#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
