r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
res_names = residues_to_move.split('_')
for n in res_names:
if n.find(':') == -1:
res = r.chains.residues.get(lambda x: x.name == n)
all_res += res
if verbose: print "get: adding ", res.name, " to ", all_res
else:
res, msg = CompoundStringSelector().select(ProteinSet([r]), n)
all_res += res
if verbose: print "css: adding ", res.name, " to ", all_res
if verbose:
print "all_res=", all_res.full_name(
), 'all_res.__class__=', all_res.__class__
#?check for duplicates
d = {}
for res in all_res:
d[res] = 1
all_res = d.keys()
all_res = ResidueSet(all_res)
#inactivate specified bonds
#disallowed_Pairs "CA_CB:CB_CG:C_CA"
all_bnds = BondSet()
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)
usage()
sys.exit()
r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename
all_res = ResidueSet()
res_names = residues_to_move.split('_')
for n in res_names:
res = r.chains.residues.get(lambda x: x.name==n)
if verbose: print "adding ", res.name, " to ", all_res
all_res += res
if verbose:
print "all_res=", all_res.full_name(), 'all_res.__class__=', all_res.__class__
#?check for duplicates
d = {}
for res in all_res: d[res] = 1
all_res = d.keys()
all_res = ResidueSet(all_res)
#inactivate specified bonds
#disallowed_Pairs "CA_CB:CB_CG:C_CA"
all_bnds = BondSet()
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)
all_bnds += bnds
res = r.chains.residues.get(lambda x: x.name==n)
all_res += res
if verbose: print "case no ':' get: adding ", res.name, " to ", all_res
else:
# 'hsg1:A:ARG8_ILE82'
n = res_names_by_chain.replace("_", ",")
if verbose: print "after comma replaced _ n is ", n
# 'hsg1:A:ARG8,ILE82'
res, msg = CompoundStringSelector().select(ProteinSet([r]), n)
if verbose: print "n selection =", res, " msg=", msg
if len(res):
all_res += res
else:
print "no residue found using string ", n
if verbose:
print "all_res=", all_res.full_name(), 'all_res.__class__=', all_res.__class__
#?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 "after all_res=", all_res.full_name()
#inactivate specified bonds
#disallowed_Pairs "CA_CB:CB_CG:C_CA"
all_bnds = BondSet()
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)
