def _get_pam5_strand_atoms_in_bond_direction(self, inputAtomList = ()):
"""
Return a list of sugar atoms in a fixed direction -- from 5' to 3'
@param inputAtomList: An optional argument. If its not provided, this
method will return a list of all atoms within the strand,
in the strand's bond direction. Otherwise, it will just return
the list <inputAtomList> whose atoms are ordered in the strand's
bond direction.
@type inputAtomList: list (with default value as an empty tuple)
@note: this is a stub and we can modify it so that
it can accept other direction i.e. 3' to 5' , as an argument.
[I think at most one atom at each end can be a bondpoint,
so we could revise this code to remove them before returning.
bruce 080205]
piotr 080411: This is a helper method for
'get_strand_atoms_in_bond_direction'. It is called for PAM5
models and should be replaced by a properly modified caller method.
Only bondpoints ('X') and sugar atoms ('Ss3', Ss5') are preserved.
@warning: for a ring, this uses an arbitrary start atom in self
(so it is not yet useful in that case). ### VERIFY
@note: this would return all atoms from an entire strand (chain or ring)
even if it spanned multiple chunks.
@TODO: THIS method is copied over from chunk class. with a minor modification
To be revised. See self.getStrandSequence() for a comment.
"""
startAtom = None
atomList = []
rawAtomList = []
if inputAtomList:
rawAtomList = inputAtomList
else:
for c in self.members:
if isinstance(c, DnaStrandChunk):
rawAtomList.extend(c.atoms.itervalues())
#Choose startAtom randomly (make sure that it's a Sugar atom
# and not a bondpoint)
for atm in rawAtomList:
if atm.element.symbol == 'Ss3' or \
atm.element.symbol == 'Ss5':
startAtom = atm
break
if startAtom is None:
print_compact_stack("bug: no Sugar atom (Ss3 or Ss5) found: " )
return []
#Build one list in each direction, detecting a ring too
#ringQ decides whether the first returned list forms a ring.
#This needs a better name in bond_chains.grow_directional_bond_chain
ringQ = False
atomList_direction_1 = []
atomList_direction_2 = []
b = None
bond_direction = 0
for bnd in startAtom.directional_bonds():
if not bnd.is_open_bond(): # (this assumes strand length > 1)
#Determine the bond_direction from the 'startAtom'
direction = bnd.bond_direction_from(startAtom)
if direction in (1, -1):
b = bnd
bond_direction = direction
break
if b is None or bond_direction == 0:
return []
#Find out the list of new atoms and bonds in the direction
#from bond b towards 'startAtom' . This can either be 3' to 5' direction
#(i.e. bond_direction = -1 OR the reverse direction
# Later, we will check the bond direction and do appropriate things.
#(things that will decide which list (atomList_direction_1 or
#atomList_direction_2) should be prepended in atomList so that it has
#atoms ordered from 5' to 3' end.
# 'atomList_direction_1' does NOT include 'startAtom'.
# See a detailed explanation below on how atomList_direction_a will be
# used, based on bond_direction
ringQ, listb, atomList_direction_1 = grow_directional_bond_chain(b, startAtom)
del listb # don't need list of bonds
if ringQ:
# The 'ringQ' returns True So its it's a 'ring'.
#First add 'startAtom' (as its not included in atomList_direction_1)
atomList.append(startAtom)
#extend atomList with remaining atoms
atomList.extend(atomList_direction_1)
else:
#Its not a ring. Now we need to make sure to include atoms in the
#direction_2 (if any) from the 'startAtom' . i.e. we need to grow
#the directional bond chain in the opposite direction.
other_atom = b.other(startAtom)
if not other_atom.is_singlet():
ringQ, listb, atomList_direction_2 = grow_directional_bond_chain(b, other_atom)
assert not ringQ #bruce 080205
del listb
#See a detailed explanation below on how
#atomList_direction_2 will be used based on 'bond_direction'
atomList_direction_2.insert(0, other_atom)
atomList = [] # not needed but just to be on a safer side.
if bond_direction == 1:
# 'bond_direction' is the direction *away from* startAtom and
# along the bond 'b' declared above. .
# This can be represented by the following sketch --
# (3'end) <--1 <-- 2 <-- 3 <-- 4 <-- (5' end)
# Let startAtom be '2' and bond 'b' be directional bond between
# 1 and 2. In this case, the direction of bond *away* from
# '2' and along 2 = bond direction of bond 'b' and thus
# atoms traversed along bond_direction = 1 lead us to 3' end.
# Now, 'atomList_direction_1' is computed by 'growing' (expanding)
# a bond chain in the direction that goes from bond b
# *towards* startAtom. That is, in this case it is the opposite
# direction of one specified by 'bond_direction'. The last atom
# in atomList_direction_1 is the (5' end) atom.
# Note that atomList_direction_1 doesn't include 'startAtom'
# Therefore, to get atomList ordered from 5'to 3' end we must
#reverse atomList_direction_1 , then append startAtom to the
#atomList (as its not included in atomList_direction_1) and then
#extend atoms from atomList_direction_2.
#What is atomList_direction_2 ? It is the list of atoms
#obtained by growing bond chain from bond b, in the direction of
#atom 1 (atom 1 is the 'other atom' of the bond) . In this case
#these are the atoms in the direction same as 'bond_direction'
#starting from atom 1. Thus the atoms in the list are already
#arranged from 5' to 3' end. (also note that after computing
#the atomList_direction_2, we also prepend 'atom 1' as the
#first atom in that list. See the code above that does that.
atomList_direction_1.reverse()
atomList.extend(atomList_direction_1)
atomList.append(startAtom)
atomList.extend(atomList_direction_2)
else:
#See a detailed explanation above.
#Here, bond_direction == -1.
# This can be represented by the following sketch --
# (5'end) --> 1 --> 2 --> 3 --> 4 --> (3' end)
#bond b is the bond betweern atoms 1 and 2.
#startAtom remains the same ..i.e. atom 2.
#As you can notice from the sketch, the bond_direction is
#direction *away* from 2, along bond b and it leads us to
# 5' end.
#based on how atomList_direction_2 (explained earlier), it now
#includes atoms begining at 1 and ending at 5' end. So
#we must reverse atomList_direction_2 now to arrange them
#from 5' to 3' end.
atomList_direction_2.reverse()
atomList.extend(atomList_direction_2)
atomList.append(startAtom)
atomList.extend(atomList_direction_1)
# Note: the bondpoint atoms are NOT included.
# ONLY consecutive sugar stoms are returned.
# piotr 080411
# extract only sugar atoms or bondpoints
# the bondpoints are extracted to make the method compatible
# with get_strand_atoms_in_bond_direction
def filter_sugars(atm):
return atm.element.symbol == 'Ss3' or \
atm.element.symbol == 'Ss5' or \
atm.element.symbol == 'X'
atomList = filter(filter_sugars, atomList)
return atomList
def _get_pam5_strand_atoms_in_bond_direction(self, inputAtomList=()):
"""
Return a list of sugar atoms in a fixed direction -- from 5' to 3'
@param inputAtomList: An optional argument. If its not provided, this
method will return a list of all atoms within the strand,
in the strand's bond direction. Otherwise, it will just return
the list <inputAtomList> whose atoms are ordered in the strand's
bond direction.
@type inputAtomList: list (with default value as an empty tuple)
@note: this is a stub and we can modify it so that
it can accept other direction i.e. 3' to 5' , as an argument.
[I think at most one atom at each end can be a bondpoint,
so we could revise this code to remove them before returning.
bruce 080205]
piotr 080411: This is a helper method for
'get_strand_atoms_in_bond_direction'. It is called for PAM5
models and should be replaced by a properly modified caller method.
Only bondpoints ('X') and sugar atoms ('Ss3', Ss5') are preserved.
@warning: for a ring, this uses an arbitrary start atom in self
(so it is not yet useful in that case). ### VERIFY
@note: this would return all atoms from an entire strand (chain or ring)
even if it spanned multiple chunks.
@TODO: THIS method is copied over from chunk class. with a minor modification
To be revised. See self.getStrandSequence() for a comment.
"""
startAtom = None
atomList = []
rawAtomList = []
if inputAtomList:
rawAtomList = inputAtomList
else:
for c in self.members:
if isinstance(c, DnaStrandChunk):
rawAtomList.extend(c.atoms.itervalues())
#Choose startAtom randomly (make sure that it's a Sugar atom
# and not a bondpoint)
for atm in rawAtomList:
if atm.element.symbol == 'Ss3' or \
atm.element.symbol == 'Ss5':
startAtom = atm
break
if startAtom is None:
print_compact_stack("bug: no Sugar atom (Ss3 or Ss5) found: ")
return []
#Build one list in each direction, detecting a ring too
#ringQ decides whether the first returned list forms a ring.
#This needs a better name in bond_chains.grow_directional_bond_chain
ringQ = False
atomList_direction_1 = []
atomList_direction_2 = []
b = None
bond_direction = 0
for bnd in startAtom.directional_bonds():
if not bnd.is_open_bond(): # (this assumes strand length > 1)
#Determine the bond_direction from the 'startAtom'
direction = bnd.bond_direction_from(startAtom)
if direction in (1, -1):
b = bnd
bond_direction = direction
break
if b is None or bond_direction == 0:
return []
#Find out the list of new atoms and bonds in the direction
#from bond b towards 'startAtom' . This can either be 3' to 5' direction
#(i.e. bond_direction = -1 OR the reverse direction
# Later, we will check the bond direction and do appropriate things.
#(things that will decide which list (atomList_direction_1 or
#atomList_direction_2) should be prepended in atomList so that it has
#atoms ordered from 5' to 3' end.
# 'atomList_direction_1' does NOT include 'startAtom'.
# See a detailed explanation below on how atomList_direction_a will be
# used, based on bond_direction
ringQ, listb, atomList_direction_1 = grow_directional_bond_chain(
b, startAtom)
del listb # don't need list of bonds
if ringQ:
# The 'ringQ' returns True So its it's a 'ring'.
#First add 'startAtom' (as its not included in atomList_direction_1)
atomList.append(startAtom)
#extend atomList with remaining atoms
atomList.extend(atomList_direction_1)
else:
#Its not a ring. Now we need to make sure to include atoms in the
#direction_2 (if any) from the 'startAtom' . i.e. we need to grow
#the directional bond chain in the opposite direction.
other_atom = b.other(startAtom)
if not other_atom.is_singlet():
ringQ, listb, atomList_direction_2 = grow_directional_bond_chain(
b, other_atom)
assert not ringQ #bruce 080205
del listb
#See a detailed explanation below on how
#atomList_direction_2 will be used based on 'bond_direction'
atomList_direction_2.insert(0, other_atom)
atomList = [] # not needed but just to be on a safer side.
if bond_direction == 1:
# 'bond_direction' is the direction *away from* startAtom and
# along the bond 'b' declared above. .
# This can be represented by the following sketch --
# (3'end) <--1 <-- 2 <-- 3 <-- 4 <-- (5' end)
# Let startAtom be '2' and bond 'b' be directional bond between
# 1 and 2. In this case, the direction of bond *away* from
# '2' and along 2 = bond direction of bond 'b' and thus
# atoms traversed along bond_direction = 1 lead us to 3' end.
# Now, 'atomList_direction_1' is computed by 'growing' (expanding)
# a bond chain in the direction that goes from bond b
# *towards* startAtom. That is, in this case it is the opposite
# direction of one specified by 'bond_direction'. The last atom
# in atomList_direction_1 is the (5' end) atom.
# Note that atomList_direction_1 doesn't include 'startAtom'
# Therefore, to get atomList ordered from 5'to 3' end we must
#reverse atomList_direction_1 , then append startAtom to the
#atomList (as its not included in atomList_direction_1) and then
#extend atoms from atomList_direction_2.
#What is atomList_direction_2 ? It is the list of atoms
#obtained by growing bond chain from bond b, in the direction of
#atom 1 (atom 1 is the 'other atom' of the bond) . In this case
#these are the atoms in the direction same as 'bond_direction'
#starting from atom 1. Thus the atoms in the list are already
#arranged from 5' to 3' end. (also note that after computing
#the atomList_direction_2, we also prepend 'atom 1' as the
#first atom in that list. See the code above that does that.
atomList_direction_1.reverse()
atomList.extend(atomList_direction_1)
atomList.append(startAtom)
atomList.extend(atomList_direction_2)
else:
#See a detailed explanation above.
#Here, bond_direction == -1.
# This can be represented by the following sketch --
# (5'end) --> 1 --> 2 --> 3 --> 4 --> (3' end)
#bond b is the bond betweern atoms 1 and 2.
#startAtom remains the same ..i.e. atom 2.
#As you can notice from the sketch, the bond_direction is
#direction *away* from 2, along bond b and it leads us to
# 5' end.
#based on how atomList_direction_2 (explained earlier), it now
#includes atoms begining at 1 and ending at 5' end. So
#we must reverse atomList_direction_2 now to arrange them
#from 5' to 3' end.
atomList_direction_2.reverse()
atomList.extend(atomList_direction_2)
atomList.append(startAtom)
atomList.extend(atomList_direction_1)
# Note: the bondpoint atoms are NOT included.
# ONLY consecutive sugar stoms are returned.
# piotr 080411
# extract only sugar atoms or bondpoints
# the bondpoints are extracted to make the method compatible
# with get_strand_atoms_in_bond_direction
def filter_sugars(atm):
return atm.element.symbol == 'Ss3' or \
atm.element.symbol == 'Ss5' or \
atm.element.symbol == 'X'
atomList = filter(filter_sugars, atomList)
return atomList
