RE: [PyMOL] MDL file

[DeLano, W. <wa...@su...>]

ChemPy has a an SDF class for processing SD files.  Here's an example of
using it to answer your question.

# Python code for reading an SDF file with
# identifier in first line of the MOL record

from pymol import cmd
from chempy.sdf import SDF
from string import join,strip

isdf =3D SDF("input.sdf")
while 1:
	r =3D isdf.read()
	if not r: break
	mol =3D r.get('MOL')
	ident =3D strip(mol[0])
	cmd.read_molstr(join(mol,''),ident)
isdf.close()

# Python code for reading an SD file with
# identifier as separate SD field 'MOLID'=20

from pymol import cmd
from chempy.sdf import SDF
from string import join

isdf =3D SDF("input.sdf")
while 1:
	r =3D isdf.read()
	if not r: break
	mol =3D r.get('MOL')
	ident =3D r.get_single('MOLID')
	cmd.read_molstr(join(mol,''),ident)
isdf.close()

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Szilveszter Juhos [mailto:sz...@ri...]
> Sent: Monday, March 11, 2002 9:27 AM
> To: pym...@li...
> Subject: [PyMOL] MDL file
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>=20
> Dear Pymol Users/Developers,
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> If I have an MDL (.sdf) file with multiple models, how can I=20
> ask pymol to
> load them into separate models? As I checked pymol is reading sdf with
> chempy's reader, so I could access the data field as well somehow.
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> Cheers:
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> Szilva
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20