PyCharm新手求助：使用Schrodinger外部模块遇初始化等问题

Hey there! Let's tackle this Schrodinger + PyCharm Python 2.7 issue step by step — I’ve helped folks work through similar library setup headaches before.

Schrodinger comes with its own dedicated Python 2.7 environment, and this is non-negotiable for proper module loading. Don’t use your system or PyCharm’s default Python 2.7!

• Locate the Schrodinger-built Python path: It’s usually something like /path/to/schrodinger/internal/bin/python (Linux/macOS) or C:\Program Files\Schrodinger\internal\python.exe (Windows).
• In PyCharm, go to File > Settings > Project: [Your Project Name] > Python Interpreter.
• Click the gear icon in the top-right, select Add, then pick System Interpreter. Navigate to the Schrodinger Python path you found and set it as your project’s default interpreter. This lets PyCharm natively recognize all Schrodinger modules.

Moving your project directory into Schrodinger’s folder is a common misstep — it creates path chaos instead of solving the problem. Schrodinger relies on specific environment variables to load modules, so here’s the right fix:

• Linux/macOS: Open a terminal, run Schrodinger’s environment setup script first (e.g., source /path/to/schrodinger/schrodinger.bashrc), then launch PyCharm directly from this terminal. PyCharm will inherit all the necessary environment variables automatically.
• Windows: Use the Schrodinger Command Prompt (found in your Schrodinger start menu folder). Open it, then type the full path to your pycharm.exe and hit enter. This boots PyCharm with Schrodinger’s pre-configured environment.

Schrodinger’s module structure is unique — don’t try to treat it like a standard pip-installed package. Use their official import patterns, for example:

# Example imports for common Schrodinger tools
from schrodinger import structure
from schrodinger.structutils import analyze
from schrodinger.job import jobcontrol

If you still get "module not found" errors, double-check that you followed step 2 correctly — missing environment variables are almost always the culprit here.

• Never mix Schrodinger’s Python with your system’s Python 2.7 — conflicting dependencies will break module loading.
• Don’t modify any files or folder structures in the Schrodinger installation directory — this can corrupt its internal module paths.
• If the "initializing" hang persists, head to Run > Edit Configurations in PyCharm. Under Environment variables, manually add key variables like SCHRODINGER=/path/to/schrodinger and PYTHONPATH=/path/to/schrodinger/python (adjust paths to match your installation).

内容的提问来源于stack exchange，提问作者Zorroman