Exploring Schema Attributes¶

Attributes are pieces of information associated with a PDB structure that can be searched for or compared to a value using an AttributeQuery. There are structure attributes and chemical attributes, which are both stored in rcsb_attributes. This can be imported as shown below:

# import rcsb_attributes as attrs for a shorter name
from rcsbsearchapi import rcsb_attributes as attrs

There are several helpful methods to search for attribute names or explore other information related to attributes.

search()¶

Given a string, this method will return an iterable of Attr objects with names that contain the given string. You can also use regular expression (regex) strings.

matching_attrs = attrs.search("author")

for attr in matching_attrs:
    print(attr)

get_attribute_details()¶

Given a full or partial attribute name, return a set of an Attr or associated Attrs with attribute names, search service types, and descriptions.

from rcsbsearchapi import rcsb_attributes as attrs

# Use a full name to get details for a specific attribute
print(attrs.get_attribute_details("rcsb_entity_source_organism.scientific_name"))

# Use a partial name to get the details of all attributes associated with that name
# Below code gets details for ".common_name", ".source_type", etc in addition to ".scientific_name"
print(attrs.get_attribute_details("rcsb_entity_source_organism"))

get_attribute_type()¶

Given a full attribute name, return the search service type (“text” for structure attributes and “text_chem” for chemical attributes).

from rcsbsearchapi import rcsb_attributes as attrs
 
print(attrs.get_attribute_type("rcsb_entity_source_organism.scientific_name"))