On 09/10/2016 12:08 PM, David Cosgrove wrote:
> On the subject of the documentation, I would encourage you to find the
> GettingStartedWithRDKit.rst in the Docs directory, find somewhere where
> this discussion fits, add it, and send the new version to Greg. If everyone
> did this every time they
Hi Rocco et al.,
I too found this a very clear explanation of the different classes of
hydrogen so many thanks for taking the time. Where would a chiral H fit in?
The sort of H from Cl[C@H](F)Br? That one needs to stay even if you
collapse all explicit H atoms to implicit.
On the subject of the
How about "explicit", rather than "physical", hydrogens?
-P.
Sent from a cell phone. Please forgive brvty and m1St@kes.
On Sep 9, 2016 1:57 AM, "Greg Landrum" wrote:
>
>
> On Thu, Sep 8, 2016 at 10:35 PM, Dimitri Maziuk
> wrote:
>
>> On
On 09/09/2016 12:56 AM, Greg Landrum wrote:
> This is absolutely correct: if you remove the Hs and then later re-add them
> it is extremely unlikely that you will end up with the same H indices
> before and after the change. It makes much more sense to just use
> removeHs=False
That's what I
On Thu, Sep 8, 2016 at 10:35 PM, Dimitri Maziuk
wrote:
> On 09/08/2016 02:26 PM, Brian Kelley wrote:
> > Dimitri, Hs are removed.
> >
> > Their is a removeHs argument in MolFromMolBlock (python) that defaults to
> > true.
> >
> > There is a corollary in SDMolSupplier if
Thanks for this writeup Rocco. You're right that there's not an easy to
find and understand collection of this information. That's one of those
gaps in the documentation that I should eventually address. This is already
a pretty good start though.
-greg
On Thu, Sep 8, 2016 at 9:37 PM, Rocco
On Thu, Sep 8, 2016 at 10:47 PM, Dimitri Maziuk
wrote:
> On 09/08/2016 02:37 PM, Rocco Moretti wrote:
>
> > (2) There's special complications here that there are certain structures,
> > such as imidazole, which needs physical or explicit hydrogens on one of
> the
> >
On 09/08/2016 02:26 PM, Brian Kelley wrote:
> Dimitri, Hs are removed.
>
> Their is a removeHs argument in MolFromMolBlock (python) that defaults to
> true.
>
> There is a corollary in SDMolSupplier if you are using that.
>
> supplier = SDMolSupplier(filename, removeHs=false)
>
> if this
On Mon, Mar 18, 2013 at 2:36 PM, Syeda Sabrina sus364...@gmail.com wrote:
Hi Greg,
If this is working as it is supposed to be then I don't understand why even
if I add only explicit Hydrogens to a molecule and check the number the of
explicit Hydrogens attached to it later why it returns
Hello Greg,
Thanks for your input. Well, basically the current version of
RunReactants() deals with the implicit Hs in some cases, so I was trying to
make some new function for my code that will replace the implicit Hs by
some other similar atom (e.g. At) and then once I am done with the
I meant to say probably current version of the RunReactants messes up with
the implicit Hs in some cases.
I am not sure though. This is a guess and trying to see how it deals with
the problematic cases if I replace those implicit Hs with some other
similar atom.
Sorry for the confusion!
Thanks
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