ndbapi is a Python API for the advanced search interface of the Nucleic Acid DB (http://ndbserver.rutgers.edu/ndbmodule/search/integrated.html).

ndbapi requires Python 2.6+ or any Python 3 (any version).

$ pip install --user git+https://github.com/gilesc/ndbapi.git

Overall, usage is simple: the user constructs a ndbapi.Client object, and then calls Client.query(params), where params is a dictionary of parameters to be searched upon. There are many possible parameters, and any parameters not supplied by the user will be left at their defaults.

The query will return a Result object containing the search parameters and results as if they had been exported to CSV. The main attribute of interest will be the Result.data attribute, which contains a pandas.DataFrame containing the result set. Alternatively, the result can be saved, which will export the result set with some metadata. For example:

from ndbapi import Client

api = Client()
rs = api.query({"citation_information.PDB_ID.value": "4WLS"})

# will print top 10 search results (in this case just one)
print(rs.data.head())

# saves results to TSV format with search parameters and search time as a header
rs.save("results.tsv")

Most of the complexity from the API comes from the fact that there are many options, each with different sets of possible values. To see the full list of options and allowed values for each, use the Client.print_options() function. The options will be printed in the same order as they appear on the NDB Advanced Search page, top to bottom and left to right. Keys which have a None as the allowed set of values accept any string (note, however, that these fields often have a specific meaning, such as PDB ID or a numeric parameter, constraining the set of strings that will in practice be useful).

Query keys come in the form of "$category.$item.$attribute". A category corresponds to one of the groupings of parameters on the Advanced Search page. An item is one particular input parameter, which may actually have several input fields, called an attribute. The type of attribute determines what valid values will be allowed. Here are a few:

• bitop : the binary operation attached to most fields on the query form (accepts "AND" or "OR")
• nop : numeric operation : ("gtEq", "ltEq", "eq")
• value : the selected button of a radio button selection (e.g., "Y"/"N"/"Ignore", "EITHER"/"RNA"/"DNA") or a free-text field
• choice : the choice from a single-choice selection box
• choices : a list of choices from a multiple-choice selection box
• minimum, maximum, and cutoff - numeric fields (accepts strings or floats)

Please use the Github issue tracker.

AGPL3+