def bond_menu_section(bond, quat = Q(1,0,0,0)):
"""
Return a menu_spec subsection for displaying info about a highlighted bond,
changing its bond_type, offering commands about it, etc.
If given, use the quat describing the rotation used for displaying it
to order the atoms in the bond left-to-right (e.g. in text strings).
"""
res = []
res.append(( bonded_atoms_summary(bond, quat = quat), noop, 'disabled' ))
res.extend( _bond_type_menu_section(bond) )
if bond.is_directional():
### REVIEW: Do we want to do this for open bonds, after mark's 071014 change
# which allows them here? Or do we want "and not bond.is_open_bond()"?
# (BTW, I'm not sure this gets called at all, for open bonds.)
# Guess: open bonds would be safe here, so allow them, though I'm
# not sure it's always a good idea. Caveat: if we treat them as non-directional
# when the base atom has three or more directional bonds, we should probably
# make that exception here too -- probably using a higher-level method in place
# of is_directional, namely directional_bond_chain_status for both atoms in bond.
# We'd want a new method on bond to call that for both atoms and look at the
# results (perhaps there's already code like that elsewhere). Without this,
# we may get a bug if a user can try to change direction on an open bond
# that hits a strand but is not in it. But since I suspect the UI never allows
# an open bond here, I won't bother to write that code just yet. [bruce 071016]
submenu_contents = bond_direction_submenu_contents(bond, quat)
left_atom = bond_left_atom(bond, quat) # same one that comes first in bonded_atoms_summary
#e ideally, for mostly vertical bonds, we'd switch to an up/down distinction for the menu text about directions
#e and whatever the direction names, maybe we should explore farther along the strand to see what they are...
# unless it hairpins or crosses over... hmm.
current_dir = bond.bond_direction_from(left_atom)
current_dir_str = _BOND_DIR_TEXTS[current_dir]
text = "strand direction (%s)" % current_dir_str
item = (text, submenu_contents)
res.append(item)
return res
def bond_direction_submenu_contents(bond, quat): #bruce 070415
res = []
left_atom = bond_left_atom(bond, quat)
direction = bond.bond_direction_from(left_atom)
## # order will be: if this bond has a dir: this dir, opp dir, unset;
## # or if not: unset, right, left. So current dir is always first. Not sure this is good! In fact, I'm sure it's not!
## if direction:
## dir_order = [direction, - direction, 0]
## else:
## dir_order = [0, 1, -1]
dir_order = [1, -1, 0]
for dir in dir_order:
text = "make it %s" % _BOND_DIR_NAMES[dir]
# how do we say concisely:
# "make the bond dirs all one way along entire strand,
# so they're going (eg) right, when they pass thru this bond"?
if dir == direction:
text += " (like this bond)" #e also use checkmark, or is that confusing since it's not a noop? for now, use it.
command = (lambda _guard = None, bond = bond, left_atom = left_atom, dir = dir:
bond.set_bond_direction_from(left_atom, dir, propogate = True))
checkmark = (dir == direction) and 'checked' or None
item = (text, command, checkmark)
res.append(item)
res.append(('set to fit minor groove (not implemented)', noop, 'disabled'))
return res
def bond_direction_submenu_contents(bond, quat): #bruce 070415
res = []
left_atom = bond_left_atom(bond, quat)
direction = bond.bond_direction_from(left_atom)
## # order will be: if this bond has a dir: this dir, opp dir, unset;
## # or if not: unset, right, left. So current dir is always first. Not sure this is good! In fact, I'm sure it's not!
## if direction:
## dir_order = [direction, - direction, 0]
## else:
## dir_order = [0, 1, -1]
dir_order = [1, -1, 0]
for dir in dir_order:
text = "make it %s" % _BOND_DIR_NAMES[dir]
# how do we say concisely:
# "make the bond dirs all one way along entire strand,
# so they're going (eg) right, when they pass thru this bond"?
if dir == direction:
text += " (like this bond)" #e also use checkmark, or is that confusing since it's not a noop? for now, use it.
command = (
lambda _guard=None, bond=bond, left_atom=left_atom, dir=dir: bond.
set_bond_direction_from(left_atom, dir, propogate=True))
checkmark = (dir == direction) and 'checked' or None
item = (text, command, checkmark)
res.append(item)
res.append(('set to fit minor groove (not implemented)', noop, 'disabled'))
return res
def bond_menu_section(bond, quat=Q(1, 0, 0, 0)):
"""
Return a menu_spec subsection for displaying info about a highlighted bond,
changing its bond_type, offering commands about it, etc.
If given, use the quat describing the rotation used for displaying it
to order the atoms in the bond left-to-right (e.g. in text strings).
"""
res = []
res.append((bonded_atoms_summary(bond, quat=quat), noop, 'disabled'))
res.extend(_bond_type_menu_section(bond))
if bond.is_directional():
### REVIEW: Do we want to do this for open bonds, after mark's 071014 change
# which allows them here? Or do we want "and not bond.is_open_bond()"?
# (BTW, I'm not sure this gets called at all, for open bonds.)
# Guess: open bonds would be safe here, so allow them, though I'm
# not sure it's always a good idea. Caveat: if we treat them as non-directional
# when the base atom has three or more directional bonds, we should probably
# make that exception here too -- probably using a higher-level method in place
# of is_directional, namely directional_bond_chain_status for both atoms in bond.
# We'd want a new method on bond to call that for both atoms and look at the
# results (perhaps there's already code like that elsewhere). Without this,
# we may get a bug if a user can try to change direction on an open bond
# that hits a strand but is not in it. But since I suspect the UI never allows
# an open bond here, I won't bother to write that code just yet. [bruce 071016]
submenu_contents = bond_direction_submenu_contents(bond, quat)
left_atom = bond_left_atom(
bond, quat) # same one that comes first in bonded_atoms_summary
#e ideally, for mostly vertical bonds, we'd switch to an up/down distinction for the menu text about directions
#e and whatever the direction names, maybe we should explore farther along the strand to see what they are...
# unless it hairpins or crosses over... hmm.
current_dir = bond.bond_direction_from(left_atom)
current_dir_str = _BOND_DIR_TEXTS[current_dir]
text = "strand direction (%s)" % current_dir_str
item = (text, submenu_contents)
res.append(item)
return res
def getToolTipInfoForBond(self, bond):
"""
Tooltip information when the cursor is over a strand bond.
As of 2008-11-09, it gives the information in the following form:
"""
#Bond direction will always be atm1 --> atm2
#@see: Bond.bond_direction_from()
atm1 = bond.atom1
atm2 = bond.atom2
strandInfo = ""
if not (atm1 and atm2):
strandInfo = self.getDefaultToolTipInfo()
return strandInfo
threePrimeEndAtom = self.get_three_prime_end_base_atom()
fivePrimeEndAtom = self.get_five_prime_end_base_atom()
allAtoms = self.get_strand_atoms_in_bond_direction(filterBondPoints = True)
tooltipDirection = "3<--5"
left_atom = bond_left_atom(bond, quat = self.assy.glpane.quat)
right_atom = bond.other(left_atom)
if bond.bond_direction_from(left_atom) == 1:
tooltipDirection = "5-->3"
else:
tooltipDirection = "3<--5"
left_atm_index = None
try:
left_atm_index = allAtoms.index(left_atom)
except:
print_compact_traceback("bug in getting strand info string "\
"atom %s not in list"%left_atom)
if left_atm_index:
#@BUG: The computation of numOfBases_next_crossover_5prime and
#numOfBases_next_crossover_3prime is wrong in some cases. So,
#that information is not displayed.
numOfBases_next_crossover_5prime, numOfBases_next_crossover_3prime = \
self._number_of_atoms_before_next_crossover(
left_atom,
tooltipDirection = tooltipDirection)
if threePrimeEndAtom and fivePrimeEndAtom:
if tooltipDirection == "3<--5":
numOfBasesDown_3PrimeDirection = len(allAtoms[left_atm_index:])
#Note: This does not include atm1 , which is intentional--
numOfBasesDown_5PrimeDirection = len(allAtoms[:left_atm_index])
##strandInfo += " 3' < " + str(numOfBasesDown_3PrimeDirection) + "/" + str(numOfBases_next_crossover_3prime)
strandInfo += " 3' < " + str(numOfBasesDown_3PrimeDirection)
strandInfo += " --(%s)-- "%(len(allAtoms))
##strandInfo += str(numOfBases_next_crossover_5prime) + "/" + str(numOfBasesDown_5PrimeDirection) + " < 5'"
strandInfo += str(numOfBasesDown_5PrimeDirection) + " < 5'"
else:
numOfBasesDown_3PrimeDirection = len(allAtoms[left_atm_index + 1:])
#Note: This does not include atm1 , which is intentional--
numOfBasesDown_5PrimeDirection = len(allAtoms[:left_atm_index + 1])
##strandInfo += " 5' > " + str(numOfBasesDown_5PrimeDirection) + "/" + str(numOfBases_next_crossover_5prime)
strandInfo += " 5' > " + str(numOfBasesDown_5PrimeDirection)
strandInfo += " --(%s)-- "%(len(allAtoms))
##strandInfo += str(numOfBases_next_crossover_3prime) + "/" + str(numOfBasesDown_3PrimeDirection) + " > 3'"
strandInfo += str(numOfBasesDown_3PrimeDirection) + " > 3'"
#Make sure that symbol like > are converted to html
strandInfo = quote_html(strandInfo)
return strandInfo