Python PDBList.download_pdb_files Examples

Example #1

File: tools.py Project: Hkethar/Conformation_predict

def getpdbs(names):
    cwd = os.getcwd()
    pdbl = PDBList()
    pdbl.download_pdb_files(names, obsolete=False, file_format="pdb", pdir=cwd)
    pdbl.download_pdb_files(names, obsolete=True, file_format="pdb", pdir=cwd)

Example #2

from Bio.PDB.PDBList import PDBList

pdblist = PDBList()
pdblist.retrieve_pdb_file(
    "127d")  # downloads structure 127D in PDBx/mmCif format
pdblist.retrieve_pdb_file(
    "127d", file_format="pdb")  # downloads structure 127D in PDB format
pdblist.retrieve_pdb_file(
    "127d", file_format="xml")  # downloads structure 127D in PDBML/XML format
pdblist.retrieve_pdb_file(
    "127d", file_format="mmtf")  # downloads structure 127D in mmtf format
pdblist.retrieve_pdb_file(
    "3k1q",
    file_format="bundle")  # downloads large structure 3K1Q in pdb-like bundle
pdblist.retrieve_pdb_file(
    "347d",
    obsolete=True)  # downloads obsolete structure 347D in PDBx/mmCif format
pdblist.download_pdb_files(
    "1esy", "127D")  # downloads structures 127D and 1ESY in PDBx/mmCif format
pdblist.download_entire_pdb(
)  # downloads entire PDB database in PDBx/mmCif format
pdblist.update_pdb()  # performs weekle update of the database