Re: [Rdkit-discuss] property of name in smilesMolSupplier

[Greg L. <gre...@gm...>]

On Thu, Oct 13, 2016 at 2:30 PM, Brian Kelley <fus...@gm...> wrote:

> I agree.  I tend to think molecules should have GetName/SetName since this
> is a common operation.
>
>
I used to argue about this point, but at this point I've either been
convinced or just gotten tired of the argument, so I'd be happy to accept
the PR.

;-)

-greg



> One note though:
>
> mol.GetPropsAsDict()
>
> Might help with introspection.  There are optionally arguments that allow
> looking at private and computed properties, I.e.
>
> mol.GetPropsAsDict(True,True)
>
> I believe will list them all.
>
> ----
> Brian Kelley
>
> On Oct 13, 2016, at 6:31 AM, 杨弘宾 <yan...@16...> wrote:
>
> Hi，
>     I spent a lot of time to explorer "How to get the property of name
> when using SmilesMolSupplier"
>
> I had a smiles file like this:
> ===
> c1ccccc1\t1\n
> ...
> ===
> where 1 means that it is positve
>
> So I wanted to read this smiles file via SMilesMolSupplier and I knew that
> the second column is the default name column.
> suppl = Chem.SmilesMolSupplier('compounds.smi',delimiter='\t',
> titleLine=False)
>
> However, I could not get the property of 1 because I had no idea what the
> property_name was.
> In the document, it shows that :
>
> If the input file has a title line and more than two columns (smiles and id), the
> additional columns will be used to set properties on each molecule.  The properties
> are accessible using the mol.GetProp(propName) method.
>
> But It was a "no title table", So I thought its property_name of "their names" should be "Name" or "name" as default. And I failed...
>
> After read the source code, I found that it should be _Name
>
> https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp#L194
>
> I think the document should be improved so that others may know how to get the name of each compound
>
> BTW, I tried to use suppl[0].GetPropNames() but only to get "<rdkit.rdBase._vectclass std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > at 0x7402e90>" that seemed tell nothing. I wondered that is there any way to make it readable in python?
>
>
>
> ------------------------------
> Hongbin Yang 杨弘宾
> Research: Toxicophore and Chemoinformatics
> Pharmaceutical Science, School of Pharmacy
> East China University of Science and Technology
>
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