def __contains__(self, res):
"""True if the given residue is in any of the mapped fragments.
@type res: L{Residue}
"""
return (res in self.fd)
def __getitem__(self, res):
"""
@type res: L{Residue}
@return: fragment classification
@rtype: L{Fragment}
"""
return self.fd[res]
if __name__ == "__main__":
import sys
p = PDBParser()
s = p.get_structure("X", sys.argv[1])
m = s[0]
fm = FragmentMapper(m, 10, 5, "levitt_data")
for r in Selection.unfold_entities(m, "R"):
print("%s:" % r)
if r in fm:
print(fm[r])
return True
return False
def _test_dist(self, c, n):
"""Return 1 if distance between atoms<radius (PRIVATE)."""
if (c - n) < self.radius:
return 1
else:
return 0
if __name__ == "__main__":
import sys
from SAP.Bio.PDB.PDBParser import PDBParser
p = PDBParser(PERMISSIVE=True)
s = p.get_structure("scr", sys.argv[1])
ppb = PPBuilder()
print("C-N")
for pp in ppb.build_peptides(s):
print(pp.get_sequence())
for pp in ppb.build_peptides(s[0]):
print(pp.get_sequence())
for pp in ppb.build_peptides(s[0]["A"]):
print(pp.get_sequence())
for pp in ppb.build_peptides(s):
for phi, psi in pp.get_phi_psi_list():
