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COD database importer

COD database importer is used to import crystal structures from the Crystallography Open Database (COD) to AiiDA.

Setup

An instance of :pyCodDbImporter <aiida.tools.dbimporters.plugins.cod.CodDbImporter> is created as follows:

from aiida.tools.dbimporters.plugins.cod import CodDbImporter
importer = CodDbImporter()

No additional parameters are required for standard queries on the main COD server.

How to do a query

A search is initiated by supplying query statements using keyword=value syntax:

results = importer.query(chemical_name="caffeine")

List of possible keywords can be listed using:

importer.get_supported_keywords()

Values for the most of the keywords can be list. In that case the query will return entries, that match any of the values (binary OR) from the list. Moreover, in the case of multiple keywords, entries, that match all the conditions imposed by the keywords, will be returned (binary AND).

Example:

results = importer.query(chemical_name=["caffeine","serotonin"],
                         year=[2000,2001])

is equivalent to the following SQL statement:

results = SELECT * FROM data WHERE
            ( chemical_name == "caffeine" OR chemical_name == "serotonin" ) AND
            ( year = 2000 OR year = 2001 )

A query returns an instance of :pyCodSearchResults <aiida.tools.dbimporters.plugins.cod.CodSearchResults>, which can be used in a same way as a list of :pyCodEntry <aiida.tools.dbimporters.plugins.cod.CodEntry> instances:

print len(results)

for entry in results:
    print entry

Using data from :pyCodEntry <aiida.tools.dbimporters.plugins.cod.CodEntry>

:pyCodEntry <aiida.tools.dbimporters.plugins.cod.CodEntry> has a few functions to access the contents of it's instances:

CodEntry.get_aiida_structure()
CodEntry.get_ase_structure()
CodEntry.get_cif_node()
CodEntry.get_parsed_cif()
CodEntry.get_raw_cif()