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():
if chain_residues_written: 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)
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():
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])
res_id=r1.get_id() 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)
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)