On 05/12/2012 00:10, Sarah Rodriguez wrote:
> Hi,
>
> I asked the earlier question:
>
> On 11/11/2012 04:01, Sarah Rodriguez wrote:
> > Hello,
> > I am wondering if I have 2 large databases that I want to compare the
> > structures in, would I be able to do this in babel?
>
> Thanks for your rep
As you found, the --canonical solution is not at all the efficient way
to do this. Here's the proper way to do this using Tim's
OBIsomorphismMapper (which uses the VF2 graph matching algorithm I
believe).
import pybel
ob = pybel.ob
mol = pybel.readstring("smi", "CC(=O)Cl")
molb = pybel.readstring(
Hello.
Yes, an input flag (at least for some input formats like cif or smiles)
meaning "please keep hydrogens as they are in the input and do not add
or remove hydrogens even if you think that they may be missing or wrong"
will surely help.
Best wishes,
Miguel Quirós
El mié, 05-12-2012 a las 09:
My comment was referring to the OB library, and your implementation is
not in there. As contributed code it may be useful to people, but
having it in the library would expand the capabilities of 'obabel' and
friends.
- Noel
On 4 December 2012 17:55, Igor Filippov [Contr] wrote:
> It's great, Noe
It's great, Noel, but... no MCS in OpenBabel? :(
I completely agree that my implementation is not perfect but it does
work within some reasonable limits...
Igor
On 12/4/2012 12:48 PM, Craig James wrote:
> Very nice ... thanks for doing this. Things like this should be
> available in the OB docu
Hi there,
I'm trying to obtain a rotation matrix between two pdb files containing the
same protein. For many of them the following script works perfectly:
# Load files in OBMol
S = next(pybel.readfile('pdb',struc))
S.removeh()
T = next(pybel.readfile('pdb',target))
T.removeh()
# Align
align = op
I think the underlying problem is that the current aromaticity code is
optimized for the situation where the location of hydrogens is
unknown. This is useful for PDB files, but in the general case, it is
solving a more difficult problem than we need to.
I'm not 100% sure of the interaction between
