Re: [OpenBabel-scripting] a question about openbabel python bindings

[Dr N. O'B. <no...@ca...>]

On Jul 22 2006, Rajarshi Guha wrote:

>I'm using the code I got on your website:
>
>obconversion = OBConversion()
>obconversion.SetInFormat("sdf")
>obmol = OBMol()
>
>notatend = obconversion.ReadFile(obmol,"test.sdf")
>while notatend:
>    print obmol.GetMolWt()
>    print obmol.NumAtoms()
>    obmol = OBMol()
>    notatend = obconversion.Read(obmol)
>
>So this is for iterating over the molecules in a single file. I would
>like to do this for multiple files. My question is do I need to make a
>new obmol object (using the first 3 lines) for each input file. Or can I
>just reuse obconversiona and obmol for each new input file?

I don't know the answer to this without checking. It would be reasonable to 
expect that it is possible. Note that you definitely need to create a new 
obmol every time or else it reads in the new atoms into the previous obmol 
(without first wiping it clean - it is more memory efficient to wipe it 
clean though if you do not need to keep the molecule).

You need to test something like the following:

obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()

for filename in ["file1.sdf", "file2.sdf"]:
    notatend = obconversion.ReadFile(obmol, filename)
    while notatend:
        print obmol.GetMolWt()
        print obmol.NumAtoms()
        obmol = OBMol()
        notatend = obconversion.Read(obmol)

Regards,
  Noel