| Row wise chemical reaction [message #718] |
Fri, 06 December 2019 19:54  |
P_Fitz
Messages: 17
Registered: November 2019
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Junior Member |
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The enumerate chemical libraries feature of data warrior is awesome, but does not do quite what I want it to for this particular application.
I have a list of Carboxylic acids that correspond with specific Amino acids that they are combined with. Enumerate chemical libraries with these sets creates all possible combinations of the two. Is there a way to just combine specific Amino acids with specific Carboxylic acids? Basically I just want to combine reactants row-wise rather than combinatorially.
Thanks!
Patrick
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| Re: Row wise chemical reaction [message #724 is a reply to message #718] |
Tue, 17 December 2019 11:22  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Hello Patrick,
I understand your aim is to bring line wise structures deposit in independent columns into a cell in common.
If so, 1) convert the structures you already have in the .dwar file as SMILES. You find this function along chemistry -> from chemical structure -> Add SMILES code, to be applied for each column of structures. 2) To concatenate the SMILES, reach for Data -> Add Calculate Values. In the new sub-menu, you define a string addition, of the SMILES, as shown below:
After confirmation by «ok», DataWarrior creates a new column with the result. You then 3) convert the concatenated SMILES string into a sketch with Chemistry -> Add Structures From Name. This equally creates a niew column, with both molecules represented in one cell:
Norwid
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| Re: Row wise chemical reaction [message #754 is a reply to message #733] |
Mon, 13 January 2020 23:02 |
P_Fitz
Messages: 17
Registered: November 2019
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Junior Member |
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Yes that is correct, I do not just want to have them next to each other, I want to react them. Thanks for your reply and for supporting Data Warrior!
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| Re: Row wise chemical reaction [message #1636 is a reply to message #1619] |
Thu, 16 June 2022 00:24 |
P_Fitz
Messages: 17
Registered: November 2019
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Junior Member |
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Hi Thomas,
Thanks so much for implementing this feature. Based on how the help screen looks (the suzuki reaction example) this is exactly how I want this feature to work. I've been trying to do the same thing with amide formation and it does not seem to be working. I went back and drew the same reaction scheme (at least I think so) for enumerating a library and that works. The numbering when I connected the bonds was slightly different there.
I'm not sure why, but after I draw the reaction, the A and B reactants seem to get switched. I think maybe the carboxylic acid is being interpreted as an fmoc amino acid and since it does not have an fmoc amino acid I'm getting an empty column as the reaction product. I've attached a screenshot of the reaction and my data columns. The output of the reaction is as I said an empty column.
As always, thanks for continuing to support Data warrior!
Patrick Fitzgerald
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| Re: Row wise chemical reaction [message #1637 is a reply to message #1636] |
Thu, 16 June 2022 00:27 |
P_Fitz
Messages: 17
Registered: November 2019
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Junior Member |
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I switched the order of my columns in the Table view and that seemed to work to do combine the molecules. This was reproducible. Switching them back stopped it from working, and then switching them again made it work.
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| Re: Row wise chemical reaction [message #1642 is a reply to message #1637] |
Mon, 20 June 2022 20:34 |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Thomas,
For the nicely working «merge by reaction» function, I would like to file for feature suggestion. May one extend the reaction editor's functionality to match the one already present when running chemistry -> enumerate combinatorial library, i.e. to add
+ define .and. save (eventually re-use) a reaction with user defined name in the .rxn format
+ access the already available templates of the combinatorial library (Stille, Wittig, etc.)
By now, the GUI of the two seem to differ:
The observations refer to DW 5.5.0 for Linux including the update by 2022-06-17.
Norwid
[Updated on: Mon, 20 June 2022 20:36] Report message to a moderator |
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| Re: Row wise chemical reaction [message #1672 is a reply to message #1656] |
Thu, 14 July 2022 10:27 |
thomas
Messages: 711
Registered: June 2014
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Senior Member |
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Dear Norwid,
thank you for the suggestion to add starting materials from an existing column. I have implemented that two or three weeks ago, but forgot to mention it in this thread.
Thomas
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