def getPeaks(self, mapNum, pos, radius=RADIUS):
"""Get a list of peaks in the map near a given position
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
pos - the coordinates to search near
OPTIONAL ARGUMENTS:
radius - how far from pos should we look for peaks?
defaults to RADIUS (defined at the top of this file)
RETURNS:
closePeaks - a list of peaks in the format [x, y, z, density]
"""
(x, y, z) = pos
#determine if we've already done a peak search for this map
if not mapNum in self.__peakList:
peakList = []
peakHash = dict()
#go through all sigma levels and do a peak search
curSigma = GET_PEAKS_STARTING_SIGMA
while curSigma >= GET_PEAKS_ENDING_SIGMA:
#do a peak search at the current sigma level
curPeaks = map_peaks_py(mapNum, curSigma)
#go through each peak we found and make sure we hadn't found it already
for peak in curPeaks:
#check peakHash for this peak
try:
peakHash[peak[0]][peak[1]][peak[2]]
except KeyError:
#if it's not there, add it to peakList and peakHash
peakList.append(peak)
if not(peakHash.has_key(peak[0])):
peakHash[peak[0]] = dict()
if not(peakHash[peak[0]].has_key(peak[1])):
peakHash[peak[0]][peak[1]] = dict()
if not(peakHash[peak[0]][peak[1]].has_key(peak[2])):
peakHash[peak[0]][peak[1]][peak[2]] = True
curSigma -= GET_PEAKS_SIGMA_STEP
#once we've found all the peaks in this map, store them
self.__peakList[mapNum] = peakList
closePeaks = map_peaks_near_point_from_list_py(mapNum, self.__peakList[mapNum], x, y, z, radius)
for curPeak in closePeaks:
(x, y, z) = curPeak
density = density_at_point(mapNum, x, y, z)
curPeak.append(density)
return closePeaks
def getPeaks(self, mapNum, pos, radius=RADIUS):
"""Get a list of peaks in the map near a given position
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
pos - the coordinates to search near
OPTIONAL ARGUMENTS:
radius - how far from pos should we look for peaks?
defaults to RADIUS (defined at the top of this file)
RETURNS:
closePeaks - a list of peaks in the format [x, y, z, density]
"""
(x, y, z) = pos
#determine if we've already done a peak search for this map
if not mapNum in self.__peakList:
peakList = []
peakHash = dict()
#go through all sigma levels and do a peak search
curSigma = GET_PEAKS_STARTING_SIGMA
while curSigma >= GET_PEAKS_ENDING_SIGMA:
#do a peak search at the current sigma level
curPeaks = map_peaks_py(mapNum, curSigma)
#go through each peak we found and make sure we hadn't found it already
for peak in curPeaks:
#check peakHash for this peak
try:
peakHash[peak[0]][peak[1]][peak[2]]
except KeyError:
#if it's not there, add it to peakList and peakHash
peakList.append(peak)
if not(peakHash.has_key(peak[0])):
peakHash[peak[0]] = dict()
if not(peakHash[peak[0]].has_key(peak[1])):
peakHash[peak[0]][peak[1]] = dict()
if not(peakHash[peak[0]][peak[1]].has_key(peak[2])):
peakHash[peak[0]][peak[1]][peak[2]] = True
curSigma -= GET_PEAKS_SIGMA_STEP
#once we've found all the peaks in this map, store them
self.__peakList[mapNum] = peakList
closePeaks = map_peaks_near_point_from_list_py(mapNum, self.__peakList[mapNum], x, y, z, radius)
for curPeak in closePeaks:
(x, y, z) = curPeak
density = density_at_point(mapNum, x, y, z)
curPeak.append(density)
return closePeaks
def findBase(self, mapNum, sugar, phos5, phos3, baseType, direction = 3):
"""Rotate the sugar center by 360 degrees in ROTATE_SUGAR_INTERVAL increments
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
sugar - the coordinates of the C1' atom
phos5 - the coordinates of the 5' phosphate
phos3 - the coordinates of the 3' phosphate
baseType - the base type (A, C, G, or U)
OPTIONAL ARGUMENTS:
direction - which direction are we tracing the chain
if it is 5 (i.e. 3'->5'), then phos5 and phos3 will be flipped
all other values will be ignored
defaults to 3 (i.e. 5'->3')
RETURNS:
baseObj - a list of [baseType, baseCoordinates]
"""
if direction == 5:
(phos5, phos3) = (phos3, phos5)
#calculate the bisector of the phos-sugar-phos angle
#first, calculate a normal to the phos-sugar-phos plane
sugarPhos5Vec = minus(phos5, sugar)
sugarPhos3Vec = minus(phos3, sugar)
normal = crossProd(sugarPhos5Vec, sugarPhos3Vec)
normal = scalarProd(normal, 1.0/magnitude(normal))
phosSugarPhosAngle = angle(phos5, sugar, phos3)
bisector = rotate(sugarPhos5Vec, normal, phosSugarPhosAngle/2.0)
#flip the bisector around (so it points away from the phosphates) and scale its length to 5 A
startingBasePos = scalarProd(bisector, -1/magnitude(bisector))
#rotate the base baton by 10 degree increments about half of a sphere
rotations = [startingBasePos] #a list of coordinates for all of the rotations
for curTheta in range(-90, -1, 10) + range(10, 91, 10):
curRotation = rotate(startingBasePos, normal, curTheta)
rotations.append(curRotation) #here's where the phi=0 rotation is accounted for
for curPhi in range(-90, -1, 10) + range(10, 91, 10):
rotations.append(rotate(curRotation, startingBasePos, curPhi))
#test electron density along all base batons
for curBaton in rotations:
curDensityTotal = 0
densityList = []
for i in range(1, 9):
(x, y, z) = plus(sugar, scalarProd(i/2.0, curBaton))
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
densityList.append(curPointDensity)
curBaton.append(curDensityTotal) #the sum of the density (equivalent to the mean for ordering purposes)
curBaton.append(median(densityList)) #the median of the density
curBaton.append(min(densityList)) #the minimum of the density
#find the baton with the max density (as measured using the median)
#Note that we ignore the sum and minimum of the density. Those calculations could be commented out,
# but they may be useful at some point in the future. When we look at higher resolutions maybe?
# Besides, they're fast calculations.)
baseDir = max(rotations, key = lambda x: x[4])
#rotate the stock base+sugar structure to align with the base baton
rotationAngle = angle(self.__baseStrucs["C"]["C4"], [0,0,0], baseDir)
axis = crossProd(self.__baseStrucs["C"]["C4"], baseDir[0:3])
orientedBase = rotateAtoms(self.__baseStrucs["C"], axis, rotationAngle)
#rotate the base about chi to find the best fit to density
bestFitBase = None
maxDensity = -999999
for curAngle in range(0,360,5):
rotatedBase = rotateAtoms(orientedBase, orientedBase["C4"], curAngle, sugar)
curDensity = 0
for curAtom in ["N1", "C2", "N3", "C4", "C5", "C6"]:
curDensity += density_at_point(mapNum, rotatedBase[curAtom][0], rotatedBase[curAtom][1], rotatedBase[curAtom][2])
#this is "pseudoChi" because it uses the 5' phosphate in place of the O4' atom
pseudoChi = torsion(phos5, sugar, rotatedBase["N1"], rotatedBase["N3"])
curDensity *= self.__pseudoChiInterp.interp(pseudoChi)
if curDensity > maxDensity:
maxDensity = curDensity
bestFitBase = rotatedBase
baseObj = ["C", bestFitBase]
#mutate the base to the appropriate type
if baseType != "C":
baseObj = self.mutateBase(baseObj, baseType)
return baseObj
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 findBase(self, mapNum, sugar, phos5, phos3, baseType, direction = 3):
"""Rotate the sugar center by 360 degrees in ROTATE_SUGAR_INTERVAL increments
ARGUMENTS:
mapNum - the molecule number of the Coot map to use
sugar - the coordinates of the C1' atom
phos5 - the coordinates of the 5' phosphate
phos3 - the coordinates of the 3' phosphate
baseType - the base type (A, C, G, or U)
OPTIONAL ARGUMENTS:
direction - which direction are we tracing the chain
if it is 5 (i.e. 3'->5'), then phos5 and phos3 will be flipped
all other values will be ignored
defaults to 3 (i.e. 5'->3')
RETURNS:
baseObj - a list of [baseType, baseCoordinates]
"""
if direction == 5:
(phos5, phos3) = (phos3, phos5)
#calculate the bisector of the phos-sugar-phos angle
#first, calculate a normal to the phos-sugar-phos plane
sugarPhos5Vec = minus(phos5, sugar)
sugarPhos3Vec = minus(phos3, sugar)
normal = crossProd(sugarPhos5Vec, sugarPhos3Vec)
normal = scalarProd(normal, 1.0/magnitude(normal))
phosSugarPhosAngle = angle(phos5, sugar, phos3)
bisector = rotate(sugarPhos5Vec, normal, phosSugarPhosAngle/2.0)
#flip the bisector around (so it points away from the phosphates) and scale its length to 5 A
startingBasePos = scalarProd(bisector, -1/magnitude(bisector))
#rotate the base baton by 10 degree increments about half of a sphere
rotations = [startingBasePos] #a list of coordinates for all of the rotations
for curTheta in range(-90, -1, 10) + range(10, 91, 10):
curRotation = rotate(startingBasePos, normal, curTheta)
rotations.append(curRotation) #here's where the phi=0 rotation is accounted for
for curPhi in range(-90, -1, 10) + range(10, 91, 10):
rotations.append(rotate(curRotation, startingBasePos, curPhi))
#test electron density along all base batons
for curBaton in rotations:
curDensityTotal = 0
densityList = []
for i in range(1, 9):
(x, y, z) = plus(sugar, scalarProd(i/2.0, curBaton))
curPointDensity = density_at_point(mapNum, x, y, z)
curDensityTotal += curPointDensity
densityList.append(curPointDensity)
curBaton.append(curDensityTotal) #the sum of the density (equivalent to the mean for ordering purposes)
curBaton.append(median(densityList)) #the median of the density
curBaton.append(min(densityList)) #the minimum of the density
#find the baton with the max density (as measured using the median)
#Note that we ignore the sum and minimum of the density. Those calculations could be commented out,
# but they may be useful at some point in the future. When we look at higher resolutions maybe?
# Besides, they're fast calculations.)
baseDir = max(rotations, key = lambda x: x[4])
#rotate the stock base+sugar structure to align with the base baton
rotationAngle = angle(self.__baseStrucs["C"]["C4"], [0,0,0], baseDir)
axis = crossProd(self.__baseStrucs["C"]["C4"], baseDir[0:3])
orientedBase = rotateAtoms(self.__baseStrucs["C"], axis, rotationAngle)
#rotate the base about chi to find the best fit to density
bestFitBase = None
maxDensity = -999999
for curAngle in range(0,360,5):
rotatedBase = rotateAtoms(orientedBase, orientedBase["C4"], curAngle, sugar)
curDensity = 0
for curAtom in ["N1", "C2", "N3", "C4", "C5", "C6"]:
curDensity += density_at_point(mapNum, rotatedBase[curAtom][0], rotatedBase[curAtom][1], rotatedBase[curAtom][2])
#this is "pseudoChi" because it uses the 5' phosphate in place of the O4' atom
pseudoChi = torsion(phos5, sugar, rotatedBase["N1"], rotatedBase["N3"])
curDensity *= self.__pseudoChiInterp.interp(pseudoChi)
if curDensity > maxDensity:
maxDensity = curDensity
bestFitBase = rotatedBase
baseObj = ["C", bestFitBase]
#mutate the base to the appropriate type
if baseType != "C":
baseObj = self.mutateBase(baseObj, baseType)
return baseObj
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