from SAP.Bio.PDB import PDBParser if len(sys.argv) != 4: print("Expects three arguments,") print(" - FASTA alignment filename (expect two sequences)") print(" - PDB file one") print(" - PDB file two") sys.exit() # The alignment fa=AlignIO.read(open(sys.argv[1]), "fasta", generic_protein) pdb_file1=sys.argv[2] pdb_file2=sys.argv[3] # The structures p=PDBParser() s1=p.get_structure('1', pdb_file1) p=PDBParser() s2=p.get_structure('2', pdb_file2) # Get the models m1=s1[0] m2=s2[0] al=StructureAlignment(fa, m1, m2) # Print aligned pairs (r is None if gap) for (r1, r2) in al.get_iterator(): print("%s %s" % (r1, r2))
for i in range(0, L): residues[i].xtra["SS_PSEA"] = ss_seq[i] #os.system("rm "+fname) class PSEA(object): def __init__(self, model, filename): ss_seq = psea(filename) ss_seq = psea2HEC(ss_seq) annotate(model, ss_seq) self.ss_seq = ss_seq def get_seq(self): """ Return secondary structure string. """ return self.ss_seq if __name__ == "__main__": import sys from SAP.Bio.PDB import PDBParser # Parse PDB file p = PDBParser() s = p.get_structure('X', sys.argv[1]) # Annotate structure with PSEA sceondary structure info PSEA(s[0], sys.argv[1])
for residue in residue_list: if not is_aa(residue): continue rd=residue_depth(residue, surface) ca_rd=ca_depth(residue, surface) # Get the key res_id=residue.get_id() chain_id=residue.get_parent().get_id() depth_dict[(chain_id, res_id)]=(rd, ca_rd) depth_list.append((residue, (rd, ca_rd))) depth_keys.append((chain_id, res_id)) # Update xtra information residue.xtra['EXP_RD']=rd residue.xtra['EXP_RD_CA']=ca_rd AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list) if __name__=="__main__": import sys from SAP.Bio.PDB import PDBParser p=PDBParser() s=p.get_structure("X", sys.argv[1]) model=s[0] rd=ResidueDepth(model, sys.argv[1]) for item in rd: print(item)
for residue in residue_list: if not is_aa(residue): continue rd = residue_depth(residue, surface) ca_rd = ca_depth(residue, surface) # Get the key res_id = residue.get_id() chain_id = residue.get_parent().get_id() depth_dict[(chain_id, res_id)] = (rd, ca_rd) depth_list.append((residue, (rd, ca_rd))) depth_keys.append((chain_id, res_id)) # Update xtra information residue.xtra['EXP_RD'] = rd residue.xtra['EXP_RD_CA'] = ca_rd AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list) if __name__ == "__main__": import sys from SAP.Bio.PDB import PDBParser p = PDBParser() s = p.get_structure("X", sys.argv[1]) model = s[0] rd = ResidueDepth(model, sys.argv[1]) for item in rd: print(item)
from SAP.Bio.PDB import PDBParser if len(sys.argv) != 4: print("Expects three arguments,") print(" - FASTA alignment filename (expect two sequences)") print(" - PDB file one") print(" - PDB file two") sys.exit() # The alignment fa = AlignIO.read(open(sys.argv[1]), "fasta", generic_protein) pdb_file1 = sys.argv[2] pdb_file2 = sys.argv[3] # The structures p = PDBParser() s1 = p.get_structure('1', pdb_file1) p = PDBParser() s2 = p.get_structure('2', pdb_file2) # Get the models m1 = s1[0] m2 = s2[0] al = StructureAlignment(fa, m1, m2) # Print aligned pairs (r is None if gap) for (r1, r2) in al.get_iterator(): print("%s %s" % (r1, r2))
if self.rotran is None: raise PDBException("No transformation has been calculated yet") rot, tran=self.rotran rot=rot.astype('f') tran=tran.astype('f') for atom in atom_list: atom.transform(rot, tran) if __name__=="__main__": import sys from SAP.Bio.PDB import PDBParser, Selection p=PDBParser() s1=p.get_structure("FIXED", sys.argv[1]) fixed=Selection.unfold_entities(s1, "A") s2=p.get_structure("MOVING", sys.argv[1]) moving=Selection.unfold_entities(s2, "A") rot=numpy.identity(3).astype('f') tran=numpy.array((1.0, 2.0, 3.0), 'f') for atom in moving: atom.transform(rot, tran) sup=Superimposer() sup.set_atoms(fixed, moving)
for i in range(0, L): residues[i].xtra["SS_PSEA"]=ss_seq[i] #os.system("rm "+fname) class PSEA(object): def __init__(self, model, filename): ss_seq=psea(filename) ss_seq=psea2HEC(ss_seq) annotate(model, ss_seq) self.ss_seq=ss_seq def get_seq(self): """ Return secondary structure string. """ return self.ss_seq if __name__=="__main__": import sys from SAP.Bio.PDB import PDBParser # Parse PDB file p=PDBParser() s=p.get_structure('X', sys.argv[1]) # Annotate structure with PSEA sceondary structure info PSEA(s[0], sys.argv[1])
if self.rotran is None: raise PDBException("No transformation has been calculated yet") rot, tran = self.rotran rot = rot.astype('f') tran = tran.astype('f') for atom in atom_list: atom.transform(rot, tran) if __name__ == "__main__": import sys from SAP.Bio.PDB import PDBParser, Selection p = PDBParser() s1 = p.get_structure("FIXED", sys.argv[1]) fixed = Selection.unfold_entities(s1, "A") s2 = p.get_structure("MOVING", sys.argv[1]) moving = Selection.unfold_entities(s2, "A") rot = numpy.identity(3).astype('f') tran = numpy.array((1.0, 2.0, 3.0), 'f') for atom in moving: atom.transform(rot, tran) sup = Superimposer() sup.set_atoms(fixed, moving)