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 <[email protected]>
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
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> Rdkit-discuss mailing list
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