Re: [Rdkit-discuss] chirality flag

[Greg L. <gre...@gm...>]

yeah. There you can/should set the flag using an unsigned int.


On Tue, Jul 9, 2013 at 5:44 AM, Igor Filippov <igo...@gm...>wrote:

> Great  - thank you!
> This will work the same way from C++, correct?
>
> Igor
>
>
> On Mon, Jul 8, 2013 at 11:42 PM, Greg Landrum <gre...@gm...>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 <gre...@gm...>wrote:
>>
>>> Hi Igor,
>>>
>>> On Tue, Jul 9, 2013 at 1:23 AM, Igor Filippov <igo...@gm...
>>> > 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
>>>
>>
>>
>