Great - thank you!
This will work the same way from C++, correct?
Igor
On Mon, Jul 8, 2013 at 11:42 PM, Greg Landrum <[email protected]>wrote:
> 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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