openmolecules.org Forum: Bug Reports » .SDF exporting conventions

Home » DataWarrior » Bug Reports » .SDF exporting conventions

Show: Today's Messages :: Polls :: Message Navigator

.SDF exporting conventions [message #2353]

Wed, 20 November 2024 19:01

cwt43361
Messages: 2
Registered: November 2024

Junior Member

Upon exporting data from data warrior using save special --> .SDF option, I noticed the following issue:

If my data has 'Compound ID' or 'Structure ID' or 'ID' or 'Name' or 'Structure Name', it seems as though upon export to .SDF it looks like the option to specify the Compound Name Column never includes these labels but rather just SMILES and other descriptors calculated within Data Warrior.

The issue I'm having is that if I use the <automatic> option it will create an additional column called 'structure no'. When I'm attempting to use this file downstream in another program where I need to have the column specifically named 'Name' or 'ID', the renaming or adding of column that data warrior is doing upon export is creating issues.

Is there a specific wording that data warrior requires for the compound name column for the program to recognize? For example, I have noticed how I include by biological activity in data sets can affect whether data warrior can interpret this as biological data (such as relative activity at 10uM).

Report message to a moderator

Re: .SDF exporting conventions [message #2355 is a reply to message #2353]

Wed, 20 November 2024 22:55

thomas
Messages: 747
Registered: June 2014

Senior Member

I checked the source code. The rule is that all alphanumerical columns qualify as 'Name column' unless one or more cells contain more than one identifier (separated by "; " or in two separate lines.

Report message to a moderator

Re: .SDF exporting conventions [message #2356 is a reply to message #2355]

Wed, 20 November 2024 23:22

cwt43361
Messages: 2
Registered: November 2024

Junior Member

God bless you! I looked at the compound library (from my college) and there is a single compound in ~30K compounds that has a semi-colin in the name! You're a legend, a hero!

Report message to a moderator

Previous Topic:	Cannot open files due to java error
Next Topic:	Superpose conformers rigid and flexible menu inverted

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Mon Aug 10 19:05:52 CEST 2026

Total time taken to generate the page: 0.00607 seconds