Re: [openbabel-scripting] Multiple molecule conversion

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

Regarding the wrapping of streams, you may find the following interesting: 
http://embedded.eecs.berkeley.edu/Alumni/pinhong/scriptEDA/pyTypemapFAQ.html#8

It appears to show a way of wrapping them.

Regards,
 Noel

On Mar 16 2006, Noel O'Boyle wrote:

>I'm not having great luck with this method.
>
>Attempt 1 Using Read after ReadFile
>=========
>from openbabel import *
>
>myfile = "3d.head.sdf"
>obConversion = OBConversion()
>obConversion.SetInFormat("sdf")
>
>mymol = OBMol()
>obConversion.ReadFile(mymol,myfile)
>print mymol.GetMolWt()
>print obConversion.Read(mymol)
>print "The program segfaults before this line"
>
>Attempt 2 Using Read after ReadString
>=========
>from openbabel import *
>
>myfilestring = open("3d.head.sdf","r").read()
>obConversion = OBConversion()
>obConversion.SetInFormat("sdf")
>
>mymol = OBMol()
>obConversion.ReadString(mymol,myfilestring)
>print mymol.GetMolWt()
>print obConversion.Read(mymol)
>print "The program aborts before this line"
>
>>From the python point of view, what is needed is a function that when
>repeatedly called, will return additional molecules. This doesn't need
>to be in the main openbabel library, but can be in the SWIG wrapper
>somewhere.
>
>Regards,
> Noel
>
>On Wed, 2006-03-15 at 14:18 -0500, Geoffrey Hutchison wrote:
>> On Mar 15, 2006, at 5:18 AM, Noel O'Boyle wrote:
>> 
>> > It seems that OBConversion.ReadFile(OBMolecule) just reads in the  
>> > first
>> > molecule, and I cannot see a way of iterating over the molecules.
>> 
>> The OBConversion.Read(OBMol) function should continue to read from  
>> the same file. However, since Python and Perl have no concept of  
>> "streams", it's not possible to use OBConversion.Read() to set up the  
>> input file or string.
>> 
>> So something like this (sorry, I haven't written much Python, so the  
>> syntax might be off):
>> 
>> import openbabel
>> 
>> mol = openbabel.OBMol()
>> conv = openbabel.OBConversion()
>> conv.SetInAndOutFormats("sdf", "sdf")
>> obConversion.ReadString(mol, "test.sdf")
>> 
>> while (obConversion.Read(mol))
>> ...
>> 
>> 
>> Cheers,
>> -Geoff
>
>
>
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