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Some tests in test_insty.py timeout when run on a single-cpu system

Status: Open.

#2236 In prody/ProDy;

· sanvila opened on Jun 1, 2026

ProDy crashes while reading an mmCIF generated using OpenFold3

Status: Open.

#2234 In prody/ProDy;

· rckormos opened on Apr 6, 2026

runDali failed to get response

Status: Open.

#2231 In prody/ProDy;

· stoneandbone opened on Mar 3, 2026

Can't pickle local object 'calcInteractionsMultipleFrames.<locals>.analyseFrame'

In progress

Status: Open.

#2192 In prody/ProDy;

· houyaxuan634-coder opened on Dec 5, 2025

AttributeError: Selection object has no attribute strip and 'strip' is not a valid selection string

In progress

Status: Open.

#2188 In prody/ProDy;

· GCS-ZHN opened on Dec 1, 2025

Not able to install prody==2.4.0 in py3.12.6

Status: Open.

#2187 In prody/ProDy;

· parasml opened on Nov 22, 2025

feature request: correct conversion from three-letter to one-letter AA code (including ncAA correct processing)

Status: Open.

#2186 In prody/ProDy;

· lokapal opened on Nov 3, 2025

Three-letter code extraction doesn't work in ProDy 2.6.1 under Python 3.12

Status: Open.

#2185 In prody/ProDy;

· lokapal opened on Nov 3, 2025

Can Prody parse residue label_seq_id from cif file ?

Status: Open.

#2180 In prody/ProDy;

· locitran opened on Oct 11, 2025

Missing key error when parsing PDB entry 7O07

Status: Open.

#2174 In prody/ProDy;

· sforli opened on Sep 4, 2025

inferBonds() method raises runtime exception due to integer types mismatch

Status: Open.

#2173 In prody/ProDy;

· SwampHiker opened on Sep 2, 2025

calcProteinInteractions() throws NumPy UFuncTypeError in ProDy 2.5.0

Status: Open.

#2142 In prody/ProDy;

· HaleHasdemir opened on Jul 11, 2025