localpdb.PDB.search*

localpdb.PDB.search(attribute, operator, value, return_type='entry', 
                    no_hits=1000, get_doc_only=False, select=False)
Performs a basic search using the RCSB API. More information available at the RCSB website. Returns the DataFrame with entries satisfying the query and, sometimes, additional scoring information.

Parameter                           Description
attribute Attribute to perform a search on - the full list is available here.
operator Operator to use in the search - full list of operators available with corresponding attributes is available here.
value Value used in the search.
return_type Format of the returned entries that satisfy the query. Available options are entry (PDBID), polymer_entity (PDBID_ENTITY), polymer_instance (PDBID_CHAIN),
no_hits Number of presented hits. Default: no_hits=1000, use no_hits=-1 to get all hits.
get_doc_only Present only the dataframe with available attributes and operators.
select If True the results of the query will be used to perform selection on lpdb.entries (if return_type=='entries') or lpdb.chains (if return_type=='polymer_instance'). Moreover, if lpdb is instantiated with auto_filter mode, the selection will be propagated to other registered dataframes. 

localpdb.PDB.search_sequence(sequence, evalue=1, identity=0.9, return_type="polymer_instance", 
                             no_hits=1000, select=False)
Search for similar sequences to the input sequence among the entries available in the PDB database. Returns the DataFrame with sequences similar to the query and similarity statistics.

Parameter                           Description
sequence Input sequence.
evalue Minimum e-value to include a sequence.
identity Minimum identity to the query to include a sequence.
return_type Format of the returned entries that satisfy the query. Available options are entry (PDBID), polymer_entity (PDBID_ENTITY), polymer_instance (PDBID_CHAIN),
no_hits Number of presented hits. Default: no_hits=1000, use no_hits=-1 to get all hits.
select If True the results of the query will be used to perform selection on lpdb.entries (if return_type=='entries') or lpdb.chains (if return_type=='polymer_instance'). Moreover, if lpdb is instantiated with auto_filter mode, the selection will be propagated to other registered dataframes. 

localpdb.PDB.search_struct(pdb_id, assembly_id=1, operator='strict_shape_match',
                           return_type="entry",  no_hits=1000, select=False)
Search for structures spatially similar to the input structures. Returns the DataFrame with structures similar to the query and similarity statistics.

Parameter                           Description
pdb_id Input structure identifier.
assembly_id Assembly identifier of the input structure.
operator Match mode type - either relaxed_shape_match or strict_shape_match.
return_type Format of the returned entries that satisfy the query. Available options are entry (PDBID), polymer_entity (PDBID_ENTITY), polymer_instance (PDBID_CHAIN),
no_hits Number of presented hits. Default: no_hits=1000, use no_hits=-1 to get all hits.
select If True the results of the query will be used to perform selection on lpdb.entries (if return_type=='entries') or lpdb.chains (if return_type=='polymer_instance'). Moreover, if lpdb is instantiated with auto_filter mode, the selection will be propagated to other registered dataframes. 

localpdb.PDB.search_seq_motif(query, type_='prosite', return_type="entry", no_hits=1000, select=False)
Search for a sequence motif in entries available in the PDB database. Returns the DataFrame with the entries containing the specified sequence motif.

Parameter                           Description
query Query motif to find in the PDB sequences, according to given type_ (i.e prosite)
type_ Type of the specified motif. Available: simple (e.g., CXCXXL), prosite (e.g., C-X-C-X(2)-[LIVMYFWC]), regex (e.g., CXCX{2}[LIVMYFWC])
return_type Format of the returned entries that satisfy the query. Available options are entry (PDBID), polymer_entity (PDBID_ENTITY), polymer_instance (PDBID_CHAIN),
no_hits Number of presented hits. Default: no_hits=1000, use no_hits=-1 to get all hits.
select If True the results of the query will be used to perform selection on lpdb.entries (if return_type=='entries') or lpdb.chains (if return_type=='polymer_instance'). Moreover, if lpdb is instantiated with auto_filter mode, the selection will be propagated to other registered dataframes.