openmolecules.org

 
Home » DataWarrior » Bug Reports » .SDF exporting conventions
.SDF exporting conventions [message #2353] Wed, 20 November 2024 19:01 Go to next message
cwt43361 is currently offline  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 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 715
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 Go to previous message
cwt43361 is currently offline  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
Goto Forum:
  

[ Syndicate this forum (XML) ] [ RSS ] [ PDF ]

Current Time: Sat Nov 23 09:20:31 CET 2024

Total time taken to generate the page: 0.03984 seconds
openmolecules.org