jinyuansun / chatmol Goto Github PK

This is the error message after typing the first line into the command line of PyMOL

PyMOL>run https://raw.githubusercontent.com/JinyuanSun/ChatMol/main/chatmol.py
Traceback (most recent call last):
File "/usr/local/Cellar/pymol/2.5.0/libexec/lib/python3.9/site-packages/pymol/parsing.py", line 467, in run
run_(path, ns_pymol, ns_pymol)
File "/usr/local/Cellar/pymol/2.5.0/libexec/lib/python3.9/site-packages/pymol/parsing.py", line 516, in run_file
execfile(file,global_ns,local_ns)
File "/usr/local/Cellar/pymol/2.5.0/libexec/lib/python3.9/site-packages/pymol/parsing.py", line 511, in execfile
exec(co, global_ns, local_ns)
File "https://raw.githubusercontent.com/JinyuanSun/ChatMol/main/chatmol.py", line 2, in
PyMOL Molecular Graphics System
ModuleNotFoundError: No module named 'openai'

But I have installed openai using PIP

(anaconda3)xxx-MacBook-Air:~ xxx$ which openai
/Users/xxx/opt/anaconda3/bin/openai

(anaconda3)xxx-MacBook-Air:~ xxx$ which pymol
/usr/local/bin/pymol

(anaconda3)xxx-MacBook-Air:~ xxx$ which python
/Users/xxx/opt/anaconda3/bin/python

Is this because my open sources PyMOL was installed at a different folder? Thanks!

Hi, thank you very much for sharing your great work. It is greatly interesting!

I have some questions regarding the ChatMol-Lite model. Specifically, I'm interested in how it was trained. Do you have any specific code or documentation outlining this process?

Any assistance or additional information would be immensely appreciated.

I was following the instruction to install chatmol plugin, and got error for module openai not found error:

load https://raw.githubusercontent.com/JinyuanSun/ChatMol/main/chatmol.py
Traceback (most recent call last):
File "/private/var/folders/0w/mjyhyf3n4_z2vr3l1d0ps7_w0000gn/T/AppTranslocation/1E319BC0-B882-44AB-B791-34B99CBF7AFC/d/PyMOL.app/Contents/lib/python3.7/site-packages/pymol/parsing.py", line 470, in run
run_(path, ns_pymol, ns_pymol)
File "/private/var/folders/0w/mjyhyf3n4_z2vr3l1d0ps7_w0000gn/T/AppTranslocation/1E319BC0-B882-44AB-B791-34B99CBF7AFC/d/PyMOL.app/Contents/lib/python3.7/site-packages/pymol/parsing.py", line 519, in run_file
execfile(file,global_ns,local_ns)
File "/private/var/folders/0w/mjyhyf3n4_z2vr3l1d0ps7_w0000gn/T/AppTranslocation/1E319BC0-B882-44AB-B791-34B99CBF7AFC/d/PyMOL.app/Contents/lib/python3.7/site-packages/pymol/parsing.py", line 514, in execfile
exec(co, global_ns, local_ns)
File "https://raw.githubusercontent.com/JinyuanSun/ChatMol/main/chatmol.py", line 3, in
Copyright (c) Schrodinger, Inc.
ModuleNotFoundError: No module named 'openai'

I do installed openai in my default env (python3.9, running python3 and import openai all look good), but the PyMol command shows the module was not found. I am relatively new to use PyMol, so maybe I am missing simple thing simple. Could you show me how to solve the issue? Many thanks.

Per OpenAI documentation it would be helpful for ChatMol to be able to read the API key from an environment variable, specifically as os.environ['OPENAI_API_KEY'].