Merge branch 'main' of https://github.com/kevinmicha/predicting-affinity

kevinmicha · Dec 11, 2023 · 182c9de · 182c9de
2 parents c3656c0 + 3883cc6
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diff --git a/checkpoints/model_unit_test.pt b/checkpoints/model_unit_test.pt
diff --git a/notebooks/[Analysis] AlphaFold can be useful if only sequences are available.ipynb b/notebooks/[Analysis] AlphaFold can be useful if only sequences are available.ipynb
diff --git a/notebooks/[Tutorial] Explaining affinity using ANTIPASTI.ipynb b/notebooks/[Tutorial] Explaining affinity using ANTIPASTI.ipynb
diff --git a/notebooks/biological_properties/aromaticity.npy b/notebooks/biological_properties/aromaticity.npy
diff --git a/notebooks/biological_properties/charge.npy b/notebooks/biological_properties/charge.npy
diff --git a/notebooks/biological_properties/hydrophobicity.npy b/notebooks/biological_properties/hydrophobicity.npy
diff --git a/notebooks/biological_properties/polarity.npy b/notebooks/biological_properties/polarity.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/1m7d.npy b/notebooks/test_data/paired_hl/dccm_map/1m7d.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/1m7d_af.npy b/notebooks/test_data/paired_hl/dccm_map/1m7d_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/1oay.npy b/notebooks/test_data/paired_hl/dccm_map/1oay.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/1oay_af.npy b/notebooks/test_data/paired_hl/dccm_map/1oay_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/1zv5.npy b/notebooks/test_data/paired_hl/dccm_map/1zv5.npy
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diff --git a/notebooks/test_data/paired_hl/dccm_map/2hkf.npy b/notebooks/test_data/paired_hl/dccm_map/2hkf.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/2hkf_af.npy b/notebooks/test_data/paired_hl/dccm_map/2hkf_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/2p44.npy b/notebooks/test_data/paired_hl/dccm_map/2p44.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/2p44_af.npy b/notebooks/test_data/paired_hl/dccm_map/2p44_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/3g5y.npy b/notebooks/test_data/paired_hl/dccm_map/3g5y.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/3g5y_af.npy b/notebooks/test_data/paired_hl/dccm_map/3g5y_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/3l95.npy b/notebooks/test_data/paired_hl/dccm_map/3l95.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/3l95_af.npy b/notebooks/test_data/paired_hl/dccm_map/3l95_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/3u0t.npy b/notebooks/test_data/paired_hl/dccm_map/3u0t.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/3u0t_af.npy b/notebooks/test_data/paired_hl/dccm_map/3u0t_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4ffz.npy b/notebooks/test_data/paired_hl/dccm_map/4ffz.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4ffz_af.npy b/notebooks/test_data/paired_hl/dccm_map/4ffz_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4jan.npy b/notebooks/test_data/paired_hl/dccm_map/4jan.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4jan_af.npy b/notebooks/test_data/paired_hl/dccm_map/4jan_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4odx.npy b/notebooks/test_data/paired_hl/dccm_map/4odx.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4odx_af.npy b/notebooks/test_data/paired_hl/dccm_map/4odx_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4w6w.npy b/notebooks/test_data/paired_hl/dccm_map/4w6w.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/4w6w_af.npy b/notebooks/test_data/paired_hl/dccm_map/4w6w_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/5alb.npy b/notebooks/test_data/paired_hl/dccm_map/5alb.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/5alb_af.npy b/notebooks/test_data/paired_hl/dccm_map/5alb_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/5dd0_af.npy b/notebooks/test_data/paired_hl/dccm_map/5dd0_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/5i8c.npy b/notebooks/test_data/paired_hl/dccm_map/5i8c.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/5i8c_af.npy b/notebooks/test_data/paired_hl/dccm_map/5i8c_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/6a0z_af.npy b/notebooks/test_data/paired_hl/dccm_map/6a0z_af.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/6eyo.npy b/notebooks/test_data/paired_hl/dccm_map/6eyo.npy
diff --git a/notebooks/test_data/paired_hl/dccm_map/6eyo_af.npy b/notebooks/test_data/paired_hl/dccm_map/6eyo_af.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/1m7d.npy b/notebooks/test_data/paired_hl/list_of_residues/1m7d.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/1oay.npy b/notebooks/test_data/paired_hl/list_of_residues/1oay.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/1zv5.npy b/notebooks/test_data/paired_hl/list_of_residues/1zv5.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/2hkf.npy b/notebooks/test_data/paired_hl/list_of_residues/2hkf.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/2p44.npy b/notebooks/test_data/paired_hl/list_of_residues/2p44.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/3g5y.npy b/notebooks/test_data/paired_hl/list_of_residues/3g5y.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/3l95.npy b/notebooks/test_data/paired_hl/list_of_residues/3l95.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/3u0t.npy b/notebooks/test_data/paired_hl/list_of_residues/3u0t.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/4ffz.npy b/notebooks/test_data/paired_hl/list_of_residues/4ffz.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/4jan.npy b/notebooks/test_data/paired_hl/list_of_residues/4jan.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/4odx.npy b/notebooks/test_data/paired_hl/list_of_residues/4odx.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/4w6w.npy b/notebooks/test_data/paired_hl/list_of_residues/4w6w.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/5alb.npy b/notebooks/test_data/paired_hl/list_of_residues/5alb.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/5i8c.npy b/notebooks/test_data/paired_hl/list_of_residues/5i8c.npy
diff --git a/notebooks/test_data/paired_hl/list_of_residues/6eyo.npy b/notebooks/test_data/paired_hl/list_of_residues/6eyo.npy
diff --git a/notebooks/test_data/structure/3g5y.pdb b/notebooks/test_data/structure/3g5y.pdb
diff --git a/notebooks/test_data/structure/3g5y_af.pdb b/notebooks/test_data/structure/3g5y_af.pdb
diff --git a/notebooks/test_data/structure/4ffz.pdb b/notebooks/test_data/structure/4ffz.pdb
diff --git a/notebooks/test_data/structure/4ffz_af.pdb b/notebooks/test_data/structure/4ffz_af.pdb
diff --git a/notebooks/test_data/structure/4jan.pdb b/notebooks/test_data/structure/4jan.pdb
diff --git a/notebooks/test_data/structure/4jan_af.pdb b/notebooks/test_data/structure/4jan_af.pdb
diff --git a/notebooks/test_data/structure/5alb.pdb b/notebooks/test_data/structure/5alb.pdb
diff --git a/notebooks/test_data/structure/5alb_af.pdb b/notebooks/test_data/structure/5alb_af.pdb
diff --git a/notebooks/test_data/structure/5dd0_af.pdb b/notebooks/test_data/structure/5dd0_af.pdb
diff --git a/notebooks/test_data/structure/5i8c.pdb b/notebooks/test_data/structure/5i8c.pdb
diff --git a/notebooks/test_data/structure/5i8c_af.pdb b/notebooks/test_data/structure/5i8c_af.pdb
diff --git a/notebooks/test_data/structure/6a0z_af.pdb b/notebooks/test_data/structure/6a0z_af.pdb
diff --git a/notebooks/test_data/structure/6eyo.pdb b/notebooks/test_data/structure/6eyo.pdb
diff --git a/notebooks/test_data/structure/6eyo_af.pdb b/notebooks/test_data/structure/6eyo_af.pdb
diff --git a/tests/explaining_test.py b/tests/explaining_test.py
@@ -60,4 +60,4 @@ def test_explaining(self):
         compute_umap(preprocessed_data, model, scheme='antigen_type', categorical=True, include_ellipses=False, numerical_values=None, external_cdict=None, interactive=True)
         compute_umap(preprocessed_data, model, scheme='antigen_species', categorical=True, include_ellipses=False, numerical_values=None, external_cdict=cdict, interactive=True)
         compute_umap(preprocessed_data, model, scheme='Random sequence', categorical=False, include_ellipses=False, numerical_values=random_sequence, external_cdict=None, interactive=True)
-        compute_umap(preprocessed_data, model, scheme='Random sequence', categorical=False, include_ellipses=False, numerical_values=random_sequence_delete, external_cdict=None, interactive=True)
+        compute_umap(preprocessed_data, model, scheme='Random sequence', categorical=False, include_ellipses=False, numerical_values=random_sequence_delete, external_cdict=None, interactive=True)