RE: [PyMOL] .xyz file loading problem from chempy module

[Warren D. <wa...@de...>]

Dmitriy,

The very latest beta versions of PyMOL can read .xyz files directly (via
the "load" or "load_raw" commands). =20

http://delsci.com/beta

load_raw usage:

my_xyz=3Dopen("some.xyz").read()
cmd.load_raw(my_xyz, 'xyz', "my_xyz")

I suspect the chempy XYZ file is limited to reading Tinker's
fixed-column XYZ format.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Dmitriy
> Sent: Friday, November 04, 2005 6:34 AM
> To: pym...@li...
> Subject: [PyMOL] .xyz file loading problem from chempy module
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> Hello everyone
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> It seems to be a problem with loading an .xyz file as a chempy model.
> For example doing
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> from chempy import io
> m =3D io.xyz.fromFile("some.xyz")
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> gives:
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> chempy: reading "some.xyz".
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File=20
> "/home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py",
> line 185, in fromFile
> TypeError: fromList() takes exactly 1 argument (2 given)
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> If I've got the right idea whats going on, there should be
> fromList(self,list)  function in xyz.py which will hide the=20
> Storage one.
> Like it's done in pdb.py (it works fine for io.pdb.fromFile)
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> I'm trying to establish a communication between my program=20
> and pymol in a simple .xyz format. Sending a list of strings,=20
> creating a chempy model and loading it into pymol will work.=20
> If there is some workaround or a fix for problem mention above.
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> Warren, Is it possible to implement a way of passing .xyz=20
> file as a string, not as a list of strings or a file? I've=20
> seen molstr, pdbstr etc. but not xyzstr.=20
> And a short description how to load pdbstr for example it in=20
> this way will be great.
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> Thanks
>   Dmitriy
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