Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates
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 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('c1c1.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 -1.14900.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.36070.1298 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.58981.2681 -0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.78661.1450 -0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.3413 -0.11240.0019 C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.5806 -1.26560.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4026 -2.04280.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.41830.2113 -0.0036 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.00752.2686 -0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
>-1.41822.0293 -0.0265 H 0 0 0 0 0 0 0 0 0 0 0 0
>-2.4222 -0.21720.0037 H 0 0 0 0 0 0 0 0 0 0 0 0
>-1.0241 -2.26520.0304 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 -0.00990.2620 N 0 0 0 0 0 0 0 0 0 0 0 0
>-0.41360.8845 -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 -1.14900.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.36070.1298 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.58981.2681 -0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.78661.1450 -0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.3413 -0.11240.0019 C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.5806 -1.26560.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.0066 -0.00990.2620 N 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4026 -2.04280.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.41830.2113 -0.0036 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.00752.2686 -0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
>-1.41822.0293 -0.0265 H 0 0 0 0 0 0 0 0 0 0 0 0
>-2.4222 -0.21720.0037 H 0 0 0 0 0 0 0 0 0 0 0 0
>-1.0241 -2.26520.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
>-0.41360.8845 -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
> 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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Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates
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('c1c1.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 -1.14900.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
1.36070.1298 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
0.58981.2681 -0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.78661.1450 -0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3413 -0.11240.0019 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5806 -1.26560.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4026 -2.04280.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
2.41830.2113 -0.0036 H 0 0 0 0 0 0 0 0 0 0 0 0
1.00752.2686 -0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.41822.0293 -0.0265 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4222 -0.21720.0037 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0241 -2.26520.0304 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 -0.00990.2620 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.41360.8845 -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 -1.14900.0150 C 0 0 0 0 0 0 0 0 0 0 0 0
1.36070.1298 -0.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
0.58981.2681 -0.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.78661.1450 -0.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3413 -0.11240.0019 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5806 -1.26560.0170 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0066 -0.00990.2620 N 0 0 0 0 0 0 0 0 0 0 0 0
1.4026 -2.04280.0267 H 0 0 0 0 0 0 0 0 0 0 0 0
2.41830.2113 -0.0036 H 0 0 0 0 0 0 0 0 0 0 0 0
1.00752.2686 -0.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.41822.0293 -0.0265 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4222 -0.21720.0037 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0241 -2.26520.0304 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.41360.8845 -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
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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[Rdkit-discuss] Chem.GetMolFrags and 3D coordinates
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
