Fix confusing default torch transform #21
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added 5 commits
September 25, 2024 16:39
…d use simpler default encoding containing the integer index of the string defined in pinder constants
… for the residue_coordinates property; also add atom names and element names separately
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* fix: element_types were left out of collate function after PR #21 * docs: re-run cached loader notebooks --------- Co-authored-by: danielkovtun <[email protected]>
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Fixed
structure2tensor_transformin thetorchPinderDatasetwas usingatom_coordinatesforresidue_coordinates. This PR fixes that by setting residue_coordinates to the coordinates of the c-alpha atomsChanged
structure2tensorencoding was previously storing a one-hot encoding of element numbers in the returnedatom_typeskey. This PR removes some of this confusion by using a consistent tensor dimension matching the convention forresidue_typesand introduces an additional keyelement_typesto store the element integer encodingsatom_typesis adjusted to represent atom names/types, not elements, and now stores the atom name integer encodings derived frompinder.core.utils.constants.ALL_ATOM_POSNSNotes
Reminder: the encodings used by default in the
PinderDatasetandPPIDatasetdataset classes are only example implementations. The default transform(s) can and likely should be customized to fit the end-user's featurization/loading workflow.Closes #20 - thanks for catching and reporting the
residue_coordinatesbug @eswan01!