Hi Paolo,
That's outstanding - thanks very much.
Best,
Andy
On Thu, Oct 12, 2017 at 10:27 AM, Paolo Tosco <paolo.to...@unito.it> wrote:
> Dear Andy,
>
> you may accomplish that within the scope of a Python script using
> functools.partial:
>
> In [1]: from rdkit import Chem
>
> In [2]: import functools
>
> In [3]: # redefine Chem.SDMolSupplier to include a custom default parameter
>
> In [4]: Chem.SDMolSupplier = functools.partial(Chem.SDMolSupplier,
> removeHs = False)
>
> In [5]: suppl = Chem.SDMolSupplier('/home/paolo/sdf/bilastine.sdf')
>
> In [6]: # hydrogens have not been stripped
>
> In [7]: suppl[0].GetNumAtoms()
> Out[7]: 71
>
> In [8]: # If you wish to invoke the original function with the original
> default parameter:
>
> In [9]: suppl = Chem.SDMolSupplier.func('/home/paolo/sdf/bilastine.sdf')
>
> In [10]: # hydrogens have been stripped as the original function was
> invoked
>
> In [11]: suppl[0].GetNumAtoms()
> Out[11]: 34
>
> HTH, cheers
> p.
> On 10/12/17 18:09, Andy Jennings wrote:
>
> Hi,
>
> First off: great work on the RDKit - a great resource for those of us that
> like to cook up our own solutions to problems.
>
> The default behavior of certain calls (e.g. Chem.SDMolSupplier,
> Chem.MolToSmiles) has default behavior that is the opposite of what I would
> generally want. For instance I might be processing docking files and want
> to keep those pesky hydrogens, or I want to keep the stereochemical
> information when I dump a smiles string.
>
> I can understand why the current defaults might have been arrived at so
> I'm not advocating the change in default behavior. Rather, I'm curious if
> one could set the default behavior for an entire script (I write mostly
> python). It maybe/is lazy of me but every so often I get caught out and
> have to backtrack through a workflow.
>
> Best,
> Andy
>
>
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