File System Connection Ports for other Readers/Writers?

[chemgirl36]

Are there any plans to create File System Connection Ports to some of the cheminformatics readers such as the SDF Reader/Writer, Molfile Reader/Writer?

Thanks,
Angie

[bruno29a]

Hi @chemgirl36 , as far as I know, these nodes exist already:

SDF Reader

SDF Writer

Molfile Reader

Molfile Writer

You will need to install the KNIME Base Chemistry Types & Nodes Extension, or you can drag any one of the above nodes onto your workflow, and Knime will get the proper extension for you.

But just in case you want to install the extension manually:

KNIME Base Chemistry Types & Nodes

EDIT: Sorry @chemgirl36 , it looks like your question was more about a Connector instead. It looks like there is no such thing yet, based on this thread:

Using SDF Reader on remote FTP files

Hello all, I have been wondering is there a way to use “SDF Reader” node with FTP files. Currently I am using “FTP Connector” and “Transfer Files” nodes to copy the files from the FTP system to my local file system and then using “SDF Reader” on the local files. For other file types excel/csv/file readers they allow to add a file system connection port and then be able to access remote files that way, but the “SDF Reader” “Click to modify ports” dots don’t seem to do anything. Is it planed to…

The workaround would be to connect to your host and download the file locally first, and then read the file.

Alternatively, you may try this Remote SDF Reader where it seems to be able to read an SDF file from an ssh server:

Remote SDF Reader

And use it in conjunction with the SDF Port To Knime node to get the data in a Knime table:

SDF Port To KNIME

Something else to try is the Maestro Connector if it’s applicable in your case:

KNIME-Maestro Connector

[chemgirl36]

Thanks for the reply I will look into those connector nodes.