Update README.md

README.md

@@ -5,11 +5,21 @@
 NB: before running the test codes,please download the procrustes package first:
 from https://github.com/theochem/procrustes
 
-
-The only file that has been changed is:
+To test the permutation codes:
+```bash
+python -m unittest tests/test_permutation.py
+```
+The files that has been changed is:
 [```openfold/utils/loss.py```](https://github.com/dingquanyu/openfold/blob/permutation/openfold/utils/loss.py), in which the forward function is modified in 
-original ```AlphaFoldLoss``` class; create a child class called ```AlphaFoldMultimerLoss``` that not only inherited all the loss calculations but also 
-has multi-chain permutation codes.
+original ```AlphaFoldLoss``` class; 
+
+create a child class called ```AlphaFoldMultimerLoss``` that not only inherited all the loss calculations but also 
+has multi-chain permutation codes; 
+
+some loss calculations have to be modified e.g. in ```fape``` loss, ```tm``` loss calculations, an extra validation was added to check if the input tensor belongs to tensor_7 or tensor_4*4
+
+[```openfold/config.py```](https://github.com/dingquanyu/openfold/blob/permutation/openfold/config.py) has seen a couple of modifications as well. Some namings were wrong and previous script forgot to update  config.loss with multimer_model_config_update
+
 
 These files are newly added:
 [```tests/test_permutation.py```](https://github.com/dingquanyu/openfold/blob/permutation/tests/test_permutation.py): A unittest script