Add support for fastidentity searchtype to enhance search capabilities #43
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ssing the operation value enables PubChemPy to execute a fast identity search with POST. The original response = request() statement was put into the else clause of the if statement.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The PubChem REST API fastidentity searchtype includes support for search by SMILES string to identify multiple stereoisomers of the same canonical SMILES string. A simple if: else: construct was added to the PubChemPy get() function to pass the operation value, thus enabling synchronous ("fast") input searches. (https://pubchemdocs.ncbi.nlm.nih.gov/pug-rest).
This was tested for the get_compounds() and get_cids() functions and found to perform as expected to return multiple isomers by canonical SMILES search.
PubChem "fast" searches cover several types, in addition to the fastidentity search, and may similarly be supported by changing the equality test to a test for presence of the searchtype in a list. This is beyond the scope of this pull request but may require little effort to implement.
The code change preserves the original result = request() expression in the else: clause and places the modified call, which includes the operation (in place of None in the original call), in the if (True): clause.