localpdb/PDB.py
def search_struct_motif(self, pdb_id, residue_ids, score_cutoff=0, exchanges=None,
                            return_type="entry", no_hits=1000, select=False):
        """
        Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
        :param pdb_id: (str) pdb id (i.e 2mnr)
        :param residue_ids: (list(dict,)) definition of motif
        :param score_cutoff: (int) return matches having scores greater than this value
        :param exchanges: (list(dict,)) definition of allowed amino acids for given residue_ids
        :param return_type: (str) type of returned data
        :param no_hits: (int) number of hits to fetch, -1 for all results
        :param select: (bool) if True results of the query will be propagated to either lpdb.entries or lpdb.chains
        (depending on the return_type parameter)
        :return: pd.DataFrame
        """
        results = self.__rest_api_commands.get('strucmotif')(pdb_id, residue_ids, score_cutoff, exchanges,
                                                             resp_type=return_type, rows=no_hits).execute()
        if select:
            if return_type == 'entry':
                self.entries = self.entries[self.entries.index.isin(results.index)]
            elif return_type == 'polymer_instance':
                self.chains = self.chains[self.chains.index.isin(results.index)]
        else:
            return results

        Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
        :param pdb_id: (str) pdb id (i.e 2mnr)
        :param residue_ids: (list(dict,)) definition of motif
        :param score_cutoff: (int) return matches having scores greater than this value
        :param exchanges: (list(dict,)) definition of allowed amino acids for given residue_ids
        :param return_type: (str) type of returned data
        :param no_hits: (int) number of hits to fetch, -1 for all results
        :param select: (bool) if True results of the query will be propagated to either lpdb.entries or lpdb.chains
        (depending on the return_type parameter)
        :return: pd.DataFrame
        
Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
def search_struct_motif(self, pdb_id, residue_ids, score_cutoff=0, exchanges=None,
                            return_type="entry", no_hits=1000, select=False):
        results = self.__rest_api_commands.get('strucmotif')(pdb_id, residue_ids, score_cutoff, exchanges,
                                                             resp_type=return_type, rows=no_hits).execute()
        if select:
            if return_type == 'entry':
                self.entries = self.entries[self.entries.index.isin(results.index)]
            elif return_type == 'polymer_instance':
                self.chains = self.chains[self.chains.index.isin(results.index)]
        else:
            return results
def search_struct_motif ( self , pdb_id , residue_ids , score_cutoff = 0 , exchanges = None , return_type = "entry" , no_hits = 1000 , select = False ) : results = self . __rest_api_commands . get ( 'strucmotif' ) ( pdb_id , residue_ids , score_cutoff , exchanges , resp_type = return_type , rows = no_hits ) . execute ( ) if select : if return_type == 'entry' : self . entries = self . entries [ self . entries . index . isin ( results . index ) ] elif return_type == 'polymer_instance' : self . chains = self . chains [ self . chains . index . isin ( results . index ) ] else : return results
Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
"""
        Get dataframe with pdb ids having structure motif similar to one defined for pdb_id
        :param pdb_id: (str) pdb id (i.e 2mnr)
        :param residue_ids: (list(dict,)) definition of motif
        :param score_cutoff: (int) return matches having scores greater than this value
        :param exchanges: (list(dict,)) definition of allowed amino acids for given residue_ids
        :param return_type: (str) type of returned data
        :param no_hits: (int) number of hits to fetch, -1 for all results
        :param select: (bool) if True results of the query will be propagated to either lpdb.entries or lpdb.chains
        (depending on the return_type parameter)
        :return: pd.DataFrame
        """
None
self
pdb_id
(str) pdb id
( str ) pdb id
residue_ids
(list(dict,)) definition of motif
( list ( dict )) definition of motif
score_cutoff
(int) return matches having scores greater than this value
( int ) return matches having scores greater than this value
exchanges
(list(dict,)) definition of allowed amino acids for given residue_ids
( list ( dict )) definition of allowed amino acids for given residue_ids
return_type
(str) type of returned data
( str ) type of returned data
no_hits
(int) number of hits to fetch, -1 for all results
( int ) number of hits to fetch - 1 for all results
select
(bool) if True results of the query will be propagated to either lpdb.entries or lpdb.chains
(depending on the return_type parameter)
( bool ) if True results of the query will be propagated to either lpdb . entries or lpdb . chains ( depending on the return_type parameter )