def test_from_url(self):
"""Check parser can fetch a record from its PDB ID."""
parser = MMTFParser()
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
struct = parser.get_structure_from_url("4ZHL")
atoms = [x for x in struct.get_atoms()]
self.assertEqual(len(atoms), 2080)
def test_from_url(self):
"""Check parser can fetch a record from its PDB ID."""
parser = MMTFParser()
with warnings.catch_warnings():
warnings.simplefilter('ignore', PDBConstructionWarning)
struct = parser.get_structure_from_url("4ZHL")
atoms = [x for x in struct.get_atoms()]
self.assertEqual(len(atoms), 2080)
def downloadUsingMmtf(pdbId, fnameOut, maxNumberOfChains=MAX_NUMBER_OF_CHAINS):
print("downloadUsingMmtf")
try:
parser = MMTFParser()
struct = parser.get_structure_from_url(pdbId)
if not 0 in struct:
return False
if len(struct[0]) > maxNumberOfChains:
raise NoValidPDBFile(
"The maximun number of allowed chains is %d (%d) for %s" %
(maxNumberOfChains, len(struct[0]), pdbId))
writter = PDBIO()
writter.set_structure(struct)
writter.save(fnameOut)
return True
except (Exception, ValueError, HTTPError) as e:
print(e)
if isinstance(e, NoValidPDBFile):
raise e
return False
from Bio.PDB import Selection
from Bio.PDB import NeighborSearch
from Bio.PDB.DSSP import DSSP
from Bio.PDB.NACCESS import *
from Bio.PDB import PDBIO
thr = 6
pdb_list = open('../437_dimers_list.merge.tsv')
for pdb_chi_chj in pdb_list:
print(pdb_chi_chj)
x = pdb_chi_chj.rstrip().split("\t")
pdb = x[0]
chi = x[1]
chj = x[2]
p = MMTFParser()
structure = MMTFParser.get_structure_from_url(pdb)
s = structure[0]
atom_list = [atom for atom in s[chi].get_atoms() if atom.name != 'H']
atom_list.extend([atom for atom in s[chj].get_atoms() if atom.name != 'H'])
RRI = NeighborSearch(atom_list).search_all(thr, 'A')
MAP = {}
for rri in RRI:
if (rri[0].get_parent().get_id()[0][0:2] == "H_"
or rri[0].get_parent().get_id()[0] == 'W'):
#print(rri[0].get_parent().get_id()[0][0:2])
continue
if (rri[1].get_parent().get_id()[0][0:2] == "H_"
or rri[1].get_parent().get_id()[0] == 'W'):
#print(rri[1].get_parent().get_id()[0][0:2])
from Bio.PDB.mmtf import MMTFParser
# read structure from file
structure = MMTFParser.get_structure("PDB/4CUP.mmtf")
# read structure from PDB
structure = MMTFParser.get_structure_from_url("4CUP")
