def debug_check_bond_direction(self, when = ""):
"""
Verify our bond direction is set correctly (if possible),
and assertfail and/or print a debug warning if not.
"""
## assert self.strandQ
assert self.baseatoms, "%r has no baseatoms" % self
if not self.strandQ:
return
assert self._bond_direction
assert not self._bond_direction_error
if self.bond_direction_is_arbitrary():
return # no way to check it
# verify it by comparing it to actual bonds
if when:
when = " (%s)" % when
# STUB: only works fully for PAM3
atom1 = self.baseatoms[0]
atom2 = self.baseatoms[1]
bond = find_bond(atom1, atom2)
errormsg = "" # might be set to an error string
actual_direction = 0 # might be set to a bond direction
if bond:
actual_direction = bond.bond_direction_from(atom1)
elif atom1.Pl_neighbors() or atom2.Pl_neighbors():
# look for atom1-Pl-atom2 (2 bonds, same direction)
bond1, bond2 = find_Pl_bonds(atom1, atom2) # might be None, None
if not bond1:
errormsg = "no Pl5 between adjacent baseatoms %r and %r" % (atom1, atom2)
else:
dir1 = bond1.bond_direction_from(atom1)
dir2 = - bond2.bond_direction_from(atom2)
if dir1 == dir2:
actual_direction = dir1 # might be 0
else:
errormsg = "Pl5 between %r and %r has inconsistent or unset bond directions" % (atom1, atom2)
else:
errormsg = "no bond between adjacent baseatoms %r and %r" % (atom1, atom2)
if not errormsg:
# check actual_direction
## not needed: assert actual_direction
recorded_direction = self._bond_direction
assert recorded_direction # redundant with earlier assert
if actual_direction != recorded_direction:
# error
errormsg = "bond direction from %r to %r: recorded %r, actual %r" % \
(atom1, atom2, recorded_direction, actual_direction)
# now errormsg tells whether there is an error.
if errormsg:
prefix = "debug_check_bond_direction%s in %r" % (when, self)
msg = "%s: ERROR: %s" % (prefix, errormsg)
print "\n*** %s ***\n" % msg
summary_format = "DNA updater: bug: [N] failure(s) of debug_check_bond_direction, see console prints"
env.history.deferred_summary_message( redmsg(summary_format))
return
def find_Pl_between(s1, s2): #bruce 080409
"""
Assume s1 and s2 are Ss3 and/or Ss5 atoms which
might be directly bonded or might have a Pl5 between them.
If they are directly bonded, return None.
If they have a Pl between them, return it.
If neither is true, raise an exception.
"""
# optimize for the Pl being found
bond1, bond2 = find_Pl_bonds(s1, s2)
if bond1:
return bond1.other(s1)
else:
assert find_bond(s1, s2)
return None
pass
def find_Pl_between(s1, s2): #bruce 080409
"""
Assume s1 and s2 are Ss3 and/or Ss5 atoms which
might be directly bonded or might have a Pl5 between them.
If they are directly bonded, return None.
If they have a Pl between them, return it.
If neither is true, raise an exception.
"""
# optimize for the Pl being found
bond1, bond2 = find_Pl_bonds(s1, s2)
if bond1:
return bond1.other(s1)
else:
assert find_bond(s1, s2)
return None
pass
