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ANNOTATION_COLS = ["can_smiles", "abbrev", "website", "externa
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Find an item in the chemical table based on a specified searchColumn and value. Will only return the first chemical result so typically only want to search by a unique identifier like "can_smiles" or "chemical_id." Returns a RowItemModel dictionary representing all of the data found in that row. In addition, count up the number of isomer3d records under the chemical and store that in an entry named count_isomer3d. |
Find an item in the chemical table based on the given SMILES string. Then trace through the whole DB schema (chemical - mixturecomponent - chemicalmix - source2chemicalmix - source - annotation) to find all of the chemicalmix and sources this chemical belongs to. Furthermore, find all of the names and values of annotations applied to such chemical mixes, ordered by the source that specified the annotation. Do an outer-join. That is, if a chemical exists under some source, but no annotations exist, still at least report a row for that source with blank annotation values. The results should be a list of RowItemModel dictionaries, at least containing the following "columns" in each model object. chemicalmix.can_smiles source.abbrev source2chemicalmix.external_id annotation.name annotation.svalue annotation.fvalue |
Given a list of dictionaries (RowItemModels) representing Annotation rows from the annotationDictsBySmiles method, see if any of the rows match items in the annotation_metadata table whose specified metadataColumn is True. If so, remove those items from the original list, and return them in a new, separate list of annotation dictionary models. |
Given one or a list of chemical can_smiles values, return an iterator over OEMolBase objects representing the chemicals. Extra value of running the annotationDictsBySmiles method for each one and recording these values as SD Tags on the molecule object. If the molecule is subsequently output in SDF format, the caller can view these in file output. Note that this returns an iterator over the same molecule object, it just gets cleared and rewritten at each iteration. If for some reason you want a separate copy for each, you'll need to do that yourself by doing something like "copy = OEGraphMol(mol)" Since a chemical can belong to multiple chemical mixes, this is a little sloppy situation. May only want to count when the chemical is the "first largest component" of the mix or something. In the meantime, only record sources and external IDs this is under. idInfoOnly: If set to True, just load the found chemical_ids and molecule titles. Don't spend time searching for 3D structures or source information. |
Find an item in the chemical table based on the given SMILES string. Then find respective records in the isomer3d table and any SDF 3D molecular data files in particular. If so, then return an oemolistream of OEMolBase objects to represent the contents of these SD Files. If the smiles provided is actually a list, will return all SDFs under those chemical SMILES. Furthermore, include SD annotation tags for:
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ANNOTATION_COLS
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