| Re: Aromaticity perception [message #974 is a reply to message #971] |
Sun, 28 June 2020 23:57   |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Hi Simon,
it was possible to replicate the problem with the .sdf shared by you. Tentatively, the
problem is caused by the existence of multiple SMILES dialects by different programs which
may be an obstacle for DW. I thus recommend to pass the .sdf to openbabel to pass the files'
content into a new .sdf file to solve the issue. Here, DataWarrior (version 5.2.1, native
installation in Linux Debian) and openbabel (version 3.1.0, June 9, 2020) were used.
Enter the directory containing the .sdf in question. From the terminal (Linux, Mac) or
cmd.exe (Windows) provide a instruction in line of
obabel -isdf Aromatised.sdf -osdf -O Aromatised_passed_obabel.sdf
With only eight molecules, this is a quick operation. Comparing the original and the new /
derived .sdf file with each other shows that the connection table in the files is adjusted,
as shown in the screen photo below:
More importantly, the issues with tetravalent nitrogen atoms are resolved:
The .dwar eventually obtained is provided as an attachment of this answer.
Openbabel is a freely available program running on Windows, Mac, and Linux to interconvert
chemical formats. Its code is open on GitHub, which equally hosts the executables. The
documentation may be accessed online, or offline. If wanted, a GUI may provide you an easier
entry into a selection of its functions, too.
---
It is equally possible to convert the SMILES as provided into an .sdf, too. The command then
would be
obabel -ismi probe.smi -osdf -O probe.sdf
to lead to the same result as above, or copy-pasting (without header row) the SMILES directly
into DW. Both .smi and .sdf of this approach equally are provided here.
Norwid
https://github.com/openbabel/openbabel
https://github.com/openbabel/openbabel/releases/tag/openbabe l-3-1-1
https://open-babel.readthedocs.io/en/latest/
https://open-babel.readthedocs.io/_/downloads/en/latest/pdf/
[Updated on: Sun, 28 June 2020 23:58] Report message to a moderator |
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