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

[Brian K. <fus...@gm...>]

I agree.  I tend to think molecules should have GetName/SetName since this is a common operation.

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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