Hi,
I'm wondering how I can match hydronium ions (H3O+) and H5O2+ using SMARTS with
OpenBabel. I created the OBMol object with only atomic number and coordinates
information, and I tried using "[#8](~[#1])(~[#1])~[#1]",
"[#8+](~[#1])(~[#1])~[#1]", and "[OH3+]" but none of them produced any matche
Hi everyone,
I’d like to modernize the Open Babel webpages, including migrating away from
MediaWiki to Markdown / Jekyll.
The idea behind the MediaWiki site was to enable anyone to edit. Unfortunately,
unlike Wikipedia, we don’t have the same level of anti-spam resilience. So we
had to move to
Sounds good.
On 24 October 2017 at 21:05, Geoffrey Hutchison
wrote:
> Hi everyone,
>
> I’d like to modernize the Open Babel webpages, including migrating away
> from MediaWiki to Markdown / Jekyll.
>
> The idea behind the MediaWiki site was to enable anyone to edit.
> Unfortunately, unlike Wikip
If you write out your molecules as SMILES strings, what do they look like?
It's possible you are missing some bonds.
On 24 October 2017 at 17:41, wrote:
> Hi,
>
> I'm wondering how I can match hydronium ions (H3O+) and H5O2+ using SMARTS
> with
> OpenBabel. I created the OBMol object with only a
Hi Noel,
I think you are right! I use `SetAtomicNum()`, `SetVector()` to build an OBMol
atom by atom, and then call `ConnectTheDots()` to add bonds. Apparently due to
valency, oxygen atoms won't have more than two bonds, hydrogen not more than
one. Therefore the molecule won't ever match H3O+ or
Hi Geoff,
When I tried to convert a multimolecule pdb file (output from obminimize)
to an sdf file, only the first molecule was converted.
I wrote my own script to split the file into multiple pdbs and put them
together as single sdf using obabel.
But any solution using obabel to that in single st
Hi,
Can anyone help me convert a single input (multimolecular) sdf file into
multiple pdb files with the molecule names (as seen in the sdf file) as
their file names instead of consecutively numbered file names?
Thanks,
Jubilant
