Hitesh,
It is certainly possible to set atom properties. I don't think any of the
output formats the rdkit can generate really support atom properties
though. What format did you envision writing and how would the atom
properties be encoded?
-greg
On Friday, July 3, 2015, Hitesh Patel <[email protected]> wrote:
> Hi Josh,
> Thanks for your quick reply. But, sorry, I want to set atom properties,
> not molecule properties. Like,
>
> atom = m.GetAtomWithIdx(5)
> atom.SetProp('my_property', 'value_of_my_property')
>
> I want to save this property associated with each atom.
>
> Regards,
>
> Hitesh Patel
>
> On Fri, Jul 3, 2015 at 3:41 PM, Campbell J.E. <[email protected]
> <javascript:_e(%7B%7D,'cvml','[email protected]');>> wrote:
>
>> Hi Hitesh
>>
>>
>>
>> I use the PropertyMol object to save molecules with properties, setting a
>> property for a molecule is fairly simple,
>>
>>
>>
>> m.SetProp("_Name",”mol_name")
>>
>>
>>
>> for m in mol_lst:
>>
>> pm = AllChem.PropertyMol(m)
>>
>> pm.SetProp("_Name", name)
>>
>> pm.SetProp("_Energy", None)
>>
>> dump_list.append(pm)
>>
>> cPickle.dump(dump_list, open(p_name, "w+"))
>>
>>
>>
>> Then something like this will allow you to act on the molecules again.
>>
>>
>>
>> mol_list = cPickle.load( open(p_name, "rb" ) )
>>
>>
>>
>> Hope this helps.
>>
>>
>>
>> Josh Campbell
>>
>>
>>
>> *From:* Hitesh Patel [mailto:[email protected]
>> <javascript:_e(%7B%7D,'cvml','[email protected]');>]
>> *Sent:* 03 July 2015 14:21
>> *To:* [email protected]
>> <javascript:_e(%7B%7D,'cvml','[email protected]');>
>> *Subject:* [Rdkit-discuss] Save files with new atom properties and read
>> again
>>
>>
>>
>> Hi there,
>>
>> I am new to RDkti.
>>
>> Is there a way to save custom property for each atoms and save that to
>> any file format and use it again?
>>
>
>
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