I encountered almost exactly the same problem with running
RD Kit using Python. So it looks like it is a swig / python
issue. (I did not write earlier because I was not sure about
the cause. Actually I have been eagerly waiting for an answer!)
So, it looks like one cannot write python functions to
I've reproduced this behaviour. As you say it's fairly subtle. In fact
I can't tell whether it's a bug at our end or a feature of swig in
general.
It appears that obmol += newmol replaces the underlying OBMol with a
new one. You can see this by printing out the obmol (the address
changes) in a non
On 05/07/2013 17:54, Brett T. Hannigan wrote:
> I have a database of molecules in pdb files. I'd like to go through
> each molecule and see if it has certain substructures, and if they do
> identify which atoms are part of that substructure. So it's easy
> enough to read the pdb file in, conve
You could also look into ProDy, if you use PDB files.
http://www.csb.pitt.edu/prody/reference/atomic/flags.html#term-hetero
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/7/8 Maciek Wójcikowski
> I think you need custom code. For python, you could use pybel. T
I've fixed this. It's a minor change so you could apply it locally if
you want. I just moved the call to DeleteHydrogens past the stereo
section when reading the InChI:
https://github.com/baoilleach/openbabel/commit/428ac8790d3b5307305912b892e9953c793b80dc
- Noel
On 26 June 2013 14:42, Jon F
I think you need custom code. For python, you could use pybel. There are
three lines that do what you want (
http://openbabel.org/docs/dev/UseTheLibrary/Python_PybelAPI.html#pybel.Smarts.findall).
You only miss one or two lines to get the atoms by their indices.
Although searching pdb files with i
