On 25/10/2017 07:55, Sundar wrote:
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?
Try:
obabel manymols.sdf -O dummy.pdb --split
Eac
Are you able to provide files that show this? Or reduce it to single compounds
that are being eliminated that can be shared?
> On Oct 24, 2017, at 8:53 PM, Sundar wrote:
>
> Hi,
>
> I am refreshing this thread for an answer.
>
> obabel input.smi -h -r -b -c --unique --gen2d --partialcharge m
You need to add the bonds somehow. If there is no way to infer the bonds
from the atomic coordinates, then it is impossible.
Regards,
- Noel
On 24 October 2017 at 22:05, wrote:
> Hi Noel,
>
> I think you are right! I use `SetAtomicNum()`, `SetVector()` to build an
> OBMol
> atom by atom, and th
> Are you able to provide files that show this? Or reduce it to single
> compounds that are being eliminated that can be shared?
Even if it’s only a subset, that would be helpful.
I’m working on a distance geometry method that should offer increased range.
Either way, having examples is crucial
> atom by atom, and then call `ConnectTheDots()` to add bonds
Not surprisingly, for a general-purpose library, Open Babel has a
general-purpose bond perception algorithm. As you note, it will ensure oxygen
atoms have a maximum of two bonds. This ensures PDB and other crystallography
files with
Hi Chris,
Worked like a charm. Thanks a lot.
But I couldn't find a documentation for --split
All I see is --splitinto docs.
-Jubilant
On Wed, Oct 25, 2017 at 4:08 AM, Chris Morley wrote:
> On 25/10/2017 07:55, Sundar wrote:
>
> Can anyone help me convert a single input (multimolecular) sdf fil
I've been working on another system where oxygen frequently exceeds a
standard valency of two (organometallics). So far, I've been getting
around the automatic bond deletion in an older version of Open Babel by
modifying the element.txt file. By changing the MaxBnd column for oxygen
to a higher v
I like the idea.
It beside the cleaner look, I think the opportunity of enabling accounts for editing the
documentation is great.
Hopefully, it will not take too much work.
Thanks!
On 10/24/2017 01:05 PM, Geoffrey Hutchison wrote:
Hi everyone,
I’d like to modernize the Open Babel webpages,
