Fw: extracting coordinates

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Fw: extracting coordinates

Andy D P

Hi,
I've identified some atoms matching a SMARTS pattern in a 3d sdf that I want to extract.  I used linecache.getline in Python to pull out the atoms by line number.  This works fine for one molecule in the sdf but with more than one molecule, all the headers for subsequent ones make it difficult to identify atoms by line number.  Is there a way in pybel to directly identify atoms.
thanks
Andy



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Re: Fw: extracting coordinates

Noel O'Boyle
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Is the documentation at http://openbabel.org/wiki/Using_OpenBabel_from_Python#Atoms_and_Molecules unclear?

- Noel

2009/11/15 macc_200 <[hidden email]>

Hi,
I've identified some atoms matching a SMARTS pattern in a 3d sdf that I want to extract.  I used linecache.getline in Python to pull out the atoms by line number.  This works fine for one molecule in the sdf but with more than one molecule, all the headers for subsequent ones make it difficult to identify atoms by line number.  Is there a way in pybel to directly identify atoms.
thanks
Andy



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