Commits · 8a38690a1efee68291fc060c5d3fc9f83e91a7ae · schwede / openstructure

Feb 06, 2023
- fix: SCHWED-5783 distinguish between 0 lDDT and no match · 8a38690a
  Xavier Robin authored 2 years ago
  
  8a38690a
- fix: SCHWED-5783 catch absence of ligands · e2e8a084
  Xavier Robin authored 2 years ago
  
  Raise a ValueError upon initialization.
  e2e8a084
Feb 01, 2023
- fix: SCHWED-5783 make element uppercase by convention · 1494e7dd
  Xavier Robin authored 2 years ago
  
  Fixes the SDF reader and documents the convention.
  1494e7dd
Jan 30, 2023
- refactor: don't expose graphs · 244eee73
  Xavier Robin authored 2 years ago
  
  Reason is, it's unclear if they are useful anywhere else
  244eee73
- refactor: SCHWED-5783 shorten calls · 8cc728bb
  Xavier Robin authored 2 years ago
  
  8cc728bb
- fix: SCHWED-5783 element case is unspecified in OST · 1d2abe08
  Xavier Robin authored 2 years ago
  
  1d2abe08
Jan 27, 2023
- cleanup: SCHWED-5783 drop assignment matrices · ed65571c
  Xavier Robin authored 2 years ago
  
  Qualified name value is not useful. Plus they are redundant with the details.
  ed65571c
- refactor: use chain/resname dict to avoid qualified name as keys · dd555b97
  Xavier Robin authored 2 years ago
  
  dd555b97
Jan 26, 2023
- feat: SCHWED-5783 add transform to output · d2fbbd73
  Xavier Robin authored 2 years ago
  
  d2fbbd73
- doc: SCHWED-5783 values for unmapped ligands · 8ce60a37
  Xavier Robin authored 2 years ago
  
  8ce60a37
Jan 24, 2023
- fix: SCHWED-5783 add bonds to copied ligand · 896a60cc
  Xavier Robin authored 2 years ago
  
  896a60cc
- fix: SCHWED-5783 assign within function · ba860473
  Xavier Robin authored 2 years ago
  
  ba860473
- refactor: SCHWED-5783 defer assignment · 13c8ab8e
  Xavier Robin authored 2 years ago
  
  13c8ab8e
- feat: SCHWED-5783 report progress during processing · ca81bec6
  Xavier Robin authored 2 years ago
  
  ca81bec6
- feat: SCHWED-5783 raise if ligands are not connected · 11565642
  Xavier Robin authored 2 years ago
  
  11565642
Jan 23, 2023
- test: SCHWED-5783 add missing test file · fbcea5c1
  Xavier Robin authored 2 years ago
  
  fbcea5c1
- feat: SCHWED-5783 enable tests in CI · dfd555b3
  Xavier Robin authored 2 years ago
  
  Loading networkX module is hopefully enough
  dfd555b3
- test: SCHWED-5783 test the right matrix · e3a209fd
  Xavier Robin authored 2 years ago
  
  e3a209fd
- doc: fix duplicate object description warning · f3b7497c
  Xavier Robin authored 2 years ago
  
  f3b7497c
- doc: SCHWED-5783 fixup doc · 997dd186
  Xavier Robin authored 2 years ago
  
  997dd186
- fix: SCHWED-5783 set graph attributes correctly · a4bb106d
  Xavier Robin authored 2 years ago
  
  This fixes substructure matches
  a4bb106d
- cleanup: SCHWED-5783 code cleanup · 88397abc
  Xavier Robin authored 2 years ago
  
  88397abc
- fix: SCHWED-5783 no longer needed · e58a2afa
  Xavier Robin authored 2 years ago
  
  Fixed elsewhere by b6270ff1
  e58a2afa
- Merge remote-tracking branch 'origin/develop' into ligand_scoring · 67c33d7b
  Xavier Robin authored 2 years ago
  
  67c33d7b
- test: SCHWED-5783 updated matrix access · 7cde8441
  Xavier Robin authored 2 years ago
  
  7cde8441
- test: SCHWED-5783 test the score results · 7f1e83e2
  Xavier Robin authored 2 years ago
  
  7f1e83e2
- refactor: SCHWED-5783 use np.inf for consistency · fbb5102e
  Xavier Robin authored 2 years ago
  
  fbb5102e
- doc: SCHWED-5783 document new properties · 67a83442
  Xavier Robin authored 2 years ago
  
  67a83442
- feat: SCHWED-5783 report qualified name in mapping · d6d2e258
  Xavier Robin authored 2 years ago
  
  d6d2e258
- feat: SCHWED-5783 skip confusing local lDDT values · b4978ef2
  Xavier Robin authored 2 years ago
  
  b4978ef2
- feat: SCHWED-5783 silence the warnings · 68d45c2a
  Xavier Robin authored 2 years ago
  
  68d45c2a
- guard against nonsense results in ChainMapper.GetRepr() · b6270ff1
  Studer Gabriel authored 2 years ago
  
  Nonsense results in that context means that the model does not cover the desired substructure in target.
  b6270ff1
- code cleanup · b68f5e4e
  Studer Gabriel authored 2 years ago
  
  b68f5e4e
- change way of selecting interface residues in order to be consistent with DockQ · f175d4c1
  Studer Gabriel authored 2 years ago
  
  f175d4c1
Jan 22, 2023
- dockq refactor · 1541e13a
  Studer Gabriel authored 2 years ago
  
  1541e13a
Jan 20, 2023
- feat: SCHWED-5783 implement ligand assignment · d5e9393e
  Xavier Robin authored 2 years ago
  
  d5e9393e
- test: SCHWED-5783 speedup test · e04275f7
  Xavier Robin authored 2 years ago
  
  e04275f7
Jan 19, 2023
- feat: SCHWED-5783 add check_resname · 7d956e81
  Xavier Robin authored 2 years ago
  
  7d956e81
- doc: SCHWED-5783 add new functions · fa54de98
  Xavier Robin authored 2 years ago
  
  fa54de98
- Merge branch 'develop' into ligand_scoring · 711872ee
  Xavier Robin authored 2 years ago
  
  711872ee