Hello all,
I've been trying to output my 3D mol object that has Gasteiger charges to
mol2 file format. How would I go about that? I've only found it for mol and
pdb.
Here is the code I'be been using if that helps:
~~~
from rdkit
ote:
> Hi James,
>
> Due to problems with the general ambiguity of the format the RDKIt does
> not have a mol2 writer.
>
> -greg
>
>
>
>
>
> On Mon, Oct 31, 2016 at 12:22 AM +0100, "James Johnson" <
> totalboron...@gmail.com> wrote:
>
>
s, here I have set each partial charge as an atom
> property. When you read in the SDF file, the partial charge for each atom
> can be accessed with
>
> partialCharge = float(atom.GetProp('molFileAlias'))
>
> In the same way you may also associate to each a name or any o
Hello all, I am trying to generate R and S from: CCC(C)(Cl)Br
Below is the code for making the smi to mol file. Can someone give me some
guidance to generate all sterochem possibilities?
The code would also need to work for 2 stereocenters such as:
RR, RS, SR, SS
or
RE, RZ, SE, SZ
etc.
Thanks!
n Thu, 8 Dec 2016 23:21:24 -0800
> James Johnson wrote:
>
> > Hello all, I am trying to generate R and S from: CCC(C)(Cl)Br
> >
> > Below is the code for making the smi to mol file. Can someone give me
> some
> > guidance to generate all sterochem possibilitie
Thank you all again for the great responses! :)
There seems to be a consensus between Andrew and Pavel that the solution is
with SetBondDir(). I've tried Pavel's functions get_unspec_double_bonds()
and set_double_bond_stereo() in python 2 (couldn't figure out how to get
RDkit set up in python 3, b
Dear All,
I'm generating analogs from a parent compound. An unfortunate side effect
is the generation of various highly strained rings among other compounds.
I'm developing filters to deal with any unwanted generated compounds, but
I'm having difficulty with strained ring systems.
Attached are so
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