extracting attributes for grover model from batch graph #3312
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arunppsg
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rbharath
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deepchem/feat/graph_data.py
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| @@ -336,6 +336,7 @@ def __init__(self, graph_list: Sequence[GraphData]): | |||
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| # graph_index indicates which nodes belong to which graph | |||
| # TODO should we rename this as node_index? | |||
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Can you remove TODO before merge?
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I have removed TODO but a question I have is should we rename graph_index as node_index because I think node_index is more descriptive. The variable here stores a mapping for every node and the graph to which the node belongs to.
deepchem/utils/grover.py
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| def _get_a2b(n_atoms, edge_index): | ||
| """a2b is a mapping between atoms and their incoming bonds |
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Can you add a Parameters section here documenting the types of the argument?
deepchem/utils/grover.py
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| def extract_grover_attributes(molgraph: BatchGraphData): | ||
| """Utility to extract grover attributes for grover model | ||
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| Parameter |
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typo: Parameters (missing "s")
rbharath
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@gusty1g Looks like some mypy errors which should be fixed before merge |
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Description
Related to #3296
This pull request proposes a new approach to extract required attributes for a grover model from a batched molecular graph.
Type of change
Please check the option that is related to your PR.
Checklist
yapf -i <modified file>and check no errors (yapf version must be 0.32.0)mypy -p deepchemand check no errorsflake8 <modified file> --countand check no errorspython -m doctest <modified file>and check no errors