[Rdkit-discuss] Question about pKa prediction using RDKit

I've been struggling to implement the SMARTS-based pKa prediction algorithm outlined by Crippen here: http://pubs.acs.org/doi/abs/10.1021/ci8001815 This same method has been mentioned elsewhere on this forum: https://sourceforge.net/p/rdkit/mailman/message/27318424/ ;

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

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

[Rdkit-discuss] what if all explicit hydrogens were actual atoms

I'm creating a public-facing data structure that uses the rdkit as the back end. I don't want to expose three different levels of existence for a hydrogen - I want them to be actual Atoms or be implied by valence. What are the consequences of always converting anything the rdkit would return via

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

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, > >

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

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

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

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 =

[Rdkit-discuss] Default behavior of certain calls

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