Comments (15)
@JSurayut is there any chance that you have pytraj source code in your desktop and you opened jupyter in the location having pytraj?
from pytraj.
from pytraj.
hi @JSurayut, how did you install pytraj?
(e.g: you can install AmberTools that includes pytraj: https://ambermd.org/GetAmber.php)
from pytraj.
from pytraj.
No, I have checked in my folder that I opened jupyter, It does not have any pytraj source code.
from pytraj.
um, that's odd. can you try import parmed; print(parmed)
to see if that works?
from pytraj.
Your issue is similar to #1565
from pytraj.
um, that's odd. can you try
import parmed; print(parmed)
to see if that works?
I try this and It show a message
ImportError Traceback (most recent call last)
in ()
----> 1 import parmed
/home/cadd/amber22/lib/python3.10/site-packages/parmed/init.py in ()
19
20 from . import exceptions, periodic_table, residue
---> 21 from . import unit, utils
22 from .topologyobjects import *
23 from .structure import Structure, StructureView
/home/cadd/amber22/lib/python3.10/site-packages/parmed/utils/init.py in ()
2 from ..exceptions import MoleculeError as _MoleculeError
3 from .pairlist import find_atom_pairs
----> 4 from ..topologyobjects import Atom
5 from shutil import which
6 from typing import List, Set, Tuple
/home/cadd/amber22/lib/python3.10/site-packages/parmed/topologyobjects.py in ()
7 import enum
8 import math
----> 9 from functools import cached_property
10 from typing import Optional
11 import warnings
ImportError: cannot import name 'cached_property'
from pytraj.
{quote}
----> 9 from functools import cached_property
10 from typing import Optional
11 import warnings
ImportError: cannot import name 'cached_property'
{quote}
This cached_property
was added to Python since 3.8 release. I bet you're mixing different python versions here.
import sys
print(sys.version_info)
print(sys.path) # check this to see any mixing.
what does this say? (e.g: you're supposed to use python 3.10)
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I encountered the same problem. Now AmberTools22 will download and install python 3.11 version miniconda. When the pytraj module is compilered, the following error appeared:
However, when I used python 3.9 in my own conda enviroment, the pytraj can be installed successfully.
from pytraj.
Thanks, Hai Nguyen. I can compile ambertools23 successfully where I noticed one update.3 you patched for AmberTools23.
And I noticed that you have fixed the compatibility issue between Python 3.11 and CPython for pytraj. Nice work! Cheers!
from pytraj.
I try it the message shows
sys.version_info(major=3, minor=6, micro=9, releaselevel='final', serial=0)
['', '/home/cadd/amber22/lib/python3.10/site-packages', '/usr/lib/python36.zip', '/usr/lib/python3.6', '/usr/lib/python3.6/lib-dynload', '/usr/local/lib/python3.6/dist-packages', '/usr/lib/python3/dist-packages', '/usr/lib/python3/dist-packages/IPython/extensions', '/home/cadd/.ipython']
from pytraj.
from pytraj.
Your jupyter notebook comes from python 3.6 but the one in amber is 3.10
What should I do, could you give me some advice please?
from pytraj.
it's hard to tell you what do to if I don't know the detail.
Basically:
- which python path did you use to compile ambertools? how (exactly) did you run jupyter?
- saying you find it, source the amber.sh as the manual suggested, then run
/path/to/python3 -m jupyter notebook
- in the notebook,
import sys; print(sys.version); print(sys)
to make sure you are using the correct python path?
from pytraj.
Related Issues (20)
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from pytraj.