Recent ProDy updates to Cavi-Finder branch - #9

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karolamik13 wants to merge 1054 commits into

karolamik13:prody-cavifinderfrom

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Commits on Feb 10, 2026

Merge pull request #2214 from jamesmkrieger/revert_scipion_parse_write
jamesmkrieger
authored
a2ee72e
fixed stuck search
AnthonyBogetti
committed
c0fc537
still trying to fix serach
AnthonyBogetti
committed
a67ae71
finishing touches
AnthonyBogetti
committed
c72acfd
add readthedocs button to readme
AnthonyBogetti
committed
8d074cc
make readme shields side by side
AnthonyBogetti
committed
60d3a56
readme formatting
AnthonyBogetti
committed
2e53bfc
Merge pull request #2217 from AnthonyBogetti/website
AnthonyBogetti
authored
30d6360
updated README shield with correct link
AnthonyBogetti
committed
6bcccb5
Merge pull request #2218 from AnthonyBogetti/website
AnthonyBogetti
authored
ab8c2e1

Commits on Feb 12, 2026

Update gui.py
Cventura18
authored
25cabae

Commits on Feb 13, 2026

Merge pull request #2219 from Cventura18/Cventura18-patch-1-updated-wording-in-DruGUI-2.0's-GUI
AnthonyBogetti
authored
c5dd484
Initial plan
Copilot
committed
ea786d2
Fix StopIteration error in getAlignedMapping for Biopython > 1.79

Copilot
and
AnthonyBogetti
committed
6a6e325
Add logging and fix length mismatch in StopIteration handling

Copilot
and
AnthonyBogetti
committed
e94c4af
Use LOGGER.warning instead of deprecated LOGGER.warn

Copilot
and
AnthonyBogetti
committed
122c8ce

Commits on Feb 18, 2026

fix alignBioPairwise for truncation
jamesmkrieger
committed
63800d3
fix for same length of excluded
jamesmkrieger
committed
7d47dd4
simplify test
jamesmkrieger
committed
6e88959

Commits on Feb 19, 2026

updated spring constants
anupam-banerjee
committed
3e85b1e

Commits on Feb 24, 2026

import Bio Phylo BaseTree and _DistanceMatrix inside
jamesmkrieger
committed
17b01e3
remove from all
jamesmkrieger
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1880a81
calcTree import from bio phylo directly
jamesmkrieger
committed
e60e937

Commits on Feb 25, 2026

add calcTree tests to confirm not broken
jamesmkrieger
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9b735e0
add more tree tests
jamesmkrieger
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3b84b0f
restore TEMPDIR to tests datafiles
jamesmkrieger
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b8aca22

Commits on Mar 5, 2026

Commits on Mar 6, 2026

MOLE 2.0 publication update
karolamik13
committed
bd211ab
Docs improvements for calcChannels()
karolamik13
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4088599

Commits on Mar 8, 2026

Docs minor change in selectChannelBySelection
karolamik13
committed
3649c89
bug fix for PQR format in calcChannelSurfaceOverlaps
karolamik13
committed
8bce624

Commits on Mar 9, 2026

parsePQR import added
karolamik13
committed
6ee0e32
fixed bug in Python 3.12 multiprocessing
AnthonyBogetti
committed
aebffdb
Merge pull request #2232 from AnthonyBogetti/wf-fix
AnthonyBogetti
authored
ae6f39f
Merge branch 'prody:main' into prody-cavifinder-reorg
karolamik13
authored
ff307c8
selectChannelBySelection - PQR parser and docs changes
karolamik13
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da9f7b3
Changes in docs
karolamik13
committed
cb5a8ca

Commits on Mar 11, 2026

additions for docs calcChannelSurfaceOverlaps
karolamik13
committed
42c595d
few changes in docs (cavitracer)
karolamik13
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57229f2

Commits on Mar 15, 2026

CaviTracer - getChannelAtoms - fix for multimodel PDB analysis
karolamik13
committed
c1fab4c

Commits on Mar 19, 2026

CaviTracer docs improvements
karolamik13
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581c083

Commits on May 1, 2026

fix pdbe emdb ftp
jamesmkrieger
committed
99488ef

Commits on May 24, 2026

Merge pull request #2018 from karolamik13/prody-cavifinder-reorg
karolamik13
authored
b425aa0

Commits on Jun 5, 2026

CaviTracer - start_point option added to calcChannels
karolamik13
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27d5667
CaviTracer - calcChannels docs
karolamik13
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15e6353
CaviTracer - start_point checking
karolamik13
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a0bec57
Merge branch 'prody:main' into prody-cavifinder-reorg
karolamik13
authored
e948f0c
CaviTracer - start_point in calcChannelsMultipleFrames (ensemble, trajectory)
karolamik13
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053a908
CaviTracer - docs for calcChannelsMultipleFrames()
karolamik13
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e6bf814

Commits on Jun 8, 2026

Commits on Jun 9, 2026

Commits on Jun 10, 2026

Commits on Jun 17, 2026

Fix PDB sequence clusters: migrate off deprecated RCSB bc-*.out files

jamesmkrieger
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claude
committed
f67a1a2
test_pdbclusters: set package path so tests don't prompt on stdin

jamesmkrieger
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claude
committed
44744e8

Commits on Jun 19, 2026

Commits on Jun 22, 2026

Commits on Jun 23, 2026

Merge branch 'prody:main' into prody-cavifinder-reorg
karolamik13
authored
27c7094
CaviTracer - docs for calcSurfaceCavities()
karolamik13
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f5355f2
CaviTracer - calcChannels docs
karolamik13
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bd57c74
CaviTracer - min_tetrahedra/max_tetrahedra added
karolamik13
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be025a6
CaviTracer - calcSurfaceCavities min/max_tetrahedra, volume
karolamik13
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cc10f92
calcSurfaceCavities - min/max volume added
karolamik13
committed
2ce30e3
calcSurfaceCavities - improved save_cavities_to_pdb
karolamik13
committed
99df3c9
calcSurfaceCavities - changes in default criteria, docs
karolamik13
committed
5e21dbd

Commits on Jul 1, 2026

CaviTracer - docs - open3D info
karolamik13
committed
c2f19dd

Commits on Jul 2, 2026

CaviTracer - removing imports that are not used
karolamik13
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f5a34f5
CaviTracer - cavities_only in one block
karolamik13
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6524e08
typo in the comment fix
karolamik13
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3368dee
CaviTracer - calcSurfaceCavitiesMultipleFrames for trajectory/multi-model analysis
karolamik13
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7b06f6f
CaviTracer - getSurfaceCavityParameters is added
karolamik13
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534718e
CaviTracer - getSurfaceCavityResidueNames added
karolamik13
committed
b3cf51f

Commits on Jul 3, 2026

Commits on Jul 4, 2026

Commits on Jul 6, 2026

Merge pull request #2235 from jamesmkrieger/jamesk/pdbe_emdb_ftp
jamesmkrieger
authored
f914353

Commits on Jul 7, 2026

Commits on Jul 8, 2026

channels: truncate channels at surface mouths to avoid their duplication.
briza81
committed
4f2e013

Commits on Jul 9, 2026

Commits on Jul 10, 2026

Commits on Jul 13, 2026

Initial plan
Copilot
authored
32ba552
Handle non-numeric mmCIF auth_seq_id values
Copilot
authored
f76446d
Add label_seq_id fallback option for mmCIF residue numbers
Copilot
authored
cd97e1e
Initial plan
Copilot
authored
2df9b68
feat: use MODRES records for correct ncAA to canonical AA conversion in parsePDBHeader
Copilot
authored
9c416c3
fix: remove incorrect sequence caching in Chain.getSequence (issue #2185)
Copilot
authored
53ffce8
Initial plan
Copilot
authored
aa60882
Initial plan
Copilot
authored
94c010f
Fix integer type mismatch in get_KDTree_indices (issue #2173)
Copilot
authored
692e02c
Fix writeNMD for large systems: renumber residues > 9999 for NMWiz/VMD PDB compatibility
Copilot
authored
164a3d0
fix: use AAMAP.get() with X fallback in _getUnobservedSeq (issue #2174)
Copilot
authored
6d405d0
Initial plan
Copilot
authored
934410e
fix: support atoms in showOccupancies
Copilot
authored
8921b5d
Initial plan
Copilot
authored
7bfcc9c
Handle extended PDB IDs in fetch and mirror paths
Copilot
authored
e372069
channels: additively weighted VD are run in serial to avoid complications with preceived per-frame parallelism
briza81
committed
b9ca70d
fix: add missing MODRES ncAA test fixture
Copilot
authored
62482c7
fix: support threeLetter sequence alias
Copilot
authored
4601f77
Make bioexcel tests optional (skip unless PRODY_BIOEXCEL_TESTS=1)
Copilot
authored
35dadde
fix: drop .gitignore exception for MODRES fixture
Copilot
authored
b8cbcf6
channels: local (enclosure-based) surface peel, removing the r1 dependence by
briza81
committed
a1a59f4

Commits on Jul 14, 2026

Commits on Jul 15, 2026

Commits on Jul 16, 2026

Commits on Jul 17, 2026

Update channels.py
karolamik13
authored
4be6430
CaviTracer - calcChannelSurfaceOverlaps() - improved with multiproc calc
karolamik13
committed
5d61cdf
CaviTracer - calcSurfaceCavityOverlaps and channels docs
karolamik13
committed
3e91bdd

Commits on Jul 18, 2026

Commits on Jul 19, 2026

capture directional perturb response vectors
jamesmkrieger
committed
dc71097
bug fix discovered from directional prs
jamesmkrieger
committed
5efc0f0
bug fix 2
jamesmkrieger
committed
0a085b9
fix directional prs output
jamesmkrieger
committed
1c8b337
fix prs no-turbo logger
jamesmkrieger
committed
6fc0f71
fix prs no-turbo
jamesmkrieger
committed
419c199
fix showAtomicMatrix
jamesmkrieger
committed
b3f818f
fix showAtomicMatrix
jamesmkrieger
committed
e80e15f
Add ref_model option to calcSignatureOverlaps with tests

jamesmkrieger
and
claude
committed
6529bdd
Add force/perturb_node knobs and comparePerturbResponses

jamesmkrieger
and
claude
committed
f4c2e3d
Merge branch 'jamesk/prs-fixes' into jamesk/prs-directional-2

jamesmkrieger
and
claude
committed
201bd26
fix: route showOccupancies through showAtomicLines
Copilot
authored
aff2a14
Merge pull request #2245 from prody/copilot/fix-system-size-limitation
jamesmkrieger
authored
2fcbae9
fix: restore showOccupancies auto_show behavior
Copilot
authored
cdb0be2
test: remove showOccupancies plotting tests
Copilot
authored
440d539
Merge pull request #2246 from prody/copilot/show-occupancies-support-atoms-kwarg
jamesmkrieger
authored
6f0d937

Commits on Jul 20, 2026

Commits on Jul 21, 2026

Thread biopython alignment arguments through mapping functions

jamesmkrieger
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claude
committed
ab60298
ClustENM: multi-start (setAtoms accepts a list of AtomGroups) + fix=False option

jamesmkrieger
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claude
committed
5461b0f
ClustENM: parallelise minimise/MD across conformers + build-once implicit-solvent system

jamesmkrieger
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claude
committed
1221349
ClustENM: round-robin Pool workers across visible GPUs for multi-GPU parallel

jamesmkrieger
and
claude
committed
8066718
prody clustenm app: accept comma-separated structures for multi-start

jamesmkrieger
and
claude
committed
c8cad9c
ClustENM: use 'spawn' for the parallel minimise/MD pool (OpenMM+CUDA can't fork)

jamesmkrieger
and
claude
committed
5223f34
ClustENM: separate parallel_sim + sim_devices (multi-GPU DeviceIndex) from parallel

jamesmkrieger
and
claude
committed
ec93297
ClustENM: record a starting CC per seed for multi-start fitting

jamesmkrieger
and
claude
committed
b3fb98a

Commits on Jul 22, 2026

Commits on Jul 23, 2026

CaviTracer - calcChannels - return_details is added
karolamik13
committed
3475efb
CaviTracer - initial version of calcPoresFromChannels() is added
karolamik13
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a801617
CaviTracer - calcPoresFromChannels() docs
karolamik13
committed
78c8a52
CaviTracer - calcPoresFromChannels - more docs
karolamik13
committed
66a0888
CaviTracer - showPores() is added
karolamik13
committed
8dcb2c6
CaviTracer - showPores as alias instead of separate func
karolamik13
committed
d534320

Commits on Jul 24, 2026

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Commits on Aug 4, 2026

Commits on Aug 6, 2026

New clustering function - DBSCAN, OPTICS for Reachability Plot
kontheodosiadis
committed
eaf54d4

Commits on Aug 9, 2026

Merge pull request #2263 from briza81/CaviTracer-parameters-update
karolamik13
authored
4484614

Commits on Aug 11, 2026

Fixed title bug in showPairwiseRMSDHeatmap
kontheodosiadis
committed
e09413d
CaviTracer - improvements for showFrequentObjectResidues()
karolamik13
committed
e7a4768
CaviTracer - scanSurfaceCavityParameters()
karolamik13
committed
af40a30
Changes accoridng to James K. suggestions
karolamik13
committed
00154d9
CaviTracer - changes in showFrequentObjectResidues() [James K suggestion]
karolamik13
committed
b15f246
Merge pull request #2266 from karolamik13/prody__main
karolamik13
authored
7969f49

Commits on Aug 12, 2026

Commits on Aug 13, 2026