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'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
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 mac...@wojcikowski.pl
I think you need custom code. For python,
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, convert
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
