#if verbose: print "now selStr", selStr # 'hsg1:A:ARG8,ILE82' #res, msg = CompoundStringSelector().select(ProteinSet([r]), n) res, msg = CompoundStringSelector().select(ProteinSet([r]), selStr) #if verbose: print selStr, " selection =", res, " msg=", msg, '\n' if len(res): all_res += res else: print "no residue found using string ", selStr #if verbose: print "built all_res=", all_res.full_name() #check for duplicates d = {} for res in all_res: d[res] = 1 all_res = d.keys() all_res = ResidueSet(all_res).uniq() all_res.sort() if verbose: print "located ", len(all_res), " residues to format:" for z in all_res: print " %s" %z.full_name() #inactivate specified bonds #disallowed_Pairs "CA_CB:CB_CG:C_CA" all_bnds = BondSet() #inactivate specified bonds #disallowed_pairs "CA_CB:CB_CG:C_CA" if len(disallowed_pairs): bnd_pairs = disallowed_pairs.split(':') for pair in bnd_pairs: names = pair.split('_') bnds = all_res.atoms.bonds[0].get(lambda x: x.atom1.name in names and x.atom2.name in names) if len(bnds):
if result.__class__ == AtomSet: resS = result.parent.uniq() else: resS = result if len(resS): all_res += resS else: print("no residue found using string ", selStr) #if verbose: print "built all_res=", all_res.full_name() #check for duplicates d = {} for res in all_res: d[res] = 1 all_res = list(d.keys()) all_res = ResidueSet(all_res).uniq() all_res.sort() if verbose: print("located ", len(all_res), " residues to format:") for z in all_res: print(" %s" % z.full_name()) all_bnds = BondSet() #inactivate bonds between specified atoms: #all_disallowed_pairs eg "1g9v_rec:A:ARG532:CA_CB,CB_CG,C_CA;1g9v_rec:B:ARG532:CA_CB,CB_CG" if len(all_disallowed_pairs): if verbose: print("line 183: all_disallowed_pairs = ", all_disallowed_pairs) disallowed_pairs = all_disallowed_pairs.split( ';') #';' between different residues for dp in disallowed_pairs: #1g9v_rec:A:ARG532:CA_CB,CB_CG,C_CA #find the residue