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Actifptm #187

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@gezmi gezmi commented Nov 29, 2024

  • added iPTM calculation
  • in predict.ipynb, the download links currently point to gezmi/Colabdesign, this needs to be corrected after merge.

gezmi added 30 commits February 11, 2024 16:27
@gezmi
returning dgram
bacf5ce
@gezmi
added calculation for interface ptm
f467bdf
@gezmi
returning if_ptm between all chain combinations
44ded08
@gezmi
correct import of get_ifptm
864ae44
@gezmi
corrected if_ptm calculations
ffa0c74
@gezmi
updated if_ptm function call
e48b3d7
@gezmi
make get_ifptm compatible with jax
ac78513
@gezmi
updated chain_indices function compatible with jax
8478135
@gezmi
getting chain indices from other source
673152e
@gezmi
geeting chain indices from other source
db3fe86
@gezmi
Update model.py
30a4e50
@gezmi
removed if_ptm code from model
1cba10f 
need to move the code outside
@gezmi
working get_ifptm
43ccdab
@gezmi
working get_ifptm
62b45be
@gezmi
get_ifptm works but gives unexpected results
34c081a
@gezmi
modified confidence to debug if_ptm
c7d1030
@gezmi
Update confidence.py
5972815
@gezmi
updated ifptm in case no interface exists
0a88639
@gezmi
Update loss.py
d08bc19
@gezmi
Update loss.py
e3201a2
@gezmi
Update model.py
1228576
@gezmi
Update confidence.py
24c68f5
@gezmi
Merge branch 'sokrypton:gamma' into gamma
9a72ff5
@gezmi
Revert "fixing jax.random.PRNGKeyArray error"
fee5405 
This reverts commit 4b30ecf.
@gezmi
Revert "Update confidence.py"
ad556f7 
This reverts commit 24c68f5.
@gezmi
Revert "Update model.py"
ebc7c96 
This reverts commit 1228576.
@gezmi
Revert "Update loss.py"
3027899 
This reverts commit e3201a2.
@gezmi
Revert "Revert "fixing jax.random.PRNGKeyArray error""
0455f6e 
This reverts commit fee5405.
@gezmi
remove error from confidence
7594bec
@gezmi
working function for getting if_ptm
07e4d0d
gezmi and others added 30 commits April 11, 2024 14:42
@gezmi
indentation correct
3bb4a24
@gezmi
update to accept custom pair_mask
c1ccdff
@gezmi
update with pairwise iptm and ifptm
dff410d
@gezmi
added 2 different ifptm calculations
f4027d7
@gezmi
calculate tm_score with contact probabilities
c8cf98f
@gezmi
update loss for ifptm
30dc15b
@gezmi
probability mask usage corrected
694cc6b 
probability is already normalized as input
@gezmi
changed input to ifptm calculation
1cfa7c3
@gezmi
changing back to pair-residue mask
e2c8414 
normalized mask needs to sum up to 1, the probability matrix will not
@gezmi
Update loss.py with correct input
77f4426
@gezmi
Update confidence.py
e1172ce
@gezmi
Created using Colab
61a0c59
added interface metrics to colabdesign
73be301
Merge remote-tracking branch 'origin/gamma' into gamma
4ae4f82
@gezmi
added interface analysis
c312f53
added interface metrics to colabdesign
e7f16c7
Merge remote-tracking branch 'origin/gamma' into gamma
3806a99
added chain ptm calculation
ff0249b
@gezmi
finished new ptm plots
f695435
@gezmi
corrected upper and lower triangle
e617dd2
@gezmi
renamed cell, cleared output
d1b6721
renamed to actifptm
3afe6dc
Merge remote-tracking branch 'origin/gamma' into gamma
803216a
@gezmi
created plotting for pariwise ptm-s and chain ptm
4557594
@gezmi
Rename chains_ptms.py to extended_metrics.py
860122e
@gezmi
adding extended metrics from colabfold
5b30946
@gezmi
Delete extended_metrics, replace from colabfold
752e475
@gezmi
fixed calculation of extended metrics
d14e96a
@gezmi
running all models by default
f155762
@gezmi
Merge branch 'sokrypton:gamma' into gamma
053c439
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