Hi,
On Friday, July 3, 2015, Hitesh Patel <[email protected]> wrote:
> Hi Greg,
>
> At first priority, I will use mol2 format. A s shown in mol2 format
> explanation, we can set user specified atom attributes. I copied the text
> below for your convenience. See the bold text.
>
The rdkit does not yet have a mol2 writer, so that isn't an option.
> For second priority, I can use mol files.
> There I have to set
> Properties block:
>
> - M ALS - atom list and exclusive list
> - M APO - Rgroup attachment point
> - M CHG - charge
> - .....
>
> But, I am not sure, whether the user defined property block is allowed or
> not.
>
M CHG and M ALS are already used by the rdkit when atoms have charges or
there are list queries. M APO is not used, but that's because I have never
managed to figure out how to adapt the MDL R Group idea to something
sensible in the context of the rdkit.
Which one looks feasible??
>
I'm still not sure of what kind of custom properties you are looking to
write.
-greg
>
>
>
> On Fri, Jul 3, 2015 at 4:45 PM Greg Landrum <[email protected]
> <javascript:_e(%7B%7D,'cvml','[email protected]');>> wrote:
>
>> 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]
>> <javascript:_e(%7B%7D,'cvml','[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]>
>>> 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]]
>>>> *Sent:* 03 July 2015 14:21
>>>> *To:* [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?
>>>>
>>>
>>> --
>
> Regards,
>
> Dr. Hitesh Patel
> Post-Doctoral Fellow,
> Technische Universität Dortmund,
> Chemische Biologie,
> Otto-Hahn-Straße 6,
> 44227, Dortmund,
> Germany
>
> Room: C1-05-181
> Work: 0231 755-4740
> Mob.: +49 (0)176 5544 6467
> Email: [email protected]
>
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