def __drawOrigCoords(origCoords):
"""Display the original pre-rotamerize coordinates as a generic object
ARGUMENTS:
origCoords - a chain object containing the atoms to be drawn
RETURNS:
drawNum - the generic object number
EFFECTS:
creates and displays a new Coot generic object
"""
#create a new generic display object
drawNum = new_generic_object_number("Pre-rotamerize coordinates")
set_display_generic_object(drawNum, 1)
lineList = [] #a list of all the bonds to be drawn
#draw bonds for each nucleotide
prevO3 = None
for curNuc in origCoords.nucs:
#draw each bond if both atoms are present
for (atom1, atom2) in (BOND_LIST_FULL["backbone"] +
BOND_LIST_FULL[curNuc.type]):
if curNuc.hasAtom(atom1) and curNuc.hasAtom(atom2):
atom1Coords = curNuc.atoms[atom1]
atom2Coords = curNuc.atoms[atom2]
lineList.append(atom1Coords + atom2Coords)
#draw a bond between O5' and the previous phosphate if both atoms are present
if prevO3 is not None and curNuc.hasAtom("P"):
lineList.append(prevO3 + curNuc.atoms["P"])
#update prevPhos
if curNuc.hasAtom("O3'"):
prevO3 = curNuc.atoms["O3'"]
else:
prevO3 = None
#actually draw the bonds
for curLine in lineList:
to_generic_object_add_line(drawNum, ORIG_COORDS_COLOR, 6, *curLine)
graphics_draw()
return drawNum
def __drawOrigCoords(origCoords):
"""Display the original pre-rotamerize coordinates as a generic object
ARGUMENTS:
origCoords - a chain object containing the atoms to be drawn
RETURNS:
drawNum - the generic object number
EFFECTS:
creates and displays a new Coot generic object
"""
#create a new generic display object
drawNum = new_generic_object_number("Pre-rotamerize coordinates")
set_display_generic_object(drawNum, 1)
lineList = [] #a list of all the bonds to be drawn
#draw bonds for each nucleotide
prevO3 = None
for curNuc in origCoords.nucs:
#draw each bond if both atoms are present
for (atom1, atom2) in (BOND_LIST_FULL["backbone"] + BOND_LIST_FULL[curNuc.type]):
if curNuc.hasAtom(atom1) and curNuc.hasAtom(atom2):
atom1Coords = curNuc.atoms[atom1]
atom2Coords = curNuc.atoms[atom2]
lineList.append(atom1Coords + atom2Coords)
#draw a bond between O5' and the previous phosphate if both atoms are present
if prevO3 is not None and curNuc.hasAtom("P"):
lineList.append(prevO3 + curNuc.atoms["P"])
#update prevPhos
if curNuc.hasAtom("O3'"):
prevO3 = curNuc.atoms["O3'"]
else:
prevO3 = None
#actually draw the bonds
for curLine in lineList:
to_generic_object_add_line(drawNum, ORIG_COORDS_COLOR, 6, *curLine)
graphics_draw()
return drawNum
def cluster_star_obj(obj, pos, thick, v_0):
delta_0 = v_0
delta_r2 = delta_0 / math.sqrt(2)
delta_r3 = delta_0 / math.sqrt(3)
delta = delta_r3
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] + delta, pos[1] + delta, pos[2] + delta
)
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] - delta, pos[1] - delta, pos[2] - delta
)
delta = delta_0
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] - delta, pos[1], pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0], pos[1] - delta, pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0], pos[1], pos[2] - delta)
delta = delta_r2
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0], pos[1] - delta, pos[2] - delta
)
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] - delta, pos[1] - delta, pos[2]
)
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] - delta, pos[1], pos[2] - delta
)
delta = delta_0
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] + delta, pos[1], pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0], pos[1] + delta, pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0], pos[1], pos[2] + delta)
delta = delta_r2
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0], pos[1] + delta, pos[2] + delta
)
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] + delta, pos[1] + delta, pos[2]
)
coot.to_generic_object_add_line(
obj, "yellowtint", thick, pos[0], pos[1], pos[2], pos[0] + delta, pos[1], pos[2] + delta
)
def cluster_star_obj(obj, pos, thick, v_0):
delta_0 = v_0
delta_r2 = delta_0 / math.sqrt(2)
delta_r3 = delta_0 / math.sqrt(3)
delta = delta_r3
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] + delta, pos[1] + delta,
pos[2] + delta)
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] - delta, pos[1] - delta,
pos[2] - delta)
delta = delta_0
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] - delta, pos[1], pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0], pos[1] - delta, pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0], pos[1], pos[2] - delta)
delta = delta_r2
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0], pos[1] - delta,
pos[2] - delta)
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] - delta, pos[1] - delta,
pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] - delta, pos[1],
pos[2] - delta)
delta = delta_0
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] + delta, pos[1], pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0], pos[1] + delta, pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0], pos[1], pos[2] + delta)
delta = delta_r2
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0], pos[1] + delta,
pos[2] + delta)
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] + delta, pos[1] + delta,
pos[2])
coot.to_generic_object_add_line(obj, "yellowtint", thick, pos[0], pos[1],
pos[2], pos[0] + delta, pos[1],
pos[2] + delta)