ModuleNotFoundError: No module named 'pytraj.core.topology_objects'

[JSurayut]

Hello, I want to use pytraj for my research but when I run on jupyter or in terminal. It shows "ModuleNotFoundError: No module named 'pytraj.core.topology_objects'", Please advice me how to fix it. Thank you

[hainm]

hi @JSurayut, how did you install pytraj?
(e.g: you can install AmberTools that includes pytraj: https://ambermd.org/GetAmber.php)

[JSurayut]

Hello, Mr. Hai Nguyen I installed pytraj by using AmberTools เมื่อ อ. 8 ส.ค. 2566 เวลา 21:50 Hai Nguyen ***@***.***> เขียนว่า:

…

hi @JSurayut <https://github.com/JSurayut>, how did you install pytraj? (e.g: you can install AmberTools that includes pytraj: https://ambermd.org/GetAmber.php) — Reply to this email directly, view it on GitHub <#1637 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBYNPYQ4SYWMW72EDWPIKU3XUJG3DANCNFSM6AAAAAA3GQNHOY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[hainm]

@JSurayut is there any chance that you have pytraj source code in your desktop and you opened jupyter in the location having pytraj?

[JSurayut]

No, I have checked in my folder that I opened jupyter, It does not have any pytraj source code.

[hainm]

um, that's odd. can you try import parmed; print(parmed) to see if that works?

[hainm]

Your issue is similar to #1565

[JSurayut]

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'

[hainm]

{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)

[freeenergylab]

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.

[hainm]

Pleaser try ambertools 23 Ps: it’s not same issue Cheers

[freeenergylab]

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!

[JSurayut]

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']

[hainm]

Your jupyter notebook comes from python 3.6 but the one in amber is 3.10

[JSurayut]

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?

[hainm]

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?