Hi Greg,
Thank you, I can reproduce your example, and my own case works fine now...
Best,
Michal
On Mon, 25 Feb 2019 at 14:26, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Michal,
>
> Which version of the RDKit are you using? This should already be working.
> Here's an example demonstrating that:
>
> In [16]: m = Chem.AddHs(Chem.MolFromSmiles('c1ccccc1.N'))
>
> In [17]: AllChem.EmbedMolecule(m)
> Out[17]: 0
>
> In [18]: fs = Chem.GetMolFrags(m,asMols=True)
>
> In [19]: print(Chem.MolToMolBlock(fs[0]))
>
> RDKit 3D
>
> 12 12 0 0 0 0 0 0 0 0999 V2000
> 0.7943 -1.1490 0.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.3607 0.1298 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.5898 1.2681 -0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7866 1.1450 -0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.3413 -0.1124 0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.5806 -1.2656 0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4026 -2.0428 0.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4183 0.2113 -0.0036 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.0075 2.2686 -0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4182 2.0293 -0.0265 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.4222 -0.2172 0.0037 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0241 -2.2652 0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 2 0
> 2 3 1 0
> 3 4 2 0
> 4 5 1 0
> 5 6 2 0
> 6 1 1 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
>
>
> In [20]: print(Chem.MolToMolBlock(fs[1]))
>
> RDKit 3D
>
> 4 3 0 0 0 0 0 0 0 0999 V2000
> -0.0066 -0.0099 0.2620 N 0 0 0 0 0 0 0 0 0 0 0 0
> -0.4136 0.8845 -0.0859 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.5574 -0.8197 -0.0901 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9775 -0.0549 -0.0860 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 1 3 1 0
> 1 4 1 0
> M END
>
>
> In [21]: print(Chem.MolToMolBlock(m))
>
> RDKit 3D
>
> 16 15 0 0 0 0 0 0 0 0999 V2000
> 0.7943 -1.1490 0.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.3607 0.1298 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.5898 1.2681 -0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7866 1.1450 -0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.3413 -0.1124 0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.5806 -1.2656 0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0066 -0.0099 0.2620 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4026 -2.0428 0.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.4183 0.2113 -0.0036 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.0075 2.2686 -0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4182 2.0293 -0.0265 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.4222 -0.2172 0.0037 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0241 -2.2652 0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.4136 0.8845 -0.0859 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.5574 -0.8197 -0.0901 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9775 -0.0549 -0.0860 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 2 0
> 2 3 1 0
> 3 4 2 0
> 4 5 1 0
> 5 6 2 0
> 6 1 1 0
> 1 8 1 0
> 2 9 1 0
> 3 10 1 0
> 4 11 1 0
> 5 12 1 0
> 6 13 1 0
> 7 14 1 0
> 7 15 1 0
> 7 16 1 0
> M END
>
>
>
> Best,
> -greg
>
>
> On Mon, Feb 25, 2019 at 5:54 AM Michal Krompiec <michal.kromp...@gmail.com>
> wrote:
>
>> Hello,
>> Let mol be a molecule with a conformer with 3D coordinates, consisting of
>> 2 fragments. Chem.GetMolFrags(mol, asMols=true) returns these fragments as
>> Molecule objects, but the 3D coordinates are lost. Is there any way to
>> preserve them?
>> Best,
>> Michal
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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