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d766458 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 | # TrDesign in JAX!
Work in Progress...
For original version implemented in keras see: https://github.com/gjoni/trDesign/tree/master/02-GD
### Google Colab
<a href="https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/tr/design.ipynb">
<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
</a>
### install
```bash
pip install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1
# download weights
if [ ! -d params/tr ]; then
mkdir -p params/tr
wget -qnc https://files.ipd.uw.edu/krypton/TrRosetta/models.zip
wget -qnc https://files.ipd.uw.edu/krypton/TrRosetta/bkgr_models.zip
unzip -qqo models.zip -d params/tr/
unzip -qqo bkgr_models.zip -d params/tr/
fi
```
### example
```python
from colabdesign import *
clear_mem()
tr_model = mk_trdesign_model(protocol="fixbb")
tr_model.prep_inputs(get_pdb("6MRR"), chain="A")
tr_model.design(100, verbose=10)
tr_model.plot()
print(tr_model.get_loss())
print(tr_model.get_seq())
```
### example
combine AfDesign and TrDesign for fixed backbone design
```python
from colabdesign import *
clear_mem()
af_model = mk_afdesign_model(protocol="fixbb")
af_model.prep_inputs(get_pdb("1TEN"))
tr_model = mk_trdesign_model(protocol="fixbb")
tr_model.prep_inputs(get_pdb("1TEN"))
af_model.restart()
af_model.design_3stage(callback=tr_model.af_callback())
```
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