Hello,
Is it possible to define my own SMARTS pattern for calculating numerical
descriptors via the command line? For example, to calculate the number of
aromatic bonds, I am using append like this:
>> obabel aspirin.sdf -osmi --append abonds
https://open-babel.readthedocs.io/en/latest/Descrip
Dear Robin,
Perhaps the NCI/NIH Chemical Identifier Resolver would work for you?
https://cactus.nci.nih.gov/chemical/structure
It can return an image through a web API with various inputs like InChI,
SMILES, and SD file. Here is an example:
https://cactus.nci.nih.gov/chemical/structure/InChIKe
Dear All,
I am trying to process a SMILES file (.smi) and calculate InChIs, where there
are some SMILES that Open Babel will not be able to read, due to syntax or
other errors. In those cases, I would like to print a string such as
"Open_Babel_Error" on the line (or something even more descript
Dear Vaibhav,
I think the pattern you specified (first one) is trying to match an oxygen
connected to aliphatic C (in 6 membered ring). I tried this more general SMARTS
pattern and it seems to match phenols:
*~[#6][OH1]
babel myfile.sdf -s"*~[#6][OH1]" sim-alcohol.smi
This web resource and re
O'Boyle
Sent: Wednesday, September 11, 2019 6:05 AM
To: Scalfani, Vincent
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] Error handling with smi file in pybel?
Hi Vin,
By default the command-line application stops on error, a behavior that can be
overridden by "-e&q
Hi Ryan,
Here is another possible choice for structure OCR:
https://spotlite.nih.gov/ncats/molvec
Vin
From: Ryan Bannen
Sent: Thursday, September 26, 2019 2:08 PM
To: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] SMILES to PNG and then PNG to SMILES? (Fredrik
Wallner)
He
Hi Peng,
In addition to the Daylight documentation on SMILES, there is also OpenSMILES,
which OpenBabel supports:
http://opensmiles.org/
And IUPAC is in the early stages of building on OpenSMILES, with IUPAC SMILES+:
https://github.com/IUPAC/IUPAC_SMILES_plus
Vin
-Original Message-
