Download PDB files¶

In [1]:

from pathlib import Path

from protein_detective.pdbe.fetch import fetch

from pathlib import Path from protein_detective.pdbe.fetch import fetch

In [2]:

ids = [
    "4NDY",  # structure of uniprot A8MT69
    "4DRA",  # structure of uniprot A8MT69
    "1XWH",  # structure of uniprot O43918
    "8WAS",  # structure for which there is no single pdb file
]

ids = [ "4NDY", # structure of uniprot A8MT69 "4DRA", # structure of uniprot A8MT69 "1XWH", # structure of uniprot O43918 "8WAS", # structure for which there is no single pdb file ]

In [3]:

save_dir = Path("pdb_files")

save_dir = Path("pdb_files")

In [4]:

files = fetch(ids, save_dir)
files

files = fetch(ids, save_dir) files

Downloading PDBe mmCIF files:   0%|          | 0/4 [00:00<?, ?it/s]

Downloading PDBe mmCIF files: 100%|██████████| 4/4 [00:00<00:00,  5.07it/s]

Out[4]:

{'4NDY': PosixPath('pdb_files/4ndy.cif'),
 '4DRA': PosixPath('pdb_files/4dra.cif'),
 '1XWH': PosixPath('pdb_files/1xwh.cif'),
 '8WAS': PosixPath('pdb_files/8was.cif')}

In [5]:

!ls pdb_files

!ls pdb_files

1xwh.cif  4dra.cif  4ndy.cif  8was.cif

Prepare pdb file for powerfit¶

In [6]:

from protein_detective.pdbe.io import write_single_chain_pdb_file

from protein_detective.pdbe.io import write_single_chain_pdb_file

In [7]:

# A8MT69	4NDY	B/D/H/L/M/N/U/V/W/X=8-81	session1/single_chain/A8MT69_pdb4ndy.ent_B2A.pdb
write_single_chain_pdb_file(save_dir / "4ndy.cif", "B", save_dir / "A8MT69_4ndy_B2A.pdb")

# A8MT69 4NDY B/D/H/L/M/N/U/V/W/X=8-81 session1/single_chain/A8MT69_pdb4ndy.ent_B2A.pdb write_single_chain_pdb_file(save_dir / "4ndy.cif", "B", save_dir / "A8MT69_4ndy_B2A.pdb")

In [8]:

# A8MT69	4DRA	E/F/G/H=1-81	session1/single_chain/A8MT69_pdb4dra.ent_E2A.pdb
write_single_chain_pdb_file(save_dir / "4dra.cif", "E", save_dir / "8MT69_4dra_E2A.pdb")

# A8MT69 4DRA E/F/G/H=1-81 session1/single_chain/A8MT69_pdb4dra.ent_E2A.pdb write_single_chain_pdb_file(save_dir / "4dra.cif", "E", save_dir / "8MT69_4dra_E2A.pdb")

In [9]:

!head pdb_files/8MT69_pdb4dra.ent_E2A.pdb
print("...")
!tail pdb_files/8MT69_pdb4dra.ent_E2A.pdb

!head pdb_files/8MT69_pdb4dra.ent_E2A.pdb print("...") !tail pdb_files/8MT69_pdb4dra.ent_E2A.pdb

head: cannot open 'pdb_files/8MT69_pdb4dra.ent_E2A.pdb' for reading: No such file or directory
...
tail: cannot open 'pdb_files/8MT69_pdb4dra.ent_E2A.pdb' for reading: No such file or directory

In [10]:

write_single_chain_pdb_file(
    "pdb_files/1xwh.cif",
    "A",
    "pdb_files/O43918_1xwh_A2A.pdb",
)

write_single_chain_pdb_file( "pdb_files/1xwh.cif", "A", "pdb_files/O43918_1xwh_A2A.pdb", )

In [12]:

# O00268      │ 8WAS    │ D/d=1-1085
write_single_chain_pdb_file(
    "pdb_files/8was.cif",
    "D",
    "pdb_files/O00268_8was_D2A.pdb",
)

# O00268 │ 8WAS │ D/d=1-1085 write_single_chain_pdb_file( "pdb_files/8was.cif", "D", "pdb_files/O00268_8was_D2A.pdb", )

In [13]:

!ls -l pdb_files/

!ls -l pdb_files/

total 18772
-rw-rw-r-- 1 verhoes verhoes  1796029 Jun  6 12:34 1xwh.cif
-rw-rw-r-- 1 verhoes verhoes  1034577 Jun  6 12:34 4dra.cif
-rw-rw-r-- 1 verhoes verhoes  3117986 Jun  6 12:34 4ndy.cif
-rw-rw-r-- 1 verhoes verhoes    92853 Jun  6 12:34 8MT69_4dra_E2A.pdb
-rw-rw-r-- 1 verhoes verhoes 12881824 Jun  6 12:34 8was.cif
-rw-rw-r-- 1 verhoes verhoes    95607 Jun  6 12:34 A8MT69_4ndy_B2A.pdb
-rw-rw-r-- 1 verhoes verhoes   110673 Jun  6 12:34 O00268_8was_D2A.pdb
-rw-rw-r-- 1 verhoes verhoes    77220 Jun  6 12:34 O43918_1xwh_A2A.pdb

In [ ]: