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])
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():
print("%f %f" % (phi, psi))
fp.write("TER\n")
if model_flag and model_residues_written:
fp.write("ENDMDL\n")
if write_end:
fp.write('END\n')
if close_file:
fp.close()
if __name__=="__main__":
from SAP.Bio.PDB.PDBParser import PDBParser
import sys
p=PDBParser(PERMISSIVE=True)
s=p.get_structure("test", sys.argv[1])
io=PDBIO()
io.set_structure(s)
io.save("out1.pdb")
with open("out2.pdb", "w") as fp:
s1=p.get_structure("test1", sys.argv[1])
s2=p.get_structure("test2", sys.argv[2])
io=PDBIO(1)
io.set_structure(s1)
io.save(fp)
io.set_structure(s2)
io.save(fp, write_end=1)
def accept_atom(self, atom):
# atoms - get rid of hydrogens
name=atom.get_id()
if _hydrogen.match(name):
return 0
else:
return 1
def extract(structure, chain_id, start, end, filename):
"""
Write out selected portion to filename.
"""
sel=ChainSelector(chain_id, start, end)
io=PDBIO()
io.set_structure(structure)
io.save(filename, sel)
if __name__=="__main__":
from SAP.Bio.PDB.PDBParser import PDBParser
import sys
p=PDBParser()
s=p.get_structure("scr", sys.argv[1])
extract(s, " ", 1, 100, "out.pdb")
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])
chain_id=r1.get_parent().get_id()
# Fill the 3 data structures
fs_map[(chain_id, res_id)]=fs
fs_list.append((r1, fs))
fs_keys.append((chain_id, res_id))
# Add to xtra
r1.xtra['EXP_CN']=fs
AbstractPropertyMap.__init__(self, fs_map, fs_keys, fs_list)
if __name__=="__main__":
import sys
p=PDBParser()
s=p.get_structure('X', sys.argv[1])
model=s[0]
# Neighbor sphere radius
RADIUS=13.0
OFFSET=0
hse=HSExposureCA(model, radius=RADIUS, offset=OFFSET)
for l in hse:
print(l)
print("")
hse=HSExposureCB(model, radius=RADIUS, offset=OFFSET)
for l in hse:
print(l)
print("")
if model_flag and model_residues_written:
fp.write("ENDMDL\n")
if write_end:
fp.write('END\n')
if close_file:
fp.close()
if __name__ == "__main__":
from SAP.Bio.PDB.PDBParser import PDBParser
import sys
p = PDBParser(PERMISSIVE=True)
s = p.get_structure("test", sys.argv[1])
io = PDBIO()
io.set_structure(s)
io.save("out1.pdb")
with open("out2.pdb", "w") as fp:
s1 = p.get_structure("test1", sys.argv[1])
s2 = p.get_structure("test2", sys.argv[2])
io = PDBIO(1)
io.set_structure(s1)
io.save(fp)
io.set_structure(s2)
io.save(fp, write_end=1)