Add ML finding and other new developments - #11

Merged

Dialpuri merged 56 commits into

add-ml-predictions

Jun 18, 2026

Commits on Oct 6, 2025

Added machine learning prediction capability to Sails
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48853b5

Commits on Oct 7, 2025

Update to gemmi 0.7.0
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f1a1c8d
Added sails-find to predicted density and updated to gemmi 0.7.3
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91a4124

Commits on Oct 9, 2025

Added sails-find multiclass capability
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bcd67d8

Commits on Oct 10, 2025

Added requests dependency
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a77f694
Added early exit when no positive predictions found
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ada2a1d
Added sails prediction submodule to pyproject.toml
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340bf8e

Commits on Oct 11, 2025

Added nullptr check and nanobind dependency
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7ae1e2f

Commits on Oct 12, 2025

Added nullptr check and nanobind dependency
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23c8a41

Commits on Oct 14, 2025

Added ability to use glycan finding in protein prediction
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1c1731e

Commits on Oct 18, 2025

Added autoglycoslate function to API
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7166e4b
Added renumber function to Glycan
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73f1c55
Added standardise residue name function
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18d5fed
Fixed bugs in density calculation
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6d4be5e

Commits on Oct 19, 2025

Added validate based on RSCC
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f6f46d6
Added chain and seqid glycoyslation options
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910005c
Added logging to sails-validate
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6663fed

Commits on Oct 20, 2025

Added masked RSCC function
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c774882
Added links to return structure
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f886814
Fixed bug with extra comma with 1 cycle jobs
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b327d5b

Commits on Oct 21, 2025

Added sails-validate global RSCC calculation
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491dc92
Added space group to structure
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bcd5618
Refactored RSCC calculation to support EM formfactors
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4d06dde

Commits on Oct 22, 2025

Added global RSCC score in per cycle removal
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d308346
Updated compare script
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72a7c95

Commits on Oct 23, 2025

Updated protein finding to use glycan prediction too
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a06f03f
Added better clash score which counts all but donor atom clash
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bb1846d
Added sequential sites to autoglycosylate
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10ce8f0
Fixed bug with chain names not going past Z
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051a5d7
Fixed bug with chain names not going past Z
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acb981b
Added functions to remove free sugars
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9ccb3ea
Added functions to remove free sugars
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1439b86

Commits on Oct 24, 2025

Added searchtype to sails-find em
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58e196a
Added preddirin to sails-find em
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5f8bf31
Added preddirin to sails-find em
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c8c4cde
Added preddirin to sails-find em
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04a7ec1

Commits on Oct 25, 2025

Added skipping of glycosites in EM mode
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5872518
Added Q Score to Sails
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528f60c

Commits on Oct 26, 2025

Added FUC clash removal
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79214f8
Added q score option to validate
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5898912

Commits on Oct 27, 2025

Added Q Score threshold calculation
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a5b9cf3
Added early stopping to X-ray cycles
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606e34d
Fixed bug in FUC clash score
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d74c267
Inlined util methods
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838f52d
Added back sites
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4be2df5

Commits on Oct 28, 2025

Commits on Nov 4, 2025

Fixed issue with missing donor atoms
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23c5523
Updated data.json
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8aa0aee

Commits on Nov 5, 2025

Removed bad clusters in data.json
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4a258a1

Commits on Dec 10, 2025

Updated prediction commandline to remove -m requirement
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5b974b6
Updated basic testing
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a477b94