Biopython > 1.79 sometimes breaks alignChains #2205
Description
Description of the bug.
When I run alignChains on the attached pdbs with Python 3.11 with Biopython > 1.79, I get the following error. With Biopython 1.79, the same code runs without any problems. This also means I can't use Python 3.12 as it doesn't support Biopython 1.79
ref_model.pdb
centered_model.pdb
Error log from code run shown below
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from ref_model (len=1132) with Chain A from centered_model:
@> Mapped: 1132 residues match with 100% sequence identity and 99% overlap.
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain B from ref_model (len=381) with Chain A from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain B from ref_model (len=381) with Chain A from centered_model:
@> Failed to match chains (seqid=33%, overlap=32%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain B from ref_model (len=381) with Chain A from centered_model:
@> Failed to match chains (seqid=12%, overlap=6%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain E from ref_model (len=709) with Chain A from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain E from ref_model (len=709) with Chain A from centered_model:
@> Failed to match chains (seqid=34%, overlap=58%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain E from ref_model (len=709) with Chain A from centered_model:
@> Failed to match chains (seqid=3%, overlap=6%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain F from ref_model (len=21) with Chain A from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain F from ref_model (len=21) with Chain A from centered_model:
@> Failed to match chains (seqid=40%, overlap=2%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain F from ref_model (len=21) with Chain A from centered_model:
@> Failed to match chains (seqid=12%, overlap=1%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from ref_model (len=1132) with Chain B from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain A from ref_model (len=1132) with Chain B from centered_model:
@> Failed to match chains (seqid=34%, overlap=29%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain A from ref_model (len=1132) with Chain B from centered_model:
@> Failed to match chains (seqid=11%, overlap=6%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain B from ref_model (len=381) with Chain B from centered_model:
@> Mapped: 346 residues match with 100% sequence identity and 99% overlap.
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain E from ref_model (len=709) with Chain B from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain E from ref_model (len=709) with Chain B from centered_model:
@> Failed to match chains (seqid=29%, overlap=46%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain E from ref_model (len=709) with Chain B from centered_model:
@> Failed to match chains (seqid=5%, overlap=15%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain F from ref_model (len=21) with Chain B from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain F from ref_model (len=21) with Chain B from centered_model:
@> Failed to match chains (seqid=28%, overlap=5%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain F from ref_model (len=21) with Chain B from centered_model:
@> Failed to match chains (seqid=6%, overlap=5%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from ref_model (len=1132) with Chain E from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain A from ref_model (len=1132) with Chain E from centered_model:
@> Failed to match chains (seqid=34%, overlap=58%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain A from ref_model (len=1132) with Chain E from centered_model:
@> Failed to match chains (seqid=5%, overlap=7%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain B from ref_model (len=381) with Chain E from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain B from ref_model (len=381) with Chain E from centered_model:
@> Failed to match chains (seqid=32%, overlap=49%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain B from ref_model (len=381) with Chain E from centered_model:
@> Failed to match chains (seqid=7%, overlap=14%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain E from ref_model (len=709) with Chain E from centered_model:
@> Mapped: 709 residues match with 100% sequence identity and 100% overlap.
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain F from ref_model (len=21) with Chain E from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain F from ref_model (len=21) with Chain E from centered_model:
@> Failed to match chains (seqid=50%, overlap=2%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain F from ref_model (len=21) with Chain E from centered_model:
@> Failed to match chains (seqid=0%, overlap=2%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from ref_model (len=1132) with Chain F from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain A from ref_model (len=1132) with Chain F from centered_model:
@> Failed to match chains (seqid=38%, overlap=6%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain A from ref_model (len=1132) with Chain F from centered_model:
@> Failed to match chains (seqid=7%, overlap=5%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain B from ref_model (len=381) with Chain F from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain B from ref_model (len=381) with Chain F from centered_model:
@> Failed to match chains (seqid=46%, overlap=21%).
@> Trying to map atoms based on CEalign:
@> Comparing Chain B from ref_model (len=381) with Chain F from centered_model:
@> Failed to match chains (seqid=4%, overlap=13%).
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain E from ref_model (len=709) with Chain F from centered_model:
@> Trying to map atoms based on local sequence alignment:
@> Comparing Chain E from ref_model (len=709) with Chain F from centered_model:
---------------------------------------------------------------------------
StopIteration Traceback (most recent call last)
Cell In[4], line 1
----> 1 prody_ref_amap = prody.alignChains(prody_ref_model, prody_model,
2 overlap=15, matchFunc=prody.sameChid)
File ~/scipion3/software/em/prody-github/ProDy/prody/proteins/compare.py:1721, in alignChains(atoms, target, match_func, **kwargs)
1715 def alignChains(atoms, target, match_func=bestMatch, **kwargs):
1716 """Aligns chains of *atoms* to those of *target* using :func:`.mapOntoChains`
1717 and :func:`.combineAtomMaps`. Please check out those two functions for details
1718 about the parameters.
1719 """
-> 1721 mappings = mapOntoChains(atoms, target, match_func, **kwargs)
1722 m, n = mappings.shape
1723 if m > n:
File ~/scipion3/software/em/prody-github/ProDy/prody/proteins/compare.py:1225, in mapOntoChains(atoms, ref, match_func, **kwargs)
1222 continue
1224 simple_target = target_chain if isinstance(target_chain, SimpleChain) else SimpleChain(target_chain, False)
-> 1225 mappings[i, j] = mapChainOntoChain(simple_target, simple_chain, **kwargs)
1227 return mappings
File ~/scipion3/software/em/prody-github/ProDy/prody/proteins/compare.py:1044, in mapChainOntoChain(mobile, target, **kwargs)
1042 result = getCEAlignMapping(simple_target, simple_mobile)
1043 elif method == 'seq':
-> 1044 result = getAlignedMapping(simple_target, simple_mobile)
1045 else:
1046 if isinstance(alignment, dict):
File ~/scipion3/software/em/prody-github/ProDy/prody/proteins/compare.py:1390, in getAlignedMapping(target, chain, alignment)
1388 b = that[i]
1389 if a not in gap_chars:
-> 1390 ares = next(aiter)
1391 amatch.append(ares.getResidue())
1392 if b not in gap_chars:
StopIteration:
What is your setup?
The same problem exists and is fixed by python and biopython version on MacOS and Linux
How did you install ProDy?
Pip install of ProDy 2.6.1 from PyPI using a uv virtual environment on Linux and pip install -Ue with a github version on my scipion branch and on tag v2.6.1 in a conda environment on MacOS all show this behaviour.
What did your code look like?
Python 3.11.0 | packaged by conda-forge | (main, Jan 14 2023, 12:26:40) [Clang 14.0.6 ]
Type 'copyright', 'credits' or 'license' for more information
IPython 9.9.0 -- An enhanced Interactive Python. Type '?' for help.
Tip: Use `--theme`, or the `%colors` magic to change IPython's themes and colors.
Cmd click to launch VS Code Native REPL
In [1]: import prody
In [2]: prody_model = prody.parsePDB("centered_model.pdb")
@> 2280 atoms and 1 coordinate set(s) were parsed in 0.07s.
In [3]: prody_ref_model = prody.parsePDB("ref_model.pdb")
@> 2243 atoms and 1 coordinate set(s) were parsed in 0.07s.
In [4]: prody_ref_amap = prody.alignChains(prody_ref_model, prody_model,
...: overlap=15, matchFunc=prody.sameChid)
Anything else?
I don't think there is anything else.
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