JW – Today, should we IP – Added atom name info to substructure dictionary, JSON now contains an additional list of the atom names to be assigned for each SMARTS. IP – Is it a good pattern to have the substructure library object delete its own contents every time we ask it to read a cif file? JW – The more reasonable behavior is probably to have it not clear itself every time it reads a new cif file. Instead we should change how we use the substructure library object, so that we only do sequential reads when we want two cif files to be combined. IP – By default it combines structures (merge information on sequential reads). Added a explicit clear_data method for removing existing data and start from scratch using the same object.
Tests for residue perception (files to add to OFF Toolkit) T4.sdf – May have unlabeled atom(s) – Should be decorated wiht pytest.mark.slow NTerminal/ALA.sdf – May have unlabeled atom(s) CTerminal/ALA.sdf – May have unlabeled atom(s) MainChain/ALA.sdf – Test that there ARE unlabeled atoms when we don’t add cap substructures, then add the cap substructure dictionary and ensure that there are ARE NOT unlabeled atoms MainChain/CYX.sdf MainChain/GLU.sdf MainChain/GLH.sdf MainChain/ARG.sdf MainChain/HIE|HID|HIP.sdf
Could make perceive_residues and from_pdb_file fill in a molecule properties entry containing the details of how the metadata was assigned We’ll make a UserDict-style class for atom metadata for now, since Pydantic will be super hard to change after the initial implementation.
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