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# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
BreakSite_Marker object wraps the functionality of identifying
the potential break sites within a DnaStrand.
NOTE: This class has nothing to do with DnaMarker class.
@author: Ninad
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
July 2008: created.
As of 2008-08-08 a comment here by Ninad said this was not used,
but was to be used for new Break options features.
As of 2009-01-21 it appears to be used (not fully verified). [--bruce]
"""
from model.bond_constants import find_bond
DEBUG_DRAW_SPHERES_AROUND_ATOMS_AT_BREAK_SITES = False
import time
class BreakSite_Marker(object):
"""
BreakSite_Marker object wraps the functionality of identifying
the potential break sites within a DnaStrand.
@see: BreakStrands_GraphicsMode
@NOTE: This class has nothing to do with DnaMarker class.
"""
def __init__(self, graphicsMode):
self.graphicsMode = graphicsMode
self.command = self.graphicsMode.command
self.win = self.graphicsMode.win
self.glpane = self.graphicsMode.glpane
self._breakSitesDict = {}
self._breakSites_atomPairs_dict = {}
self._startAtoms_dict = {}
self._endAtoms_dict = {}
def getBreakSitesDict(self):
return self._breakSitesDict
def getStartAtomsDict(self):
return self._startAtoms_dict
def getEndAtomsDict(self):
return self._endAtoms_dict
def getBreakSites_atomPairsDict(self):
return self._breakSites_atomPairs_dict
def full_update(self):
self._startAtoms_dict = {}
self._endAtoms_dict = {}
self.update()
def update(self):
self.clearDictionaries()
self._updateBreakSites()
def clearDictionaries(self):
self._breakSitesDict = {}
self._breakSites_atomPairs_dict = {}
##self._startAtoms_dict = {}
##self._endAtoms_dict = {}
def updateStartAtomsDict(self, atm):
strand = atm.getDnaStrand()
if strand in self.command.getStrandList():
self._startAtoms_dict[strand] = atm
self._updateBreakSitesForStrand(strand)
def updateEndAtomsDict(self, atm):
strand = atm.getStrand()
if strand in self.command.getStrandList():
self._endAtoms_dict[strand] = atm
self._updateBreakSitesForStrand(strand)
def _updateBreakSites(self):
##print "***BEFORE updating the breaksites:", time.clock()
strands_to_be_searched = self.command.getStrandList()
basesBeforeNextBreak = self.command.getNumberOfBasesBeforeNextBreak()
if basesBeforeNextBreak == 0:
return #not possible
for strand in strands_to_be_searched:
self._updateBreakSitesForStrand(strand)
##print "***AFTER updating the breaksites:", time.clock()
def _updateBreakSitesForStrand(self, strand):
"""
"""
basesBeforeNextBreak = self.command.getNumberOfBasesBeforeNextBreak()
rawStrandAtomList = strand.get_strand_atoms_in_bond_direction()
strandAtomList = filter(lambda atm: not atm.is_singlet(),
rawStrandAtomList)
if len(strandAtomList) < 3:
return #skip this strand. It doesn't have enough bases
if len(strandAtomList) < basesBeforeNextBreak:
return
#First create a dict to store the information about the bond
#that will be stored in the atom pairs.
atomPair_dict = {}
# =============================================
#If start and end atoms are specified between which the break sites
#need to be computed --
startAtom = None
endAtom = None
startAtomIndex = 0
endAtomIndex = len(strandAtomList) - 1
if self._startAtoms_dict.has_key(strand):
startAtom = self._startAtoms_dict[strand]
#@@BUG METHOD NOT FINISHED YET
#-- sometimes it gives error x not in list after breaking
#a strand etc. CHECK this -- Ninad 2008-07-02
startAtomIndex = strandAtomList.index(startAtom)
if self._endAtoms_dict.has_key(strand):
endAtom = self._endAtoms_dict.index(endAtom)
endAtomIndex = strandAtomList.index(endAtom)
if startAtom and endAtom:
if startAtomIndex > endAtomIndex:
strandAtomList.reverse()
startAtomIndex = strandAtomList.index(startAtom)
endAtomIndex = strandAtomList.index(endAtom)
# =============================================
i = 1
listLength = len(strandAtomList[startAtomIndex: endAtomIndex + 1])
for atm in strandAtomList[startAtomIndex: endAtomIndex + 1]:
#Add '1' to the following actual atom index within the list.
#This is done because the start atom itself will be counted
#as '1st base atom to start with -- INCLUDING THAT ATOM when we
#mark the break sites.
#Example: User want to create a break after every 1 base.
#So, if we start at 5' end, the 5' end atom will be considred
#the first base, and a bond between the 5'end atom and the next
#strand atom will be a 'break site'. Then the next break site
#will be the bond '1 base after that strand atom and like that
idx = strandAtomList.index(atm)
if (i%basesBeforeNextBreak) == 0 and i < listLength:
next_atom = strandAtomList[idx + 1]
bond = find_bond(atm, next_atom)
if not atomPair_dict.has_key(bond):
atomPair_dict[bond] = (atm, next_atom)
if DEBUG_DRAW_SPHERES_AROUND_ATOMS_AT_BREAK_SITES:
for a in (atm, next_atom):
if not self._breakSitesDict.has_key(id(a)):
self._breakSitesDict[id(a)] = a
i += 1
self._breakSites_atomPairs_dict[strand] = atomPair_dict
def _updateBreakSitesForStrand_ORIG(self, strand):
"""
"""
basesBeforeNextBreak = self.command.getNumberOfBasesBeforeNextBreak()
rawStrandAtomList = strand.get_strand_atoms_in_bond_direction()
strandAtomList = filter(lambda atm: not atm.is_singlet(),
rawStrandAtomList)
if len(strandAtomList) < 3:
return #skip this strand. It doesn't have enough bases
if len(strandAtomList) < basesBeforeNextBreak:
return
# =============================================
#If start and end atoms are specified between which the break sites
#need to be computed --
startAtom = None
endAtom = None
startAtomIndex = 0
endAtomIndex = len(strandAtomList) - 1
if self._startAtoms_dict.has_key(strand):
startAtom = self._startAtoms_dict[strand]
#@@BUG METHOD NOT FINISHED YET
#-- sometimes it gives error x not in list after breaking
#a strand etc. CHECK this -- Ninad 2008-07-02
startAtomIndex = strandAtomList.index(startAtom)
if self._endAtoms_dict.has_key(strand):
endAtom = self._endAtoms_dict.index(endAtom)
endAtomIndex = strandAtomList.index(endAtom)
if startAtom and endAtom:
if startAtomIndex > endAtomIndex:
strandAtomList.reverse()
startAtomIndex = strandAtomList.index(startAtom)
endAtomIndex = strandAtomList.index(endAtom)
# =============================================
i = 1
listLength = len(strandAtomList[startAtomIndex: endAtomIndex + 1])
for atm in strandAtomList[startAtomIndex: endAtomIndex + 1]:
#Add '1' to the following actual atom index within the list.
#This is done because the start atom itself will be counted
#as '1st base atom to start with -- INCLUDING THAT ATOM when we
#mark the break sites.
#Example: User want to create a break after every 1 base.
#So, if we start at 5' end, the 5' end atom will be considred
#the first base, and a bond between the 5'end atom and the next
#strand atom will be a 'break site'. Then the next break site
#will be the bond '1 base after that strand atom and like that
##idx = strandAtomList.index(atm) + 1
idx = strandAtomList.index(atm)
##if (idx%basesBeforeNextBreak) == 0 and idx < len(strandAtomList):
if (i%basesBeforeNextBreak) == 0 and i < listLength:
next_atom = strandAtomList[idx + 1]
bond = find_bond(atm, next_atom)
if not self._breakSites_atomPairs_dict.has_key(bond):
self._breakSites_atomPairs_dict[bond] = (atm, next_atom)
for a in (atm, next_atom):
if not self._breakSitesDict.has_key(id(a)):
self._breakSitesDict[id(a)] = a
i += 1
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