Merge pull request #7 from kevinmicha/kevinmicha-patch-1

Update citing.rst

antipasti/preprocessing/preprocessing.py

@@ -580,9 +580,9 @@ def load_training_images(self):
 
         assert labels == [item for item in self.selected_entries if item not in self.pathological]
 
-        for pdb in self.selected_entries:
-            if pdb not in self.pathological and self.affinity_entries_only:
-                assert np.float16(10**kds[[item for item in self.selected_entries if item not in self.pathological].index(pdb)] == np.float16(self.df[self.df['pdb']==pdb]['affinity'])).all()
+        #for pdb in self.selected_entries:
+        #    if pdb not in self.pathological and self.affinity_entries_only:
+        #        assert np.float16(10**kds[[item for item in self.selected_entries if item not in self.pathological].index(pdb)] == np.float16(self.df[self.df['pdb']==pdb]['affinity'])).all()
 
         return np.array(imgs), np.array(kds), labels, raw_imgs
 
@@ -623,4 +623,4 @@ def load_test_image(self):
                 h = h[0]
                 l = l[0]
 
-        return self.generate_masked_image(raw_sample, 0, test_h=int(h), test_l=int(l))[0]
+        return self.generate_masked_image(raw_sample, 0, test_h=int(h), test_l=int(l))[0]

docs/citing.rst

@@ -3,4 +3,4 @@ Citing ANTIPASTI in a publication
 
 If you want to acknowledge ANTIPASTI in a publication, we suggest you to cite:
 
-Kevin Michalewicz, Mauricio Barahona and Barbara Bravi. ANTIPASTI: interpretable prediction of antibody binding affinity exploiting Normal Modes and Deep Learning. bioRxiv 2023.12.22.572853; doi: `https://doi.org/10.1101/2023.12.22.572853 <https://doi.org/10.1101/2023.12.22.572853>`_
+Kevin Michalewicz, Mauricio Barahona and Barbara Bravi (2024). ANTIPASTI: Interpretable prediction of antibody binding affinity exploiting normal modes and deep learning. Structure, `https://doi.org/10.1016/j.str.2024.10.001 <https://doi.org/10.1016/j.str.2024.10.001>`_

docs/conf.py

@@ -147,5 +147,5 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/', None)}