def excercise(code):
print('\nAtom names')
print(get_atom_names(code))
print('\nAlternate atom names')
print(get_atom_names(code, alternate=True))
print('\nHydrogen names')
print(get_hydrogen_names(code))
print('\nAlternate hydrogen names')
print(get_hydrogen_names(code, alternate=True))
print('\nWrapped hydrogen names')
print(get_hydrogen_names(code, wrap=True))
print('\nBond pairs')
print(get_bond_pairs(code))
print('\nAlternate name bond pairs')
print(get_bond_pairs(code, alternate=True))
def excercise(code): print '\nAtom names' print get_atom_names(code) print '\nAlternate atom names' print get_atom_names(code, alternate=True) print '\nHydrogen names' print get_hydrogen_names(code) print '\nAlternate hydrogen names' print get_hydrogen_names(code, alternate=True) print '\nWrapped hydrogen names' print get_hydrogen_names(code, wrap=True) print '\nBond pairs' print get_bond_pairs(code) print '\nAlternate name bond pairs' print get_bond_pairs(code, alternate=True)
def rotamer_outliers(chain, pdbID, rot_outliers):
mc_atoms = ["N", "C", "O", "OXT"]
rot_out = "@subgroup {Rota outliers} dominant\n"
rot_out += "@vectorlist {chain %s} color= gold master= {Rota outliers}\n" % chain.id
outlier_list = []
for outlier in rot_outliers.results :
if (not outlier.is_outlier()) : continue
outlier_list.append(outlier.atom_group_id_str())
for residue_group in chain.residue_groups():
for atom_group in residue_group.atom_groups() :
check_key = atom_group.id_str()
if (check_key in outlier_list) :
key_hash = {}
xyz_hash = {}
for atom in atom_group.atoms():
key = "%s %s %s%s B%.2f %s" % (
atom.name.lower(),
atom_group.resname.lower(),
chain.id,
residue_group.resid(),
atom.b,
pdbID)
key_hash[atom.name.strip()] = key
xyz_hash[atom.name.strip()] = atom.xyz
bonds = get_bond_pairs(code=atom_group.resname)
for bond in bonds:
if bond[0] in mc_atoms or bond[1] in mc_atoms:
continue
elif bond[0].startswith('H') or bond[1].startswith('H'):
continue
if (key_hash.get(bond[0]) == None or
key_hash.get(bond[1]) == None or
xyz_hash.get(bond[0]) == None or
xyz_hash.get(bond[1]) == None):
continue
rot_out += kin_vec(key_hash[bond[0]],
xyz_hash[bond[0]],
key_hash[bond[1]],
xyz_hash[bond[1]])
if len(rot_out.splitlines()) == 2:
rot_out = ""
return rot_out
