def do_select(self, name):
if self.pick_count < 1:
self.atom1 = self.get_Atom(name)
if len(self.atom1) > 0:
if int(self.atom1[2]) == self.ResSeq and self.atom1[1] == 'LIG':
self.pickNextAtom()
self.highlight_Atom(self.atom1)
else:
self.ErrorStatus = [ "You can only select atoms from the object " + self.LigDisplay + ". Try again." ]
else:
self.ErrorStatus = [ "No atoms could be selected in the object " + self.LigDisplay + ". Try again." ]
else:
self.atom2 = self.get_Atom(name)
if len(self.atom2) > 0:
if int(self.atom2[2]) == self.ResSeq and self.atom2[1] == 'LIG':
self.pickNextAtom()
self.highlight_Atom(self.atom2)
if not self.is_Valid(self.atom1, self.atom2):
self.ErrorStatus = [ "The selected bond cannot be set as flexible. Try again." ]
else:
# Already existing Possible Bond
if self.FlexIndex != 0:
if self.dictFlexBonds[self.FlexIndex][0]:
self.dictFlexBonds[self.FlexIndex][0] = 0
else:
self.dictFlexBonds[self.FlexIndex][0] = 1
# Force new bond
else:
self.Force_NewBond(General_cmd.get_ID(self.atom1[0], self.LigDisplay),
General_cmd.get_ID(self.atom2[0], self.LigDisplay))
self.show_SelectedBonds()
self.pick_count = 0
cmd.refresh_wizard()
cmd.delete(self.AtomDisplay)
cmd.refresh()
else:
self.ErrorStatus = [ "No atoms could be selected in the object " + self.LigDisplay + ". Try again." ]
else:
self.ErrorStatus = [ "You can only select atoms from the object " + self.LigDisplay + ". Try again." ]
def is_Valid(self, atom1, atom2):
# 2 hydrogens
if atom1[4].strip()[0] == 'H' and atom2[4].strip()[0] == 'H':
return 0
# Distance is too far
elif Geometry.distance(atom1[5:],atom2[5:]) > 2.0:
return 0
self.FlexIndex = self.is_Flexible(General_cmd.get_ID(atom1[0], self.LigDisplay),
General_cmd.get_ID(atom2[0], self.LigDisplay))
# The bond cannot be defined
if self.FlexIndex == -1:
return 0
# The bond can only be defined using force
elif self.FlexIndex == 0 and not self.Force:
return 0
return 1
def do_select(self, name):
lt = cmd.index(name + ' & !hydrogens')
for t in lt:
if t[0] != self.LigDisplay:
self.ErrorStatus = [ "You can only select a non-Hydrogen from the object " + self.LigDisplay + ". Try again." ]
else:
self.AnchorAtom = General_cmd.get_ID(t[1],t[0])
self.RefreshDisplay()
break
cmd.deselect()
def do_select(self, name):
lt = cmd.index(name + ' & !hydrogens')
for t in lt:
if t[0] != self.LigDisplay:
self.ErrorStatus = [
"You can only select a non-Hydrogen from the object " +
self.LigDisplay + ". Try again."
]
else:
self.AnchorAtom = General_cmd.get_ID(t[1], t[0])
self.RefreshDisplay()
break
cmd.deselect()
def get_Coords(self, atom_number, point):
found = False
try:
atom_number = int(atom_number)
atoms = cmd.get_model(self.LigDisplay, state=cmd.get_state())
for at in atoms.atom:
if General_cmd.get_ID(at.index, self.LigDisplay) == atom_number:
point.extend([at.coord[0],at.coord[1],at.coord[2]])
found = True
break
if not found:
return 1
except:
return 1
return 0