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Aromaticity perception [message #967] Thu, 25 June 2020 22:38 Go to next message
richards99 is currently offline  richards99
Messages: 42
Registered: May 2020
Location: UK
Member
Hi,
There appears to be consistent issues with the import of certain aromatised structures.
Ones I especially notice are N-methylated pyridinones, pyrimidinones, and bicyclic structures.
Data Warrior puts double bonds into the wrong positions, quaternising nitrogens.

It would be useful if the aromaticity perception can be improved otherwise it creates lots of invalid smiles which require manually altering.

Thanks,

Simon.
Re: Aromaticity perception [message #968 is a reply to message #967] Fri, 26 June 2020 10:13 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 204
Registered: June 2019
Senior Member
Hi Simon,

may you add from which software / file format you import into DW to observe these issues and share a typical minimal input/output file? For now, it reads related to the (intermediate) representation of 2-pyridone with SMILES either as lactam C1=CC=CNC(=O)1, or lactim Oc1ccccn1.

Norwid
Re: Aromaticity perception [message #969 is a reply to message #968] Sun, 28 June 2020 00:09 Go to previous messageGo to next message
richards99 is currently offline  richards99
Messages: 42
Registered: May 2020
Location: UK
Member
Hi Norwid,
I cannot find a way to attach an SDF file, but basically this set of smiles below causes a problem.
If you create a CSV/TXT file of these and import them into DW, then all is fine.
But if you create an SDF file of these smiles using Marvin Sketch for example (kept as aromatised), and then import them into DW, then all the double bonds are messed up!
Other programmes such as Marvin, RDKit do not seem to have issues with these.

Cn1ccccc1=O
Cn1cccnc1=O
Cn1ccncc1=O
Cn1ccn(C)c(=O)c1=O
Cn1ccc(=O)cc1
Cn1ccc2ncccc2c1=O
Cn1ccc(=O)c2cccnc12
Cn1c2cccnc2ccc1=O
Re: Aromaticity perception [message #971 is a reply to message #967] Sun, 28 June 2020 00:14 Go to previous messageGo to next message
richards99 is currently offline  richards99
Messages: 42
Registered: May 2020
Location: UK
Member
index.php?t=getfile&id=214&private=0

Okay, worked out now how to attach the file.
Attached is the SDF file which is problematic for DW, and a snapshot showing the difference between importing as smiles or SDF.

Simon.

Re: Aromaticity perception [message #974 is a reply to message #971] Sun, 28 June 2020 23:57 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 204
Registered: June 2019
Senior Member
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:

index.php?t=getfile&id=221&private=0

More importantly, the issues with tetravalent nitrogen atoms are resolved:

index.php?t=getfile&id=222&private=0


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]

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Re: Aromaticity perception [message #980 is a reply to message #974] Thu, 02 July 2020 14:41 Go to previous message
thomas is currently offline  thomas
Messages: 646
Registered: June 2014
Senior Member
many thanks Simon and Norwid for pointing to this issue suggesting work-arounds.

The problem was that DataWarrior didn't expect finding compounds with aromatic bond types in molfiles,
which are based on the Daylight aromaticity model into the bargain, e.g. having carbonyl carbon atoms being
maked as aromatic. This is unusual for two reasons: First, molfiles typically store alternating single
and double bonds for aromatic rings rather than using the delocalized bond type, unless it encodes
a substructure with query features. Second, for the rare cases that the delocalized bond types may be used
one would expect an MDL/Symex/Hueckel aromaticity concept to be applied.

Nevertheless, since Marvin Sketch seems to read SMILES based atom aromaticity encodings and writes them directly into
written molfiles using aromatic bond types, I have updated DataWarrior to normalize this kind of encoding before
generating and writing idcodes (DataWarrior's canonical structure representation) into its native files.

The current developments version should not have this issue anymore.

Thomas

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