Re: [Rdkit-discuss] Deep Copy of Molecule

[Rich L. <rl...@ca...>]

Hi Dave,

I actually came across this perculiarity yesterday!  I think the problem is that the copy built-in module only works properly with Python objects, and rdkit Mol objects are really C++ objects (I’m sure someone else can give a better explanation). The solution that seemed to work for me is to call the Mol constructor rather than use the copy module:

In [1]: from rdkit import Chem
In [2]: mol = Chem.MolFromSmiles('c1ccccc1')
In [3]: mol.SetProp('_Name', 'One')
In [4]: mol.SetProp('Prop', '1')
In [5]: mol2 = Chem.Mol(mol)
In [6]: print mol2.GetProp('_Name')
One
In [7]: print mol2.GetProp('Prop')
1

This seems to create a copy rather than just another reference to the same C++ object.

In [8]: mol.SetProp('check_if_same', 'mol')
In [9]: mol2.SetProp('check_if_same', 'mol2')
In [10]: mol.GetProp('check_if_same')
Out[10]: 'mol'
In [11]: mol2.GetProp('check_if_same')
Out[11]: 'mol2'

Hope this helps!

Rich
--
Richard Lewis
PhD Candidate
Centre for Molecular Informatics
University of Cambridge
http://www.ch.cam.ac.uk/group/bender <http://www.ch.cam.ac.uk/group/bender>
> On 27 Mar 2015, at 09:41, Dave Wood <dav...@mo...> wrote:
> 
> Dear All,
> 
> I was a little suprised by this behaviour when making a copy of a molecule. Is it the expected behaviour?
> 
> It isn't a problem for me as I can copy the properties across seperately, but I thought it could be worth mentioning.
> 
> Dave
> 
> IPython 1.2.1 -- An enhanced Interactive Python.
> ?         -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help      -> Python's own help system.
> object?   -> Details about 'object', use 'object??' for extra details.
> 
> In [1]: from rdkit import Chem
> In [2]: import copy
> In [3]: mol = Chem.MolFromSmiles("c1ccccc1")
> In [4]: mol.SetProp("_Name", "One")
> In [5]: mol.SetProp("Prop", "1")
> In [6]: mol2 = copy.deepcopy(mol)
> In [7]: print mol2.GetProp("_Name")
> ---------------------------------------------------------------------------
> KeyError                                  Traceback (most recent call last)
> <ipython-input-7-9ad92b63b870> in <module>()
> ----> 1 print mol2.GetProp("_Name")
> 
> KeyError: '_Name'
> 
> In [8]: print mol2.GetProp("Prop")
> ---------------------------------------------------------------------------
> KeyError                                  Traceback (most recent call last)
> <ipython-input-8-668c3857671a> in <module>()
> ----> 1 print mol2.GetProp("Prop")
> 
> KeyError: 'Prop'
> 
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