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AlphaPulldown/conda/bin
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Dima fc41c1a5eb AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues 
- Strip _entity_poly_seq from generated template mmCIF so AF3 reconstructs _pdbx_poly_seq_scheme from _atom_site, avoiding UNK/gap mismatches
- Build query_to_template_map using only residues with atoms to prevent OOB indexing in template features
- Add --debug_templates flag to optionally dump generated template mmCIFs into templates_debug/
- Keep templates enabled; test test__chopped_dimer now passes
2025-08-12 14:04:33 +02:00
..
2to3
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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2to3-3.12
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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activate
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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adig
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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ahost
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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archspec
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bsdcat
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bsdcpio
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bsdtar
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bsdunzip
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bunzip2
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bzcat
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bzcmp
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bzdiff
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bzegrep
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bzfgrep
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bzgrep
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bzip2
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
bzip2recover
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bzless
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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bzmore
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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c_rehash
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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captoinfo
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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clear
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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compile_et
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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conda
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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conda2solv
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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conda-env
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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cph
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
curl-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
deactivate
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
distro
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
dumpsolv
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
gss-client
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
idle3
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
idle3.12
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
infocmp
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
infotocap
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
installcheck
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
jsondiff
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
jsonpatch
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
jsonpointer
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
k5srvutil
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
kadmin
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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kdestroy
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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keyctl
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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kinit
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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klist
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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kpasswd
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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krb5-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
ksu
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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kswitch
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
ktutil
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
kvno
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
lz4
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
lz4c
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
lz4cat
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
mamba
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
mamba-package
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
mergesolv
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
ncurses6-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
ncursesw6-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
nghttp
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
nghttpd
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
nghttpx
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
normalizer
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
openssl
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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pip
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
pip3
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
pydoc
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
pydoc3
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
pydoc3.12
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
python
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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python3
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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python3-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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python3.1
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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python3.12
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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python3.12-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
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repo2solv
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
reset
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
sclient
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
sim_client
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
sqlite3_analyzer
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tabs
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tclsh
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tclsh8.6
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
testsolv
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tic
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
toe
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tput
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tqdm
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
tset
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
unlz4
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
unzstd
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
uuclient
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
wheel
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
wish
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
wish8.6
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
x86_64-conda_cos6-linux-gnu-ld
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
x86_64-conda-linux-gnu-ld
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
xml2-config
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
xmlcatalog
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
xmllint
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
zstd
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
zstdcat
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
zstdgrep
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
zstdless
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00
zstdmt
AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues
2025-08-12 14:04:33 +02:00