Functionality expansion requrest for SDF download

Questions
,
1

Dear Datagrok team,

Thank you for your continued support.

Regarding the CSV (optional) feature, I would like to inquire if it would be possible to implement a similar output functionality for SDF format, hopefully where only the displayed information is exported?

image
image379×499 16.1 KB

I am making this request because my team has noticed that to some extent number of users in my side find SDF format more convenient to work with compared to CSV.

I would greatly appreciate it if you could kindly consider this suggestion.

Best regards,

Kosuke

1 Like
2

Hi Kosuke,
Thank you for your suggestion and for reaching out.

We have already begun discussing the possible implementation of this feature for the SDF format. To ensure we meet your needs, could you please clarify whether you’re looking for full CSV-like export functionality or just the ‘Visible Columns Only’ option?

Best regards,
Olena

1 Like
3

Dear Olena,
Thank you for your consideration.

The most important requirement to export SDF format is the ability to limit the number of rows.
Therefore, I would like to have the following two conditions for rows:

  • Filtered Rows Only
  • Selected Rows Only

Regarding columns,
The “Visible Columns Only” option becomes very effective when there are tens of columns, so I would like this to be considered as well. This is the second most important factor.

For chemical structures, I noticed users will need to specify which column should be used as the molfile in the SDF. Personally, I think it would be fine to set New line as “\n” and Missing value as empty string by default.

If you have any questions or comments, please let me know.
Best,
Kosuke

1 Like
4

Here’s a ticket to track the request:

2 Likes
5

Hi Kosuke,

We’ve recently improved the SDF Export feature, and here’s how it will look in the upcoming Datagrok 1.26 release:

image
image273×298 8.63 KB

Users can now:

  • select the molecule column to convert;
  • choose to export only selected or visible columns;
  • export only selected or filtered rows.

We hope this aligns with what you were looking for and that it will be useful in your workflow!

Kind regards,
Dmytro

2 Likes
6

Dear Dmytro,
Thank you for useful update and your effort. I will check it ASAP once new version is released.
Best,
Kosuke

1 Like
7

Dear Dmytro,
Regarding SDF downloads, I have one more point to inform you about the download behavior. While this may no longer be an issue in newer versions, I’m sharing this for your reference.

We noticed a phenomenon when the property type is “qnum”: there is a discrepancy between the displayed data and the exported data, as you can see below. This appears to be due to floating-point precision errors.

image
image1214×557 87 KB

However, there are pros and cons to whether empty cells should be treated as empty strings or Null values - please decide based on Datagrok’s philosophy. The most important point for me is that the downloaded SDF values should match what is displayed in the grid.

Best regards,
Kosuke

2 Likes
8

Hi Kosuke,

You’re right — thanks for pointing that out!
Just like with CSV export, we should represent None values as empty strings, and the same logic should apply here as well. We’ve already addressed this, and the updated SDF export now correctly treats empty cells as empty strings.

Kind regards,
Dmytro

2 Likes
9

Dear Dmytro,
I’m happy to hear you have already dealt with it. If I should find new issues after releasing new features I will let you know.
Best regards,
Kosuke

2 Likes