Tutorials

pip install --upgrade pip

pip install pdb-profiling

pip install --upgrade pdb-profiling

from pdb_profiling import default_config

default_config(your_output_folder)

from pdb_profiling.processors import PDB

pdb_object = PDB('3hl2')

dfrm = pdb_object.fetch_from_pdbe_api('api/pdb/entry/molecules/', PDB.to_dataframe).result()

pdb_object.fetch_from_pdbe_api('api/pdb/entry/molecules/').result()
# >>> WindowsPath('./api/pdb/entry/molecules/api%pdb%entry%molecules%+3hl2.tsv')

from pdb_profiling.processors.pdbe.record import API_SET
print(API_SET)

from pdb_profiling.processors import PDBs

pdb_objects = PDBs(['1a01', '2xyn', '3hl2', '4hho'])

(<PDB 1a01>, <PDB 2xyn>, <PDB 3hl2>, <PDB 4hho>)

res = pdb_objects.fetch(
    'fetch_from_pdbe_api', 
    api_suffix='api/pdb/entry/summary/', 
    then_func=PDB.to_dataframe).run().result()

from pandas import concat
concat(res, sort=False, ignore_index=True)

from pandas import DataFrame

exp_res = pdb_objects.fetch(PDBs.fetch_exp_pipe).run().result()

DataFrame(
    (j for i in exp_res for j in i),
    columns=['pdb_id',
             'resolution',
             'experimental_method_class',
             'experimental_method',
             'multi_method'])

date_res = pdb_objects.fetch(PDBs.fetch_date).run().result()
DataFrame(date_res, columns=['pdb_id', 'revision_date', 'deposition_date'])

from pdb_profiling.processors import SIFTS, SIFTSs

sifts_from_pdb_demo = SIFTS('1a01')    # <SIFTS PDB Entry 1a01>
sifts_from_unp_demo = SIFTS('Q5VST9')  # <SIFTS UniProt Q5VST9>

sifts_from_pdb_demo.fetch_from_pdbe_api('api/mappings/all_isoforms/', SIFTS.to_dataframe).result()

sifts_from_unp_demo.fetch_from_pdbe_api('api/mappings/all_isoforms/', SIFTS.to_dataframe).result()

SIFTS('P21359-2').fetch_from_pdbe_api('api/mappings/all_isoforms/', SIFTS.to_dataframe
    ).then(SIFTS.reformat
    ).then(SIFTS.dealWithInDel
    ).then(SIFTS.fix_range
    ).then(SIFTS.add_residue_conflict).result()

SIFTSs(('P21359', 'Q5VST9', 'P21359-5')).fetch('fetch_from_pdbe_api', api_suffix='api/mappings/all_isoforms/', then_func=SIFTS.to_dataframe).run().result()

sifts_info, score_detail, experimental_info = SIFTS('P21359-3').pipe_score().result()

pdb_object.profile_id().result()

pdb_object.set_assembly().result()
assemblies = pdb_object.assembly
'''
>>> assemblies  # Note a python dictionary
>>> {0: <PDBAssembly 3hl2/0>, 1: <PDBAssembly 3hl2/1>, 2: <PDBAssembly 3hl2/2>}
'''

from pdb_profiling.processors import PDBAssembly

pdb_assembly_object = PDBAssembly('3hl2/1')
pdb_assembly_object.Assembly_summary
'''
{'preferred': True, 'form': 'hetero', 'name': 'pentamer', 'assembly_id': '1'}
'''

pdb_assembly_object = assemblies[1]
pdb_assembly_object.pipe_protein_protein_interface().result()
interfaces = pdb_assembly_object.interface
interfaces
'''
{1: <PDBInterface 3hl2/1/1>,
 2: <PDBInterface 3hl2/1/2>,
 3: <PDBInterface 3hl2/1/3>,
 4: <PDBInterface 3hl2/1/4>,
 13: <PDBInterface 3hl2/1/13>,
 14: <PDBInterface 3hl2/1/14>}
'''

from pdb_profiling.processors import PDBInterface

pdb_interface_object = PDBInterface('3hl2/1/3')
pdb_interface_object.get_interface_res_dict().result()
'''
{'entity_id_1': 1,
 'chain_id_1': 'A',
 'struct_asym_id_1': 'A',
 'struct_asym_id_in_assembly_1': 'AA',
 'asym_id_rank_1': 2,
 'model_id_1': 2,
 'molecule_type_1': 'polypeptide(L)',
 'surface_range_1': '[[23,61],[63,109],[111,120],[123,124],[127,130],[132,139],[141,146],[148,151],[153,164],[168,178],[180,204],[206,208],[210,216],[223,223],[225,227],[230,234],[236,237],[240,241],[243,246],[248,248],[252,252],[254,255],[257,262],[264,265],[267,268],[270,276],[281,284],[286,292],[298,302],[304,305],[307,321],[324,325],[328,329],[331,373],[375,390],[392,424],[426,437],[439,456],[458,463]]',
 'interface_range_1': '[[23,25],[27,28],[31,31],[47,50],[52,53],[56,57],[60,61],[65,68],[82,82],[86,86],[89,90],[109,109]]',
 'entity_id_2': 1,
 'chain_id_2': 'B',
 'struct_asym_id_2': 'B',
 'struct_asym_id_in_assembly_2': 'B',
 'asym_id_rank_2': 1,
 'model_id_2': 1,
 'molecule_type_2': 'polypeptide(L)',
 'surface_range_2': '[[21,61],[63,109],[111,121],[123,125],[127,130],[132,139],[141,146],[149,150],[153,164],[167,178],[180,204],[206,208],[210,216],[223,223],[225,227],[230,234],[236,237],[240,241],[243,246],[248,248],[252,252],[254,255],[257,262],[264,265],[267,268],[270,276],[280,284],[286,292],[294,294],[298,302],[304,305],[307,326],[328,329],[331,424],[426,437],[439,446],[448,453],[455,456],[458,463]]',
 'interface_range_2': '[[21,22],[24,25],[27,28],[31,31],[47,50],[52,53],[56,57],[60,61],[65,68],[82,82],[86,86],[90,90]]',
 'pdb_id': '3hl2',
 'assembly_id': 1,
 'interface_id': 3,
 'use_au': False}
'''

from pdb_profiling.processors.i3d.api import Interactome3D

Interactome3D.pipe_init_interaction_meta().result()

SIFTS.search_partner_from_i3d('P21359', ('ho','he')).result()

sifts_demo = SIFTS('P21359-2')
df1 = sifts_demo.pipe_select_mo().result()
df1

df2 = sifts_demo.pipe_select_ho(run_as_completed=True).result()
df2

df3 = sifts_demo.pipe_select_ho_iso(run_as_completed=True).result()
df3