Thanks, Stephan, for the quick response! OK, I think I can do the patch for the current version installation instead of numpy downgrade, and for future versions this will be solved.
João
From: Stephan Schott <s.schott-verdugo.fz-juelich.de>
Sent: Tuesday, August 8, 2023 3:51 PM
To: Damas Joao CHST <Joao.Damas.syngenta.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Issue with deprecated np.float when using packmol-memgen
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Hi again,
Indeed there are 2 calls for np.float which should be changed. I will pass a patch for this. In the meantime, if this is needed urgently, you can either downgrade numpy within miniconda to 1.23, or change the calls in v3numpy.py<
http://v3numpy.py>
sed -i "s/np.float/float/" /progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py
Best regards,
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
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Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
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El mar, 8 ago 2023 a las 11:51, Stephan Schott (<s.schott-verdugo.fz-juelich.de<mailto:s.schott-verdugo.fz-juelich.de>>) escribió:
Hi Joao,
I haven't those aliases, so indeed it could be the case this is failing. I'll have a look and get back to you.
Cheers,
Stephan Schott Verdugo
Biochemist
Computational Biophysical Chemistry
Institut für Bio- und Geowissenschaften / Bioinformatik (IBG-4)
Forschungszentrum Jülich GmbH
Wilhelm-Johnen-Straße, 52425 Jülich
Germany
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
El mar, 8 ago 2023 a las 11:26, Damas Joao CHST via AMBER (<amber.ambermd.org<mailto:amber.ambermd.org>>) escribió:
Dear all,
I have AmberTools 23 installed through the source on a cluster, and recently one of my users reported the following when using packmol-memgen:
Traceback (most recent call last):
File "/progs/all/opensource/ambertools/23/bin/packmol-memgen", line 189, in <module>
packmol_memgen.main(args)
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/main.py", line 895, in main
grid = pdbvol(pdb)
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/main.py", line 784, in pdbvol
atoms = pdbatoms.read_pdb("temp.pdb")
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py", line 212, in read_pdb
atoms.append(AtomFromPdbLine(line))
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py", line 128, in AtomFromPdbLine
atom = Atom()
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py", line 43, in __init__
self.pos = v3.vector() if pos is None else pos
File "/progs/all/opensource/ambertools/23/lib/python3.10/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py", line 29, in vector
return np.zeros(3, dtype=np.float)
File "/progs/all/opensource/ambertools/23/miniconda/lib/python3.10/site-packages/numpy/__init__.py", line 305, in __getattr__
raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'float'.
`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations<
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations>. Did you mean: 'cfloat'?
I did not change any parameters other than the prefix, so I assume the code just needs to be updated to match the more recent version of NumPy. The one that gets installed on my system is version 1.24. Or is there something that I should change from the installation perspective?
Thank you,
João
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Received on Tue Aug 08 2023 - 07:00:02 PDT
