I am trying to read a small molecule from PDB file and match its atom
numbers to the same molecule in a SDF file. I have tried both matching
SMART patterns and using OBIsomorphismMapper, both work for 70% of cases.
However there are cases for which OpenBabel can not simply get the right
SMILES from
al SMILES from the ligand repository at the
> PDB and use that for your analysis.
>
> Best,
>
> S
>
>
>
> On 08/31/2016 01:51 PM, Sam Tonddast-Navaei wrote:
>
>> I am trying to read a small molecule from PDB file and match its atom
>> numbers to the s
ng of 1st->16th, 2nd -> 15th.
>
> Hopefully the attached script gives an idea of how to incorporate this
> idea into your code.
>
>
> On Wed, Aug 31, 2016 at 4:51 PM, Sam Tonddast-Navaei > wrote:
>
>> I am trying to read a small molecule from PDB file and matc
Hello,
I am trying to adjust the protonization based on the PH for a given
molecule and I am using pybel and openbabel for python. I am using the
following code:
>>> mol = pybel.readstring('smi', 'C1=CC=C(C=C1)C[C@H](C(=O)[O-])[NH3+]')
> >>> len(mol.atoms)
> 16
> >>> mol.OBMol.AddHydrogens(True,
Hello everyone,
I was trying to filter through the SMILES with missing stereochemistry
information. So I am using the below script to loop over the atoms and
check if the atom is a chiral center and if so, is the stereochemistry
information there or not.
mol = pybel.readstring('smi', smi)
>
mes all nitrogens can invert and are therefore
> non-chiral.
>
> Would you be willing to upload this example as a SMILES or Mol to the
> issue tracker for 2.4.1?
> http://github.com/openbabel/openbabel/issues
>
> Thanks!
> -Geoff
>
>
> On Sep 16, 2016, at 6:28 PM
Hello all,
I am trying to break a molecule into two fragments using Pybel yet keeping
the cis/trans stereochemisty information at the cleavage point when I
substitute it by a dummy atom. Currently I am trying to copy the bond
property (IsUp or IsDown) and assign it to the new bonds (bonds assign
k at the docs for OBStereoFacade and related classes. Stereo is stored
> in a Config object with refs to the four IDs of the atoms connected to the
> atoms of the double bond.
>
> On 19 Nov 2016 11:35 p.m., "Sam Tonddast-Navaei"
> wrote:
>
>> Hello all,
>&
g, and then use
>>> setconfig or something like this.
>>>
>>> On 26 Dec 2016 8:09 p.m., "Sam Tonddast-Navaei"
>>> wrote:
>>>
>>>> Thanks Noel, I figured it out thanks to your hint. Is there a function
>>>> that a
4L)
> OC.C(=CCl)F
Could you please let me know if I am missing something and how I can update
the SMILES?
On Mon, Dec 26, 2016 at 3:41 PM, Sam Tonddast-Navaei
wrote:
> Hahaha, I actually do suck and still stuck :)
> An example script is always helpful and I would really appreciate it i
ng HasCisTransStereo(atom_index).
Could anyone elaborate why is this the case?
Thanks,
Sam
On Mon, Dec 26, 2016 at 5:08 PM, Sam Tonddast-Navaei
wrote:
> Hi Noel,
>
> I made this script:
>
> #!/usr/bin/python
>> import pybel
>> import openbabel as ob
>>
>> mo
ol.AddBond(3, a.GetIdx(), 1)
>
> # Note that the refs uses atom Ids (4294967294 is used to mark an
> implicit stereo ref)
> config.refs = (a.GetId(), 4294967294, 4, 4294967294)
> stereo.SetConfig(config)
>
> print mol.write('smi') # OC.C(=C\Cl)/F
>
>
> On 27 Decembe
Hello all,
Thank you in advance for taking your time and I hope to explain the
problem well. I am trying to find the largest induced subfragment given two
molecules. For example given ATP (Adenosine Triposphate) and Guanine, I
would like the algorithm to return the Purine ring.
I wrote a piece
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