def testIdAtom(self):
cmd.fragment('gly', 'm1')
self.assertEqual(cmd.id_atom('ID 3'), 3)
self.assertEqual(cmd.id_atom('ID 3', 1), ('m1', 3))
cmd.feedback("disable", "cmd", "errors")
self.assertRaises(CmdException, cmd.id_atom, 'ID 3+4')
self.assertRaises(CmdException, cmd.id_atom, 'ID 100')
def selectProt(self):
index_a = cmd.id_atom("pw2")
index_A = cmd.id_atom("pw3")
cmd.select(
"bounded", "(bound_to id {0:d}) and not "
"(hydrogens or name H* or id {0:d} or id {1:d})".format(
index_A, index_a))
atoms = cmd.get_model("bounded")
cmd.delete("bounded")
if not atoms.atom:
cmd.select(
"bounded", "(id {0:d} around 2.2) and not "
"(hydrogens or name H* or id {0:d} or id {1:d})".format(
index_A, index_a))
atoms = cmd.get_model("bounded")
cmd.delete("bounded")
if not atoms.atom:
showerror(self.parent, "Error",
"Not found atoms bonded or around (b)")
self.reset()
at = atoms.atom[0]
index_B = at.id
cmd.select("pw4", "id {:d}".format(index_B))
self.createAtomObj(4)
cmd.select(
"bounded", "(bound_to id {0:d}) and not "
"(hydrogens or name H* or id {0:d} or id {1:d} or id {2:d})".
format(index_B, index_a, index_A))
atoms = cmd.get_model("bounded")
cmd.delete("bounded")
if not atoms.atom:
cmd.select(
"bounded", "(id {0:d} around 2.2) and not "
"(hydrogens or name H* or id {0:d} or id {1:d} or id {2:d})".
format(index_B, index_a, index_A))
atoms = cmd.get_model("bounded")
cmd.delete("bounded")
if not atoms.atom:
showerror(self.parent, "Error",
"Not found atoms bonded or around (b)")
self.reset()
at = atoms.atom[0]
index_C = at.id
cmd.select("pw5", "id {:d}".format(index_C))
self.createAtomObj(5)
def doFinish(self):
r_aA = cmd.get_distance(atom1="pw2", atom2="pw3", state=0)
cmd.distance(self.params_str[0], "pw2", "pw3")
th_a = cmd.get_angle(atom1="pw1", atom2="pw2", atom3="pw3", state=0)
cmd.angle(self.params_str[1], "pw1", "pw2", "pw3")
th_A = cmd.get_angle(atom1="pw2", atom2="pw3", atom3="pw4", state=0)
cmd.angle(self.params_str[2], "pw2", "pw3", "pw4")
if not (r_aA and th_a and th_A):
showerror(self.parent, "Error!",
"Maybe you made a mistake when choosing atoms!")
self.reset()
phi_ba = cmd.get_dihedral(atom1="pw0",
atom2="pw1",
atom3="pw2",
atom4="pw3",
state=0)
cmd.dihedral(self.params_str[3], "pw0", "pw1", "pw2", "pw3")
phi_aA = cmd.get_dihedral(atom1="pw1",
atom2="pw2",
atom3="pw3",
atom4="pw4",
state=0)
cmd.dihedral(self.params_str[4], "pw1", "pw2", "pw3", "pw4")
phi_AB = cmd.get_dihedral(atom1="pw2",
atom2="pw3",
atom3="pw4",
atom4="pw5",
state=0)
cmd.dihedral(self.params_str[5], "pw2", "pw3", "pw4", "pw5")
index_c = cmd.id_atom("pw0")
index_c_name = getAtomString('pw0')
index_b = cmd.id_atom("pw1")
index_b_name = getAtomString('pw1')
index_a = cmd.id_atom("pw2")
index_a_name = getAtomString('pw2')
index_A = cmd.id_atom("pw3")
index_A_name = getAtomString('pw3')
index_B = cmd.id_atom("pw4")
index_B_name = getAtomString('pw4')
index_C = cmd.id_atom("pw5")
index_C_name = getAtomString('pw5')
self.setBondForceParam(r_aA, th_a, th_A, phi_ba, phi_aA, phi_AB,
index_c, index_b, index_a, index_A, index_B,
index_C)
self.setAtomsDef(index_c_name, index_b_name, index_a_name,
index_A_name, index_B_name, index_C_name)
top = Toplevel(
self.parent) # <- freeze when open gro file in pymol 1.X
Output(top, self.bondForceParams, self.atoms_def)
cmd.set_wizard()
def rpcIdAtom(what='all', mode=0):
""" returns the results of cmd.id_atom(what) """
return cmd.id_atom(what, mode=mode)
def rpcIdAtom(what='all', mode=0): """ returns the results of cmd.id_atom(what) """ return cmd.id_atom(what, mode=mode)
def get_ID(index, sel):
return int(cmd.id_atom('index ' + str(index) + ' & ' + sel + ' & present'))