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nifets · May 20, 2023 · d1bf11c · d1bf11c
1 parent 46d796c
commit d1bf11c
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Showing 7 changed files with 10,920 additions and 11,194 deletions.
diff --git a/.ipynb_checkpoints/Globins Experiment-checkpoint.ipynb b/.ipynb_checkpoints/Globins Experiment-checkpoint.ipynb
diff --git a/.ipynb_checkpoints/Simulated Experiment-checkpoint.ipynb b/.ipynb_checkpoints/Simulated Experiment-checkpoint.ipynb
diff --git a/Globins Experiment.ipynb b/Globins Experiment.ipynb
diff --git a/Simulated Experiment.ipynb b/Simulated Experiment.ipynb
diff --git a/data/pdb/1M4F.pdb b/data/pdb/1M4F.pdb
diff --git a/src/inference/AncestorSampling.jl b/src/inference/AncestorSampling.jl
@@ -27,7 +27,7 @@ end
 end
 
 
-function sample_anc_coords_wn(p, descs, t; burn_in=300)
+function sample_anc_coords_wn(p, descs, t; burn_in=600)
     sampler = MH(:x => v -> MixtureModel([WrappedNormal(v, I), WrappedNormal(v, 20*I)], [0.8, 0.2]))
     n = size(descs[1], 2)
     D = length(descs)
@@ -56,9 +56,17 @@ function sample_anc_coords_sub(p, descs, t; burn_in=5)
     return X
 end
 
+function sample_anc_coords_sub2(p, descs, t; burn_in=5)
+    n = size(descs[1], 2)
+    for i ∈ 1:n
+        X[1, i] = 1
+    end
+    return X
+end
+
 function sample_anc_coords(p, descs, t)
     if eltype(p) <: Integer
-        return sample_anc_coords_sub(p, descs, t)
+        return sample_anc_coords_sub2(p, descs, t)
     else
         return sample_anc_coords_wn(p, descs, t)
     end

diff --git a/src/objects/Backbone.jl b/src/objects/Backbone.jl
@@ -86,7 +86,7 @@ function backbone_bond_angles_and_lengths(chain::BioChain)
         for j ∈ 1:3
             atoms[j] = new_atoms[j]
             bond_angles[j, i] = bondangle(atoms[j%3+1], atoms[(j+1)%3+1], atoms[j])
-            bond_lengths[j, i] = distance(atoms[(j+1)%3+1], atoms[j])
+            bond_lengths[j, i] = BioStructures.distance(atoms[(j+1)%3+1], atoms[j])
         end
     end
     return bond_angles, bond_lengths