Home » DataWarrior » Functionality » Filter out nasty functions (to design a macro to filter all nasty functions their names should be included )
| Re: Filter out nasty functions [message #1898 is a reply to message #1897] |
Sun, 14 May 2023 22:24   |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Julio,
I would like to add two suggestions; how the task is presented/shared, and a revision of the SMILES string.
a) After recording a DW macro, it is possible to export this via Macro -> Export Macro as a file with file extension .dwam. This offers the advantage for an easier/faster import to replicate your observations (Macro -> Import Macro in a first step, Macro -> Run Macro to apply the instructions) by any subsequent reader of your post, because it typically is small enough to be attached to a message here (up to five files in total [e.g. incl. a small test data set] for a maximum over all files of 2MB). It equally prevents the omission of lines; in your most recent example, the opening how the macro is named (for the display within the DW session) and closing line </macro> was missing.
For the purpose of illustration, I enclose a small test set .dwar, and a macro to assign SMILES and compute Mw as .dwam.
b) Curious about the structure the SMILES strings describes, I relayed it to openbabel to write a .sdf, however without success.
$ obabel -:"Nc1c([C@@H](CC(C2=CNC(Nc3ccccc3)=CC2=O)=O)C(C(O[C@@H]2[C@@H] 3CCCC2)=O)=C3O)cccc1" -h --gen3d -O test.sdf -xv3000
==============================
*** Open Babel Warning in ParseSmiles
Invalid SMILES string: 2 unmatched ring bonds.
0 molecules converted
With regards,
Norwid
[1] https://chemdrawdirect.perkinelmer.cloud/js/sample/index.htm l#
[2] https://www.simolecule.com/cdkdepict/depict.html
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