 1) and will contain the following information:


Picture 5. Not found output data


How to start work with MolPort KNIME node

1. KNIME set up

KNIME set up is free. Find out how to install KNIME. To install KNIME just re-archive the files from the KNIME website and follow the instructions.


2. MolPort nodes set up

With MolPort nodes you can verify if a particular compound is present in our database. To install node you can use our automatic KNIME install/update website with address: https://www.molport.com/knime/. Here is detailed instruction how to make installation.

You can also download our examples of workflows. They contain file examples and description:
       1. MolPort SimpleSearch from SMILES (with files examples).knwf
       2. MolPort ChemicalSearch from SDF (with files examples).knwf.



Other ways to access information from MolPort
       1. Download files from FTP.
       2. Application programing interface (API) for integration with your existing software.
       3. Web services for Microsoft Excel.
       4. Structure search on web site.
       5. List Search for a list of compounds for the optimal purchasing selection.

Contact us to receive your personal login and password! Let us know if you require more information about KNIME or other services!

2017 MolPort, v2.32, release date 08-12-2017 10:00 (+0200). All rights reserved.