This is way cleaner than the whole "SetData(...)" hack.
Well done. And thanks for pointing it out.
-
Jean-Paul Ebejer
Early Stage Researcher
On 29 January 2012 12:13, Greg Landrum <[email protected]> wrote:
> Hi Jean-Paul,
>
> On Sat, Jan 28, 2012 at 3:18 PM, JP <[email protected]> wrote:
> >
> > I would like to use ForwardSDMolSupplier to read directly from standard
> in.
> >
> > This is possible using the normal SDMolSupplier by using something like:
> >
> > supp = Chem.SDMolSupplier()
> > data = sys.stdin.read()
> > ## NB This is not the nicest way to do it - especially if the file is
> > massive (it is held in variable data) - but will do.
> > suppl.SetData(data, sanitize = True)
> > data = None # <- do this last step to free up memory in case the file
> is
> > large
> >
> > Can the empty constructor and SetData be added to ForwardSDMolSupplier ?
> > (possibly this is common behaviour across all Suppliers... and its
> righteous
> > place is in the superclass)
>
> All you need to do is construct a ForwardSDMolSupplier using sys.stdin.
> Here's an example:
>
> ~/Projects/Benchmarks > cat mols_from_stdin.py
> from rdkit import Chem
> import sys
>
> nGood=0
> nBad=0
> for mol in Chem.ForwardSDMolSupplier(sys.stdin):
> if mol is None:
> nBad+=1
> else:
> nGood+=1
>
> print '%d good, %d bad'%(nGood,nBad)
>
> ~/Projects/Benchmarks > python mols_from_stdin.py < PubChemBackground.sdf
> 10000 good, 0 bad
>
> Best,
> -greg
>
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