prody

library2.6.1pypypi✓ verified 87d ago

ProDy is an open-source Python package for protein dynamics analysis, including structure analysis, normal mode analysis (ANM, GNM, PCA), sequence analysis, trajectory parsing, and protein-ligand interactions. Current version 2.6.1 supports Python >=3.10, NumPy 2, and Python 3.12. Releases occur roughly every few months with bug fixes and new features.

ai-ml data

pip install prody

github ↗package ↗homepage ↗docs ↗

INSTALL

IMPORT

SIG · PRODY

prody

ai-mlpythonv2.6.1

Install

9.7s avg

Import

4520ms

Disk

419MB

Pass rate

1/ 10

Env Coverage1 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.6.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

glibc

py 3.10

✕ build_error

py 3.11

✕ build_error

py 3.12

✕ build_error

✓ 9.7s

py 3.13

✕ build_error

py 3.9

✕ build_error

419MB installed

● package 419MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

parsePDB

✓ from prody import parsePDB

✗ import prody; prody.parsePDB()

Function is in top-level prody namespace after import

ANM

✓ from prody import ANM

✗ from prody.proteins import ANM

ANM is in top-level namespace

calcRMSD

✓ from prody import calcRMSD

✗ from prody.measure import calcRMSD

Direct import from prody is preferred

Parse a PDB, build ANM Hessian, and compute normal modes.

from prody import * from prody import parsePDB, ANM, calcModes pdb = parsePDB('1ake') anm = ANM('example') anm.buildHessian(pdb) modes = calcModes(anm) print(modes[:3])

prody --version

Debug

Known issues

breakingPython 3.11 or earlier and Python 3.13+ are not supported; requires Python >=3.10 and <3.13.

fix

Use Python 3.10-3.12. Check with `python --version`.

affects: <=2.5.0: Python 3.9; 2.6.0+ requires Python 3.10-3.12

breakingNumPy 2 support introduced in v2.6.0; earlier versions may fail with NumPy 2.

fix

Upgrade ProDy to v2.6.0+ or pin NumPy <2.

affects: <2.6.0

deprecatedThe `imp.find_module` workaround in apps is removed; use `importlib`.

fix

If using custom scripts that relied on `prody.apps`, update to avoid deprecated module loading.

affects: >=2.3.0

gotchaProDy uses a global logger that may override your logging level. Call `prody.LOGGER.setLevel(logging.WARNING)` to suppress verbose output.

fix

Add `import logging; prody.LOGGER.setLevel(logging.WARNING)` at the start of your script.

affects: all

gotchaWildcard import `from prody import *` pollutes namespace with many internal symbols; prefer explicit imports.

fix

Use explicit imports: `from prody import parsePDB, ANM, ...`

affects: all

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'prody'

ProDy not installed or installed in wrong environment.

fix

Run `pip install prody` in the correct Python environment.

ImportError: numpy.core.multiarray failed to import

NumPy version incompatible with ProDy (e.g., NumPy 2 with ProDy <2.6.0).

fix

Upgrade ProDy: `pip install --upgrade prody` or downgrade NumPy: `pip install 'numpy<2'`

AttributeError: module 'prody' has no attribute 'parsePDB'

ProDy not imported correctly (e.g., `import prody` instead of `from prody import parsePDB`).

fix

Use `from prody import parsePDB` or `import prody; pdb = prody.parsePDB(...)`

ValueError: 4-letter PDB ID is not supported

ProDy <2.6.0 does not support extended PDB IDs (4-letter codes).

fix

Upgrade to ProDy >=2.6.0: `pip install --upgrade prody`

Upgrade

Version history

2.6.1latest on PyPI · released Aug 19, 2025

Audit

Dependencies

No dependency data recorded yet.

Agent activity

8 hits · last 30 days

node

Resources

githubhttps://github.com/prody/ProDy ↗

packagehttps://pypi.org/project/prody/ ↗

homepagehttp://www.bahargroup.org/prody ↗

docshttp://www.bahargroup.org/prody/tutorials.html ↗