I have some structures from SMILES and I want to show them as SMILES text in the report. But when I selected the SMI field into the report it showes some stranger HEX data in the report. I don't know how to convert a structure into a plain text SMILES.
How to create SMILES from structure?
Thank you very much.
Use the cast node to cast smiles to structure. It should then be seen as a structure in the report. If not use the marvin node to convert the cast column into sdf and connect to report once more.
Set/Change the structure viewer in knime preferences if necessary.
Thank you for your reply.
But if fact i am not want to see "structure". I want to see "SMILES" in text format. My fields is in "SMI" format and it can be rendered as "Marvin" or "String". But when I imported it into report it can only view as a image or a bunch of meaning less hex data. There are many nodes which can convert a smiles into a "Structure", but none of them can convert the structure back to a "SMILES". Someone, such as OpenBabel, can convert an "SDF" strcuture to a "SMI" structure, but none of them can convert a "Structure" back to a plain text "smiles". :(
In KNIME there is no such thing as a "structure". The molecules can be in a variety of formats, thet standard formats being SDF and Smiles. If they are in a vendor specific format (RDKit, CDK, Schrödinger, etc.) they can be converted into SDF or Smiles with the correspoding converter nodes. The reason that you usually onyl see the graphical depiction is that the default renderer for Smiles or SDF is the graphical renderer. This one is also used when creating the report contents. If you want to have the textual representation I suggest to use the "Column Rename" node and changet the type of the Smiles column to StringValue.
Use the cast node to cast smiles to structure. It should then be seen as a structure in the report. If not use the marvin node to convert the cast column into sdf and connect to report once more.
Yes. It works thank you very much.
Yes. Thank you. I know how to show structure in report.
But if I use the default setting the image resolution is poor. When I try to fix the image size to a larger number it will stretch the structure and the molecule showed ugly. Many tools can convert structure to pretty picture but it seems that they are not imported into KNIME.
Is there anyway to do that? Thank you.
Structures can be made to look really good in the report tool.
first, in the data to report node, increase the values in the use custom scaling section to say 500 by 500.
then make sure your structures are represented as SDF going ino the data to report node.
Go to knime preferences, chemistry section and for SDF choose Marvin as default renderer.
now find the Marvin preferences in the Knime preferences and under renderer section increase the bond thickness and atom label size. You should now find that the structure images generated in your report look much better.
simon.
Dear richards,
It works greatly. Thank you very much. :)