Re: [Rdkit-discuss] AddHs()

2016-09-13 Thread Dimitri Maziuk
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

Re: [Rdkit-discuss] AddHs()

2016-09-10 Thread David Cosgrove
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

Re: [Rdkit-discuss] AddHs()

2016-09-09 Thread Peter S. Shenkin
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

Re: [Rdkit-discuss] AddHs()

2016-09-09 Thread Dimitri Maziuk
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

Re: [Rdkit-discuss] AddHs()

2016-09-08 Thread Greg Landrum
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

Re: [Rdkit-discuss] AddHs()

2016-09-08 Thread Greg Landrum
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

Re: [Rdkit-discuss] AddHs()

2016-09-08 Thread Greg Landrum
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 > >

Re: [Rdkit-discuss] AddHs()

2016-09-08 Thread Dimitri Maziuk
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

Re: [Rdkit-discuss] AddHs returns weird results

2013-03-19 Thread Greg Landrum
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

Re: [Rdkit-discuss] AddHs returns weird results

2013-03-19 Thread Syeda Sabrina
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

Re: [Rdkit-discuss] AddHs returns weird results

2013-03-19 Thread Syeda Sabrina
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