Re: [Rdkit-discuss] Default behavior of certain calls

[Greg Landrum]

That's really cool. Thanks for pointing it out Paolo.

On Thu, Oct 12, 2017 at 7:27 PM, Paolo Tosco  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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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
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Re: [Rdkit-discuss] Default behavior of certain calls

[George Papadatos]

Great example of functools.partial. 
For those who like functional programming, it can also be used with map and 
imap when a function needs more than one parameters. 

George. 

Sent from my giPhone

> On 12 Oct 2017, at 19:04, Andy Jennings  wrote:
> 
> Hi Paolo,
> 
> That's outstanding - thanks very much.
> 
> Best,
> Andy
> 
>> On Thu, Oct 12, 2017 at 10:27 AM, Paolo Tosco  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
>>> 
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> 
>>> 
>>> ___
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>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> 
> 
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Re: [Rdkit-discuss] Default behavior of certain calls

[Andy Jennings]

Hi Paolo,

That's outstanding - thanks very much.

Best,
Andy

On Thu, Oct 12, 2017 at 10:27 AM, Paolo Tosco  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
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> ___
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> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
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Re: [Rdkit-discuss] Default behavior of certain calls

[Paolo Tosco]

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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