def get_beads(self):
"""
Generates steric beads required for checking for steric clashes between
motifs. Each residues has three beads modeled after the typical three
bead models used in coarse grain modeling. The three beads are,
Phosphate (P, OP1, OP2) Sugar (O5',C5',C4',O4',C3',O3',C1',C2',O2')
and Base (All remaining atoms).
"""
phos_atoms,sugar_atoms,base_atoms = [],[],[]
for i,a in enumerate(self.atoms):
if a is None:
continue
if i < 3:
phos_atoms.append(a)
elif i < 12:
sugar_atoms.append(a)
else:
base_atoms.append(a)
beads = []
types = [residue.BeadType.PHOS, residue.BeadType.SUGAR, residue.BeadType.BASE]
for i,alist in enumerate([phos_atoms,sugar_atoms,base_atoms]):
if len(alist) > 0:
beads.append(residue.Bead(util.center(alist), types[i]))
return beads
def draw(self, view_mode=0):
self.view_mode = view_mode
self.drawn = 1
for r in self.residues:
r.draw(view_mode)
if view_mode == 2:
points = []
for r in self.residues:
atoms = []
for i in (0,1,2,3,4,5):
if r.atoms[i] is not None:
atoms.append(r.atoms[i])
center = util.center(atoms)
points.append(center)
self.obj = curve(radius=0.5, color=color.orange)
for p in points:
self.obj.append(pos=p)
center=(5, 0, 0),
background=(1, 1, 1),
ambient=color.gray(0.5))
"""c = controls(x=0, y=0, width=250, height=250, range=60)
m1 = menu(pos=(0,0,0), height=7, width=25, text='Options')
bl = button(pos=(-30,30), height=30, width=40, text='Mode', action=lambda: change())
m1.items.append(('Mode', lambda: change())) # specify menu item title and action to perform"""
atoms = []
s = structure.structure_from_pdb("nodes.0.pdb")
atoms.extend(s.atoms())
s = structure.structure_from_pdb("nodes.1.pdb")
atoms.extend(s.atoms())
v_atoms = []
center = util.center(atoms)
for a in atoms:
v_atoms.append(VAtom(a))
scene.center = center
scene.range = np.array([20, 20, 20])
range = np.array([20, 20, 20])
points = []
lines = []
pick = None
dragpos = []
while 1:
rate(100)
if scene.kb.keys: # event waiting to be processed?
def d(self):
atoms = self._get_atoms()
return util.center(atoms)
x=0, y=0, width=800, height=800,
center=(5,0,0), background=(1,1,1), ambient=color.gray(0.5))
"""c = controls(x=0, y=0, width=250, height=250, range=60)
m1 = menu(pos=(0,0,0), height=7, width=25, text='Options')
bl = button(pos=(-30,30), height=30, width=40, text='Mode', action=lambda: change())
m1.items.append(('Mode', lambda: change())) # specify menu item title and action to perform"""
atoms = []
s = structure.structure_from_pdb("nodes.0.pdb")
atoms.extend(s.atoms())
s = structure.structure_from_pdb("nodes.1.pdb")
atoms.extend(s.atoms())
v_atoms = []
center = util.center(atoms)
for a in atoms:
v_atoms.append(VAtom(a))
scene.center = center
scene.range = np.array([20,20,20])
range = np.array([20,20,20])
points = []
lines = []
pick = None
dragpos = []
