I can't seem to reproduce the problem.
Here's an example showing that the original atom coordinates are preserved
when Chem.AddHs is called with the addCoords argument:
#--------------------------------
In [9]: mb="""
...: Mrv0541 08211405312D
...:
...: 6 6 0 0 0 0 999 V2000
...: -3.5578 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0
...: -4.2723 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0
...: -4.2723 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0
...: -3.5578 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0
...: -1.8268 -0.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0
...: -2.8433 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
0
...: 1 2 1 0 0 0 0
...: 1 6 2 0 0 0 0
...: 2 3 2 0 0 0 0
...: 3 4 1 0 0 0 0
...: 4 5 2 0 0 0 0
...: 5 6 1 0 0 0 0
...: M END
...: """
In [10]: m = Chem.MolFromMolBlock(mb)
In [11]: nm = Chem.AddHs(m,addCoords=True)
In [12]: print Chem.MolToMolBlock(nm)
RDKit 2D
12 12 0 0 0 0 0 0 0 0999 V2000
-3.5578 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.2723 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.2723 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5578 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8268 -0.7219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8433 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5578 1.9250 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
-5.2249 0.9625 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
-5.2249 -0.9625 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
-3.8108 -1.8955 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
-0.8095 -1.1404 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
-2.1500 1.2665 0.0000 H 0 0 0 0 0 1 0 0 0 0 0 0
1 2 2 0
1 6 1 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
1 7 1 0
2 8 1 0
3 9 1 0
4 10 1 0
5 11 1 0
6 12 1 0
M END
#--------------------------------
Note that addCoords does add the Hs in 3D:
#--------------------------------
In [5]: print Chem.MolToMolBlock(m)
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
-0.7500 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
In [7]: nm=Chem.AddHs(m,addCoords=True)
In [8]: print Chem.MolToMolBlock(nm)
RDKit 2D
8 7 0 0 0 0 0 0 0 0999 V2000
-0.7500 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1167 0.0000 1.0371 H 0 0 0 0 0 1 0 0 0 0 0 0
-1.1167 0.8981 -0.5185 H 0 0 0 0 0 1 0 0 0 0 0 0
-1.1167 -0.8981 -0.5185 H 0 0 0 0 0 1 0 0 0 0 0 0
1.1167 -0.0000 1.0371 H 0 0 0 0 0 1 0 0 0 0 0 0
1.1167 -0.8981 -0.5185 H 0 0 0 0 0 1 0 0 0 0 0 0
1.1167 0.8981 -0.5185 H 0 0 0 0 0 1 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
#--------------------------------
It is probably feasible to modify the code to add Hs in 2D when the
conformer is 2D, but it's likely a non-trivial amount of work and, as
Dimitri pointed out, there are many situations where the results aren't
going to look particularly good.
-greg
On Wed, Aug 20, 2014 at 7:34 PM, Greg Landrum <[email protected]>
wrote:
>
>
> On Wednesday, August 20, 2014, Michał Nowotka <[email protected]> wrote:
>
>>
>> I've just checked and actually adding this flag doesn't solve my problem.
>> It seems that adding this flag actually calls Compute2dCoords (at
>> least this is how it looks like), because all coordinates are computed
>> from scratch, for example if my compound was translated by some vector
>> on 2D plane, after executing addHs it will be centered, if the
>> compound had one atom dragged unusually, it will be aligned back.
>>
>> The only difference between this flag and calling Compute2dCoords is
>> that H bonds are longer, which actually looks worse...
>>
>>
> Hmmm, that doesn't sound like what is supposed to happen. I think that
> it should just add coords for the Hs that it adds. I will take a look
> tomorrow morning to see what is going on. There may be something odd for
> 2d conformers, but I really don't think it should redo the whole
> coordinate generation.
>
> -greg
>
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