def get_residues_from_radius(radius, ref):
asl = 'fillres ((within %i ligand ) and not (res.ptype "T3P"))' % (int(float(radius)))
st=StructureReader(ref).next()
atoms=evaluate_asl(st, asl)
if len(atoms)==0:
print "NO LIGAND IN REFERENCE FILE"
print "no ligand in reference file"
sys.exit()
pocket=st.extract(atoms)
resnames=[i.pdbres for i in pocket.residue]
resnums=[i.resnum for i in pocket.residue]
chains=[i.chain for i in pocket.residue]
data=dict()
for chain in set(chains):
for (n,c) in zip(resnums, chains):
if c not in data.keys():
data[c]=[]
if str(n) not in data[c]:
data[c].append(str(n))
selection=[]
for chain in data.keys():
selection.append(','.join(data[chain]) + '.%s' % chain)
if len(selection)==1:
selection=[selection,]
return selection
def get_residues_from_radius(radius, ref):
asl = 'fillres ((within %i ligand ) and not (res.ptype "T3P"))' % (int(
float(radius)))
st = StructureReader(ref).next()
atoms = evaluate_asl(st, asl)
if len(atoms) == 0:
print "NO LIGAND IN REFERENCE FILE"
print "no ligand in reference file"
sys.exit()
pocket = st.extract(atoms)
resnames = [i.pdbres for i in pocket.residue]
resnums = [i.resnum for i in pocket.residue]
chains = [i.chain for i in pocket.residue]
data = dict()
for chain in set(chains):
for (n, c) in zip(resnums, chains):
if c not in data.keys():
data[c] = []
if str(n) not in data[c]:
data[c].append(str(n))
selection = []
for chain in data.keys():
selection.append(','.join(data[chain]) + '.%s' % chain)
if len(selection) == 1:
selection = [
selection,
]
return selection
def check_selection_boolean(ref, target):
st=StructureReader(ref).next()
atoms=evaluate_asl(st, 'all')
sub=st.extract(atoms)
resnames=[i.pdbres.rstrip() for i in sub.residue]
if target in resnames:
verdict=True
else:
verdict=False
return verdict
def check_selection_boolean(ref, target):
st = StructureReader(ref).next()
atoms = evaluate_asl(st, 'all')
sub = st.extract(atoms)
resnames = [i.pdbres.rstrip() for i in sub.residue]
if target in resnames:
verdict = True
else:
verdict = False
return verdict