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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