Fix and enhance geometric node features #305
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## master #305 +/- ##
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+ Coverage 40.27% 44.10% +3.83%
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Files 48 113 +65
Lines 2811 7817 +5006
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+ Hits 1132 3448 +2316
- Misses 1679 4369 +2690
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Without this, `vec`s are of type object, which for example breks the smooth conversion to torch tensors.
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anton-bushuiev
changed the title
graphein/ml/visualisation.py
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| @@ -115,13 +116,17 @@ def plot_pyg_data( | |||
| d["coords"] = x.coords[i] | |||
| if node_colour_tensor is not None: | |||
| d["colour"] = float(node_colour_tensor[i]) | |||
| if hasattr(x, "c_beta_vector"): | |||
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This is a really nice idea. I think it would be better to generalise this and provide these as default arguments.
E.g.:
for node_vec in node_vector_features:
if hasattr(x, node_vec):
d[node_feat] = getattr(x, node_feat)[i]
graphein/ml/visualisation.py
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| @@ -135,3 +140,12 @@ def plot_pyg_data( | |||
| colour_nodes_by if node_colour_tensor is None else "colour", | |||
| colour_edges_by if edge_colour_tensor is None else "colour", | |||
| ) | |||
| if hasattr(x, "c_beta_vector"): | |||
|
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Hi, @a-r-j! Can you take another look at this? It would be nice if you could merge this. |
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Hey @anton-bushuiev sorry for being slow on this. Recently started a new job & this PR slipped through the cracks. Appreciate the contribution, as always. |
Reference Issues/PRs
rgroup_df=compute_rgroup_dataframe(remove_insertions(raw_pdb_df))#304H:CYS:104in3SE8).object, which breaks for example their smooth conversion to PyTorch tensors, when converting to PyG data.add_k_nn_edgesfor the case when some residues were dropped before (e.g. when some alt_locs are removed). The code ofadd_k_nn_edgesassumes the dataframe to have continuous index which is not true if some residues are dropped. For example the following line constructs continuousoutgoingwhich are then used to index dataframe:graphein/graphein/protein/edges/distance.py
Line 1127 in 371ce9a
I have also added the functionality to test whether a warning is raised by
loguruaccording to Delgan/loguru#59.What does this implement/fix? Explain your changes
What testing did you do to verify the changes in this PR?
Pull Request Checklist
./CHANGELOG.mdfile (if applicable)./graphein/tests/*directories (if applicable)./notebooks/(if applicable)python -m py.test tests/and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,python -m py.test tests/protein/test_graphs.py)black .andisort .