def setUp(self):
self.line = ("ATOM 158 C LEU A 135 -42.160 -11.386 54.208"
" 1.00 43.54 C \n")
self.web = PDBFile.fetch('4K5Y')
self.file_ = PDBFile.from_file('tests/resources/4K5Y.pdb')
def setUp(self):
self.pdb = PDBFile.from_file('tests/resources/4K5Y.pdb')
self.chain_a = self.pdb.select(chain__eq='A', nres__lt=263)
def setUp(self):
self.pdb = PDBFile.from_file('tests/resources/1hpv.pdb')
self.lig = self.pdb.ligand()
self.prot = self.pdb.protein()
from protutils.pdb import PDBFile
# Download 4k5Y.pdb from the RCSB Protein Data Bank
pdb = PDBFile.fetch('4K5Y')
# Select residues less than 263 on chain A, then chain B
chain_a = pdb.select(chain__eq='A', nres__lt=263)
chain_b = pdb.select(chain__eq='B', nres__lt=263)
# Align selection with another selection that contains the same number of atoms
aligned_chain_b = chain_b.align(chain_a)
# prints: RMSD = 0.983960869568
# write structures to pdb files
chain_a.write_pdb('chain_a.pdb')
chain_b.write_pdb('chain_b.pdb')
aligned_chain_b.write_pdb('aligned_chain_b.pdb')
from protutils.pdb import PDBFile
# Download 4k5Y.pdb from the RCSB Protein Data Bank
pdb = PDBFile.fetch('4K5Y')
# Select residues less than 263 on chain A, then chain B
chain_a = pdb.select(chain__eq='A', nres__lt=263)
chain_b = pdb.select(chain__eq='B', nres__lt=263)
# Align selection with another selection that contains the same number of atoms
aligned_chain_b = chain_b.align(chain_a)
# prints: RMSD = 0.983960869568
# write structures to pdb files
chain_a.write_pdb('chain_a.pdb')
chain_b.write_pdb('chain_b.pdb')
aligned_chain_b.write_pdb('aligned_chain_b.pdb')
from protutils.pdb import PDBFile
from protutils.ncbi.blastp import BLASTPDBRecord
pdb = PDBFile.fetch('4K5Y')
chain_a = pdb.select(chain='A', nres__lt=1000)
# Get sequence
sequence = chain_a.sequence.replace('-', '')
# search for similar sequences to 4K5Y_A
query = BLASTPDBRecord(sequence)
# Get top hit
PDB = query.get_best()['pdb']
similar = PDBFile.fetch(PDB)
similar.select(chain='A', nres__lt=1000)
# Compare aligned structures
aligned = similar.cealign(chain_a)
chain_a.write_pdb('4k5y_A.mod.pdb')
aligned.write_pdb('{0}_A.mod.pdb'.format(PDB))
from protutils.pdb import PDBFile
# write a small helper function
def get_residue_list(selected, pdbfile):
"""Get all residues atoms for a selection
"""
residues = {atm.nres for atm in selected}
return pdbfile.select(nres__isin=residues)
pdb = PDBFile.fetch('1HPV')
# Select ligand
ligand = pdb.ligand()
# select protein atoms with 5 Angstroms of the ligand
atoms = pdb.protein().within(5.0, ligand)
prot = get_residue_list(atoms, pdb)
ligand.write_pdb('ligand.pdb')
prot.write_pdb('prot.pdb')
def setUp(self):
self.line = ("ATOM 158 C LEU A 135 -42.160 -11.386 54.208"
" 1.00 43.54 C \n")
self.web = PDBFile.fetch('4K5Y')
self.file_ = PDBFile.from_file('tests/resources/4K5Y.pdb')
def setUp(self):
self.pdb = PDBFile.from_file('tests/resources/1hpv.pdb')
self.lig = self.pdb.ligand()
self.prot = self.pdb.protein()
def setUp(self):
self.pdb = PDBFile.from_file('tests/resources/4K5Y.pdb')
self.chain_a = self.pdb.select(chain__eq='A', nres__lt=263)