def secondPhos(self, mapNum, curPhos, direction = 3):
"""find the second phosphate in a chain using phosphate distance data
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
curPhos - the coordinates of the first phosphate
OPTIONAL ARGUMENTS:
direction - which direction to trace the chain: 3 implies 5'->3'
5 implies 3'->5'
defaults to 3 (5'->3')
RETURNS:
peakList - a list of potential phosphate peaks
sugarList - a list of potential C1' locations for each phosphate peak
"""
peaks = self.getPeaks(mapNum, curPhos)
#calculate the score for each peak
peakScores = []
for curPeak in peaks:
#exclude any peaks that are within an Angstom of the current phosphate position
#this will exclude the peak corresponding to the current phosphate position
if dist(curPhos, curPeak) >= 1:
#do a sugar search for the current phosphate
if direction == 3:
sugarLocs = self.findSugar(mapNum, curPhos, curPeak)
else: #direction == 5:
sugarLocs = self.findSugar(mapNum, curPeak, curPhos)
densityScore = sugarLocs[0][3] + curPeak[3]
score = ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))) + (SECOND_PHOS_DENSITY_WEIGHT * ln(densityScore))
peakScores.append((curPeak, score, sugarLocs))
#sort the peaks according to score
peakScores.sort(key = lambda x: x[1], reverse = 1)
#return only the coordinates, not the scores
peakList = [x[0] for x in peakScores]
sugarList = [x[2] for x in peakScores]
return (peakList, sugarList)
def secondPhos(self, mapNum, curPhos, direction = 3):
"""find the second phosphate in a chain using phosphate distance data
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
curPhos - the coordinates of the first phosphate
OPTIONAL ARGUMENTS:
direction - which direction to trace the chain: 3 implies 5'->3'
5 implies 3'->5'
defaults to 3 (5'->3')
RETURNS:
peakList - a list of potential phosphate peaks
sugarList - a list of potential C1' locations for each phosphate peak
"""
peaks = self.getPeaks(mapNum, curPhos)
#calculate the score for each peak
peakScores = []
for curPeak in peaks:
#exclude any peaks that are within an Angstom of the current phosphate position
#this will exclude the peak corresponding to the current phosphate position
if dist(curPhos, curPeak) >= 1:
#do a sugar search for the current phosphate
if direction == 3:
sugarLocs = self.findSugar(mapNum, curPhos, curPeak)
else: #direction == 5:
sugarLocs = self.findSugar(mapNum, curPeak, curPhos)
densityScore = sugarLocs[0][3] + curPeak[3]
score = ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))) + (SECOND_PHOS_DENSITY_WEIGHT * ln(densityScore))
peakScores.append((curPeak, score, sugarLocs))
#sort the peaks according to score
peakScores.sort(key = lambda x: x[1], reverse = 1)
#return only the coordinates, not the scores
peakList = [x[0] for x in peakScores]
sugarList = [x[2] for x in peakScores]
return (peakList, sugarList)
def firstPhos(self, mapNum, curPos):
"""find the first phosphate in a chain
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
curPos - where to start the search (i.e. the current screen center coordinates)
RETURNS:
peaks - a list of potential phosphate peaks
"""
peaks = self.getPeaks(mapNum, curPos)
#sort the peaks based on how close they are to curPos
peaks.sort(key=lambda x: dist(curPos, x))
return peaks
def firstPhos(self, mapNum, curPos):
"""find the first phosphate in a chain
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
curPos - where to start the search (i.e. the current screen center coordinates)
RETURNS:
peaks - a list of potential phosphate peaks
"""
peaks = self.getPeaks(mapNum, curPos)
#sort the peaks based on how close they are to curPos
peaks.sort(key=lambda x: dist(curPos, x))
return peaks
def startingSugarDist(self):
"""Calculate the sugar-sugar distance for the starting suite of this nucleotide
ARGUMENTS:
None
RETURNS:
the distance from the sugar atom (i.e. C1') of the previous nucleotide to the sugar atom (C1') of this nucleotide
None if there is no previous nucleotide
NOTE:
Behavior of this function is undefined if this nucleotide is not part of a chain.
(Currently, it returns None.)
"""
if self.connectedToPrev() and self.hasAtom(SUGARATOM) and self.prevNuc().hasAtom(SUGARATOM):
return dist(self.atoms[SUGARATOM], self.prevNuc().atoms[SUGARATOM])
else:
return None
def phosDist(self):
"""Calculate the phosphate-phosphate distance
ARGUMENTS:
None
RETURNS:
The distance from the phosphate of this nucleotide to the phosphate of the next nucleotide
None if no next phosphate if present
NOTE:
Behavior of this function is undefined if this nucleotide is not part of a chain.
(Currently, it raises an error.)
"""
if self.connectedToNext() and self.hasAtom("P") and self.nextNuc().hasAtom("P"):
return dist(self.atoms["P"], self.nextNuc().atoms["P"])
else:
return None
def startingSugarDist(self):
"""Calculate the sugar-sugar distance for the starting suite of this nucleotide
ARGUMENTS:
None
RETURNS:
the distance from the sugar atom (i.e. C1') of the previous nucleotide to the sugar atom (C1') of this nucleotide
None if there is no previous nucleotide
NOTE:
Behavior of this function is undefined if this nucleotide is not part of a chain.
(Currently, it returns None.)
"""
if self.connectedToPrev() and self.hasAtom(SUGARATOM) and self.prevNuc().hasAtom(SUGARATOM):
return dist(self.atoms[SUGARATOM], self.prevNuc().atoms[SUGARATOM])
else:
return None
def phosDist(self):
"""Calculate the phosphate-phosphate distance
ARGUMENTS:
None
RETURNS:
The distance from the phosphate of this nucleotide to the phosphate of the next nucleotide
None if no next phosphate if present
NOTE:
Behavior of this function is undefined if this nucleotide is not part of a chain.
(Currently, it raises an error.)
"""
if self.connectedToNext() and self.hasAtom("P") and self.nextNuc().hasAtom("P"):
return dist(self.atoms["P"], self.nextNuc().atoms["P"])
else:
return None
def findSugar(self, mapNum, phos5, phos3):
"""find potential C1' locations between the given 5' and 3' phosphate coordinates
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
phos5 - the coordinates of the 5' phosphate
phos3 - the coordinates of the 3' phosphate
RETURNS:
sugarMaxima - a list of potential C1' locations, each listed as [x, y, z, score]
"""
#calculate the distance between the two phosphatse
phosPhosDist = dist(phos5, phos3)
#calculate a potential spot for the sugar based on the phosphate-phosphate distance
#projDist is how far along the 3'P-5'P vector the sugar center should be (measured from the 3'P)
#perpDist is how far off from the 3'P-5'P vector the sugar center should be
#these functions are for the sugar center, which is what we try to find here
#since it will be more in the center of the density blob
perpDist = -0.185842*phosPhosDist**2 + 1.62296*phosPhosDist - 0.124146
projDist = 0.440092*phosPhosDist + 0.909732
#if we wanted to find the C1' instead of the sugar center, we'd use these functions
#however, finding the C1' directly causes our density scores to be less accurate
#so we instead use the functions above to find the sugar center and later adjust our
#coordinates to get the C1' location
#perpDist = -0.124615*phosPhosDist**2 + 0.955624*phosPhosDist + 2.772573
#projDist = 0.466938*phosPhosDist + 0.649833
#calculate the normal to the plane defined by 3'P, 5'P, and a dummy point
normal = crossProd([10,0,0], minus(phos3, phos5))
#make sure the magnitude of the normal is not zero (or almost zero)
#if it is zero, that means that our dummy point was co-linear with the 3'P-5'P vector
#and we haven't calculated a normal
#if the magnitude is almost zero, then the dummy point was almost co-linear and we have to worry about rounding error
#in either of those cases, just use a different dummy point
#they should both be incredibly rare cases, but it doesn't hurt to be safe
if magnitude(normal) < 0.001:
#print "Recalculating normal"
normal = crossProd([0,10,0], minus(phos5, phos3))
#scale the normal to the length of perpDist
perpVector = scalarProd(normal, perpDist/magnitude(normal))
#calculate the 3'P-5'P vector and scale it to the length of projDist
projVector = minus(phos3, phos5)
projVector = scalarProd(projVector, projDist/magnitude(projVector))
#calculate a possible sugar location
sugarLoc = plus(phos5, projVector)
sugarLoc = plus(sugarLoc, perpVector)
#rotate the potential sugar location around the 3'P-5'P vector to generate a list of potential sugar locations
sugarRotationPoints = self.__rotateSugarCenter(phos5, phos3, sugarLoc)
#test each potential sugar locations to find the one with the best electron density
for curSugarLocFull in sugarRotationPoints:
curSugarLoc = curSugarLocFull[0:3] #the rotation angle is stored as curSugarLocFull[4], so we trim that off for curSugarLoc
curDensityTotal = 0
#densityList = [] #if desired, this could be used to generate additional statistics on the density (such as the median or quartiles)
#check density along the 5'P-sugar vector
phosSugarVector = minus(curSugarLoc, phos5)
phosSugarVector = scalarProd(phosSugarVector, 1.0/(DENSITY_CHECK_POINTS+1))
for i in range(1, DENSITY_CHECK_POINTS+1):
(x, y, z) = plus(phos5, scalarProd(i, phosSugarVector))
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
#densityList.append(curPointDensity)
#check at the sugar center
(x, y, z) = curSugarLoc
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
#densityList.append(curPointDensity)
#check along the sugar-3'P vector
sugarPhosVector = minus(phos3, curSugarLoc)
sugarPhosVector = scalarProd(sugarPhosVector, 1.0/(DENSITY_CHECK_POINTS+1))
for i in range(1, DENSITY_CHECK_POINTS+1):
(x, y, z) = plus(curSugarLoc, scalarProd(i, sugarPhosVector))
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
#densityList.append(curPointDensity)
curSugarLocFull.append(curDensityTotal)
#curSugarLocFull.extend([curDensityTotal, median(densityList), lowerQuartile(densityList), min(densityList)])#, pointList])
#find all the local maxima
sugarMaxima = []
curPeakHeight = sugarRotationPoints[-1][4]
nextPeakHeight = sugarRotationPoints[0][4]
sugarRotationPoints.append(sugarRotationPoints[0]) #copy the first point to the end so that we can properly check the last point
for i in range(0, len(sugarRotationPoints)-1):
prevPeakHeight = curPeakHeight
curPeakHeight = nextPeakHeight
nextPeakHeight = sugarRotationPoints[i+1][4]
if prevPeakHeight < curPeakHeight and curPeakHeight >= nextPeakHeight:
sugarMaxima.append(sugarRotationPoints[i])
#sort the local maxima by their density score
sugarMaxima.sort(key = lambda x: x[4], reverse = True)
#adjust all the sugar center coordinates so that they represent the corresponding C1' coordinates
for i in range(0, len(sugarMaxima)):
curSugar = sugarMaxima[i][0:3]
#rotate a vector 148 degrees from the phosphate bisector
phosAngle = angle(phos5, curSugar, phos3)
phos5vector = minus(phos5, curSugar)
axis = crossProd(minus(phos3, curSugar), phos5vector)
axis = scalarProd(axis, 1/magnitude(axis))
c1vec = rotate(phos5vector, axis, 148.539123-phosAngle/2)
#scale the vector to the appropriate length
c1vec = scalarProd(c1vec, 1.235367/magnitude(c1vec))
#rotate the vector about the phosphate bisector
phosBisectorAxis = rotate(phos5vector, axis, -phosAngle/2)
phosBisectorAxis = scalarProd(phosBisectorAxis, 1/magnitude(phosBisectorAxis))
c1vec = rotate(c1vec, phosBisectorAxis, -71.409162)
sugarMaxima[i][0:3] = plus(c1vec, curSugar)
return sugarMaxima
def nextPhos(self, mapNum, curPhos, prevPhos, prevSugar, direction = 3):
"""Find the next phosphate in a chain using phosphate distance and angle data
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
curPhos - the coordinates of the current phosphate
prevPhos - the coordinates of the previous phosphate
prevSugar - the coordinates of the previous C1' atom
OPTIONAL ARGUMENTS:
direction - which direction to trace the chain: 3 implies 5'->3'
5 implies 3'->5'
defaults to 3 (5'->3')
RETURNS:
peakList - a list of potential phosphate peaks
sugarList - a list of potential C1' locations for each phosphate peak
"""
peaks = self.getPeaks(mapNum, curPhos)
#calculate the score for each peak
peakScores = []
for curPeak in peaks:
#exclude any peaks that are within an Angstom of the current phosphate position
#this will exclude the peak corresponding to the current phosphate position
if dist(curPhos, curPeak) >= 1:
#do a sugar search for the current phosphate
if direction == 3:
sugarLocs = self.findSugar(mapNum, curPhos, curPeak)
else:
sugarLocs = self.findSugar(mapNum, curPeak, curPhos)
densityScore = sugarLocs[0][3] + curPeak[3]
score = ((PHOS_DIST_WEIGHT * ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))))
+ ln(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak)))
+ ln(self.__sugarPhosSugarAngleInterp.interp(angle(prevSugar, curPhos, sugarLocs[0][0:3])))
+ (DENSITY_WEIGHT * ln(densityScore))
)
peakScores.append((curPeak, score, sugarLocs))
#FOR DEBUGGING OUTPUT
#peakScores.append((curPeak, score, sugarLocs, ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))), ln(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak))), ln(self.__sugarPhosSugarAngleInterp.interp(angle(prevSugar, prevPhos, sugarLocs[0][0:3]))), sugarLocs[0][3], sugarLocs[0][4], sugarLocs[0][5], sugarLocs[0][6], curPeak[3], sugarLocs[0][7]))
#peakScores.append((curPeak, score, sugarLocs, ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))), ln(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak))), ln(self.__sugarPhosSugarAngleInterp.interp(angle(prevSugar, curPhos, sugarLocs[0][0:3]))), ln(densityScore), DENSITY_WEIGHT * ln(densityScore), sugarLocs[0][3], curPeak[3]))
#print "Score for peak %(curPeak)s is %(score)f" % vars()
#print "\tDist: " + str(dist(curPhos, curPeak)) + "\t" + str(self.__phosDistInterp.interp(dist(curPhos, curPeak)))
#print "\tAngle: " + str(angle(prevPhos, curPhos, curPeak)) + "\t" + str(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak)))
#sort the peaks according to score
peakScores.sort(key = lambda x: x[1], reverse = 1)
#return only the coordinates, not the scores
peakList = [x[0] for x in peakScores]
sugarList = [x[2] for x in peakScores]
#FOR DEBUGGING OUTPUT
#print "Current scores:"
#print "overall\t\tphosDist\tphosAngle\tsPsAngle\tdensity score\tw. den score\tsugar score\tphos score"
#for x in peakScores:
# #print "SCORE: %f\tSUGAR SCORE: %f" % (x[1], x[2][0][3])
# print "\t".join(map(str, (x[1],) + x[3:]))
return (peakList, sugarList)
def findSugar(self, mapNum, phos5, phos3):
"""find potential C1' locations between the given 5' and 3' phosphate coordinates
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
phos5 - the coordinates of the 5' phosphate
phos3 - the coordinates of the 3' phosphate
RETURNS:
sugarMaxima - a list of potential C1' locations, each listed as [x, y, z, score]
"""
#calculate the distance between the two phosphatse
phosPhosDist = dist(phos5, phos3)
#calculate a potential spot for the sugar based on the phosphate-phosphate distance
#projDist is how far along the 3'P-5'P vector the sugar center should be (measured from the 3'P)
#perpDist is how far off from the 3'P-5'P vector the sugar center should be
#these functions are for the sugar center, which is what we try to find here
#since it will be more in the center of the density blob
perpDist = -0.185842*phosPhosDist**2 + 1.62296*phosPhosDist - 0.124146
projDist = 0.440092*phosPhosDist + 0.909732
#if we wanted to find the C1' instead of the sugar center, we'd use these functions
#however, finding the C1' directly causes our density scores to be less accurate
#so we instead use the functions above to find the sugar center and later adjust our
#coordinates to get the C1' location
#perpDist = -0.124615*phosPhosDist**2 + 0.955624*phosPhosDist + 2.772573
#projDist = 0.466938*phosPhosDist + 0.649833
#calculate the normal to the plane defined by 3'P, 5'P, and a dummy point
normal = crossProd([10,0,0], minus(phos3, phos5))
#make sure the magnitude of the normal is not zero (or almost zero)
#if it is zero, that means that our dummy point was co-linear with the 3'P-5'P vector
#and we haven't calculated a normal
#if the magnitude is almost zero, then the dummy point was almost co-linear and we have to worry about rounding error
#in either of those cases, just use a different dummy point
#they should both be incredibly rare cases, but it doesn't hurt to be safe
if magnitude(normal) < 0.001:
#print "Recalculating normal"
normal = crossProd([0,10,0], minus(phos5, phos3))
#scale the normal to the length of perpDist
perpVector = scalarProd(normal, perpDist/magnitude(normal))
#calculate the 3'P-5'P vector and scale it to the length of projDist
projVector = minus(phos3, phos5)
projVector = scalarProd(projVector, projDist/magnitude(projVector))
#calculate a possible sugar location
sugarLoc = plus(phos5, projVector)
sugarLoc = plus(sugarLoc, perpVector)
#rotate the potential sugar location around the 3'P-5'P vector to generate a list of potential sugar locations
sugarRotationPoints = self.__rotateSugarCenter(phos5, phos3, sugarLoc)
#test each potential sugar locations to find the one with the best electron density
for curSugarLocFull in sugarRotationPoints:
curSugarLoc = curSugarLocFull[0:3] #the rotation angle is stored as curSugarLocFull[4], so we trim that off for curSugarLoc
curDensityTotal = 0
#densityList = [] #if desired, this could be used to generate additional statistics on the density (such as the median or quartiles)
#check density along the 5'P-sugar vector
phosSugarVector = minus(curSugarLoc, phos5)
phosSugarVector = scalarProd(phosSugarVector, 1.0/(DENSITY_CHECK_POINTS+1))
for i in range(1, DENSITY_CHECK_POINTS+1):
(x, y, z) = plus(phos5, scalarProd(i, phosSugarVector))
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
#densityList.append(curPointDensity)
#check at the sugar center
(x, y, z) = curSugarLoc
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
#densityList.append(curPointDensity)
#check along the sugar-3'P vector
sugarPhosVector = minus(phos3, curSugarLoc)
sugarPhosVector = scalarProd(sugarPhosVector, 1.0/(DENSITY_CHECK_POINTS+1))
for i in range(1, DENSITY_CHECK_POINTS+1):
(x, y, z) = plus(curSugarLoc, scalarProd(i, sugarPhosVector))
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
#densityList.append(curPointDensity)
curSugarLocFull.append(curDensityTotal)
#curSugarLocFull.extend([curDensityTotal, median(densityList), lowerQuartile(densityList), min(densityList)])#, pointList])
#find all the local maxima
sugarMaxima = []
curPeakHeight = sugarRotationPoints[-1][4]
nextPeakHeight = sugarRotationPoints[0][4]
sugarRotationPoints.append(sugarRotationPoints[0]) #copy the first point to the end so that we can properly check the last point
for i in range(0, len(sugarRotationPoints)-1):
prevPeakHeight = curPeakHeight
curPeakHeight = nextPeakHeight
nextPeakHeight = sugarRotationPoints[i+1][4]
if prevPeakHeight < curPeakHeight and curPeakHeight >= nextPeakHeight:
sugarMaxima.append(sugarRotationPoints[i])
#sort the local maxima by their density score
sugarMaxima.sort(key = lambda x: x[4], reverse = True)
#adjust all the sugar center coordinates so that they represent the corresponding C1' coordinates
for i in range(0, len(sugarMaxima)):
curSugar = sugarMaxima[i][0:3]
#rotate a vector 148 degrees from the phosphate bisector
phosAngle = angle(phos5, curSugar, phos3)
phos5vector = minus(phos5, curSugar)
axis = crossProd(minus(phos3, curSugar), phos5vector)
axis = scalarProd(axis, 1/magnitude(axis))
c1vec = rotate(phos5vector, axis, 148.539123-phosAngle/2)
#scale the vector to the appropriate length
c1vec = scalarProd(c1vec, 1.235367/magnitude(c1vec))
#rotate the vector about the phosphate bisector
phosBisectorAxis = rotate(phos5vector, axis, -phosAngle/2)
phosBisectorAxis = scalarProd(phosBisectorAxis, 1/magnitude(phosBisectorAxis))
c1vec = rotate(c1vec, phosBisectorAxis, -71.409162)
sugarMaxima[i][0:3] = plus(c1vec, curSugar)
return sugarMaxima
def nextPhos(self, mapNum, curPhos, prevPhos, prevSugar, direction = 3):
"""Find the next phosphate in a chain using phosphate distance and angle data
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
curPhos - the coordinates of the current phosphate
prevPhos - the coordinates of the previous phosphate
prevSugar - the coordinates of the previous C1' atom
OPTIONAL ARGUMENTS:
direction - which direction to trace the chain: 3 implies 5'->3'
5 implies 3'->5'
defaults to 3 (5'->3')
RETURNS:
peakList - a list of potential phosphate peaks
sugarList - a list of potential C1' locations for each phosphate peak
"""
peaks = self.getPeaks(mapNum, curPhos)
#calculate the score for each peak
peakScores = []
for curPeak in peaks:
#exclude any peaks that are within an Angstom of the current phosphate position
#this will exclude the peak corresponding to the current phosphate position
if dist(curPhos, curPeak) >= 1:
#do a sugar search for the current phosphate
if direction == 3:
sugarLocs = self.findSugar(mapNum, curPhos, curPeak)
else:
sugarLocs = self.findSugar(mapNum, curPeak, curPhos)
densityScore = sugarLocs[0][3] + curPeak[3]
score = ((PHOS_DIST_WEIGHT * ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))))
+ ln(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak)))
+ ln(self.__sugarPhosSugarAngleInterp.interp(angle(prevSugar, curPhos, sugarLocs[0][0:3])))
+ (DENSITY_WEIGHT * ln(densityScore))
)
peakScores.append((curPeak, score, sugarLocs))
#FOR DEBUGGING OUTPUT
#peakScores.append((curPeak, score, sugarLocs, ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))), ln(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak))), ln(self.__sugarPhosSugarAngleInterp.interp(angle(prevSugar, prevPhos, sugarLocs[0][0:3]))), sugarLocs[0][3], sugarLocs[0][4], sugarLocs[0][5], sugarLocs[0][6], curPeak[3], sugarLocs[0][7]))
#peakScores.append((curPeak, score, sugarLocs, ln(self.__phosDistInterp.interp(dist(curPhos, curPeak))), ln(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak))), ln(self.__sugarPhosSugarAngleInterp.interp(angle(prevSugar, curPhos, sugarLocs[0][0:3]))), ln(densityScore), DENSITY_WEIGHT * ln(densityScore), sugarLocs[0][3], curPeak[3]))
#print "Score for peak %(curPeak)s is %(score)f" % vars()
#print "\tDist: " + str(dist(curPhos, curPeak)) + "\t" + str(self.__phosDistInterp.interp(dist(curPhos, curPeak)))
#print "\tAngle: " + str(angle(prevPhos, curPhos, curPeak)) + "\t" + str(self.__phosAngleInterp.interp(angle(prevPhos, curPhos, curPeak)))
#sort the peaks according to score
peakScores.sort(key = lambda x: x[1], reverse = 1)
#return only the coordinates, not the scores
peakList = [x[0] for x in peakScores]
sugarList = [x[2] for x in peakScores]
#FOR DEBUGGING OUTPUT
#print "Current scores:"
#print "overall\t\tphosDist\tphosAngle\tsPsAngle\tdensity score\tw. den score\tsugar score\tphos score"
#for x in peakScores:
# #print "SCORE: %f\tSUGAR SCORE: %f" % (x[1], x[2][0][3])
# print "\t".join(map(str, (x[1],) + x[3:]))
return (peakList, sugarList)
