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New main #53

Merged
merged 366 commits into from
Jan 10, 2024
Merged

New main #53

merged 366 commits into from
Jan 10, 2024

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Dingel321
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adds the current code to the main branch

Dingel321 and others added 30 commits March 14, 2023 19:35
@Dingel321
changed that ctf is randomly selected at each image
e208ed9
@Dingel321
changed that ctf is randomly selected at each image
3698158
@Dingel321
chnaged calculation of ctf (less copying of tensors), add log prior f…
e348b86 
…or snr
@Dingel321
chnaged calculation of ctf (less copying of tensors), add log prior f…
f4a5e38 
…or snr
@Dingel321
minor changes to external files
329c538
@Dingel321
minor changes to external files
3b51d1a
@Dingel321
updated readme with training
377b739
@Dingel321
updated readme with training
2abfbf2
fix memory error in simulator
9713be0
fix memory error in simulator
5273692
removed unwanted dir
97f3c5e
removed unwanted dir
3eb19c6
Merge branch 'iss7' of github.com:DSilva27/cryo_em_SBI into iss7
7430bd4
Merge branch 'iss7' of github.com:DSilva27/cryo_em_SBI into iss7
03d48d7
fix return error in simulator
e520b39
fix return error in simulator
4269889
update tutorial
4fda03b
update tutorial
b025278
Merge branch 'develop' into iss6
1501de7 
include fixes from Lars
Merge branch 'develop' into iss6
8d46d7a 
include fixes from Lars
fixes some default variables in inference methods
242fc0f
fixes some default variables in inference methods
a00524d
implement unit tests for the simulator
f31e472
implement unit tests for the simulator
245766a
@DSilva27
Create python-package.yml
60630b0
@DSilva27
Create python-package.yml
9aa29f8
@DSilva27
Merge pull request #10 from DSilva27/iss8
d34f9d3 
Create python-package.yml
@DSilva27
Merge pull request #10 from DSilva27/iss8
7d27ed9 
Create python-package.yml
@DSilva27
Revert "Create python-package.yml"
a67db6a
@DSilva27
Revert "Create python-package.yml"
532e853
Dingel321 and others added 27 commits July 3, 2023 20:07
@Dingel321
notebook update
7cb0ca0
@Dingel321
notebook update
ca27183
@Dingel321
added all functions to simulator
3867c34
@Dingel321
new version gpu simulator
f34e26b
@Dingel321
added backbone of eval_log_prob class
3debf9a
@Dingel321
small bug fixes and changes in the embeddings
23e0a65
@DSilva27
include physical information in simulator and implement pdb/traj parser
d953d01 
closes #24
@DSilva27
replace SIGMA for RES in every instance
2f03b8c
@Dingel321
updated all atom branch
2905945
@Dingel321
changed code formatting
6fc6c22
@Dingel321
fixed bug in traj parser and npewithembedding
b9f8ddb
@Dingel321
changed definition of atom sigma to bioEM radius
f4e2481
@Dingel321
added embedding nets for all expermental setups
29353ec
@Dingel321
ficed bug in pdb parser
ecf0020
@Dingel321
introduced goarse grained lipid bead
d8e708e
@Dingel321
Merge branch 'iss42' of https://github.com/DSilva27/cryo_em_SBI into …
7a92214 
…iss42
@Dingel321
batched simulator in CryoEmSimulator class
47631ef
@Dingel321
all beads are the same in simulator
121bb32
@Dingel321
removed old notebooks and experiment files
1688086
@Dingel321
removed deprecated tests and added config files and models for tests
c0cffdf
@Dingel321
updated the readme
902805b
@Dingel321
chnaged title of repo in readme
84a5ceb
@Dingel321
titile typo
4d7002a
@Dingel321
added pdb and traj parser to generate_model.pdb
9c5b59b
@Dingel321
added eval_log_prob function
6225a18
@Dingel321
cleaned train_npe
762b900
@Dingel321
updated doc strings in generate models
a5c9bf9
@Dingel321
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adds current cryoSBI code to the main branch

@Dingel321 Dingel321 requested a review from DSilva27 January 8, 2024 14:07
@Dingel321 Dingel321 merged commit c6d4db6 into main Jan 10, 2024
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@Dingel321 @DSilva27