Ok, it's checked in:
In [2]: m = Chem.MolFromSmiles('C[C@H](F)Cl')
In [3]: print Chem.MolToMolBlock(m)
RDKit
4 3 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 0
M END
In [5]: m.SetProp("_MolFileChiralFlag","1")
In [6]: print Chem.MolToMolBlock(m)
RDKit
4 3 0 0 1 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 0
M END
The same flag will be set if the chiral flag is set when the mol block is
parsed.
-greg
On Tue, Jul 9, 2013 at 5:08 AM, Greg Landrum <[email protected]> wrote:
> Hi Igor,
>
> On Tue, Jul 9, 2013 at 1:23 AM, Igor Filippov
> <[email protected]>wrote:
>
>> I noticed that RDKit generated MDL MOL file without the chirality flag
>> set on the top of the mol
>> block (there are stereo atoms with wedge and hash bonds present in the
>> molecule):
>>
>> RDKit 2D
>>
>> 796808 0 0 0 0 0 0 0 0999 V2000
>>
>> Is there any way to tell MolToMolBlock() to set the chirality flag?
>>
>>
> There currently is no way to do this. I will add support for it (via a
> molecule property) for the next release.
>
> -greg
>
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