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
On 09/09/2016 12:07 PM, Peter S. Shenkin wrote:
> How about "explicit", rather than "physical", hydrogens?
As a programmer I'd prefer the obmol in a dependable known state at all
times. I'd always put all H atom nodes in the molecule graph: calculate
them from "explicit" charges and/or "implicit"
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 09/08/2016 02:26 PM, Brian Kelley wrote:
>> > Dimitri, H
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 expe
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 you are using that.
> >
>
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 More
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
> > nitrogens in order to Kekuliz
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
> nitrogens in order to Kekulize properly. If you're implicit only, the RDKit
> sanitizer will chok
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 helps.
Greg can correct me if I'm wrong(1), but in RDKit there's actually three
"levels" of hydrogens:
* "Physical" hydrogens, which are represented as actual, independent atoms
in the atom graph. ("Physical hydrogens" is what I'm calling them - I don't
know if RDKit has an official term for them.)
* "E
False should be capitalized in python:
supplier = SDMolSupplier(filename, removeHs=False)
And their == there of course :) Sometime I type faster than I think.
On Thu, Sep 8, 2016 at 3:26 PM, Brian Kelley wrote:
> Dimitri, Hs are removed.
>
> Their is a removeHs argument in MolFromMolBlock (
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 helps.
On Thu, Sep 8, 2016 at 2:46 PM, Dimitri Maziuk
wrote:
> On 0
On 09/08/2016 10:25 AM, Greg Landrum wrote:
...
> Why do you want 2D drawings that include H atoms?
On the subject of H atoms: when I read in the MOL file that has them, I
need to explicitly call AddHs() in order to have them drawn.
Question: do they actually get stripped off by the reader and re
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
S
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
RunReacta
On Mon, Mar 18, 2013 at 2:36 PM, Syeda Sabrina 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 zero and in case o
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 zero and in case of
implicit hydrogen it is returning the other one?
>> m = Chem.
Hi,
On Fri, Mar 15, 2013 at 3:56 PM, Syeda Sabrina wrote:
> I was trying to how understand how the AddHs ()works and how I can relate
> its output with the GetNumExplicitHs() to see how many explicit hydrogens
> were added. But It seems like AddHs does not work correctly. Below is the
> code that
I was trying to how understand how the AddHs ()works and how I can relate
its output with the GetNumExplicitHs() to see how many explicit hydrogens
were added. But It seems like AddHs does not work correctly. Below is the
code that I used.
m = Chem.MolFromSmiles('C')
for a in m.GetAtoms():
pr
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