def findCoilPoints(self, s0, s1, s2, displacement_s2_m2,
displacement_m2_m1,
displacement_m1_m0,
alpha_s0_s1_s2_m2,
beta_s1_s2_m2,
alpha_s1_s2_m2_m1,
beta_s2_m2_m1,
alpha_s2_m2_m1_m0,
beta_m2_m1_m0):
# function identifies the positions of the ends of a free coil in terms of the
# end point it is connecting to and certain bond information.
# Our objective is to define m2, m1 and m0 in terms of this information.
# the names s0, s1, s2 and m2, m1, m0 are defined in the building block function
# for connecting two blocks together.
# m2 atom in terms of s0, s1 and s2
TNB1 = coords.constructTNBFrame(s0, s1, s2)
m2 = s2 + displacement_s2_m2 * coords.generateTNBVecXYZ(TNB1, beta_s1_s2_m2, alpha_s0_s1_s2_m2)
# m1 atom in terms of s1, s2 and m2
TNB2 = coords.constructTNBFrame(s1, s2, m2)
m1 = m2 + displacement_m2_m1 * coords.generateTNBVecXYZ(TNB2, beta_s2_m2_m1, alpha_s1_s2_m2_m1)
# m0 atom in terms of s2, m2 and m1
TNB3 = coords.constructTNBFrame(s2, m2, m1)
m0 = m1 + displacement_m1_m0 * coords.generateTNBVecXYZ(TNB3, beta_m2_m1_m0, alpha_s2_m2_m1_m0)
return [m0, m1, m2]
def findLastTwoPoints(self, startPoints, endPoints, pointsToAvoid):
TNB = coords.constructTNBFrame(startPoints[-2],
startPoints[-1],
endPoints[-1])
# see page 173 in book 2
l = np.linalg.norm(startPoints[-1] - endPoints[-1])
tComponent = np.abs(l-self.bondLength)/2.0
bComponent = np.sqrt(self.bondLength**2 - tComponent**2)
if l>self.bondLength:
newPoint1 = startPoints[-1] - tComponent* TNB[0] - bComponent * TNB[2]
else:
newPoint1 = startPoints[-1] + tComponent* TNB[0] - bComponent * TNB[2]
newPoint2 = newPoint1 + self.bondLength * TNB[0]
# whizz check point 1 as if newPoint2 was at the end of endPoints
newPoint1, inBounds1 = self.whizzCheck(startPoints, endPoints + [newPoint2], pointsToAvoid, newPoint1)
if inBounds1:
# Now whizz check point 2 as if the new newPoint1 was at the end of startPoints.
newPoint2, inBounds2 = self.whizzCheck(startPoints + [newPoint1], endPoints, pointsToAvoid, newPoint2)
listsAreGood = False
if inBounds1 and inBounds2: # only return true if both the new points are golden.
listsAreGood = True
return newPoint1, newPoint2, listsAreGood
def constructLoop(self, BB1, BB2, loopGen, pointsToAvoid):
connectorA = BB1.getConnectionAtoms(
1) # 1 is the C terminus of interest
connectorB = BB2.getConnectionAtoms(
0) # 0 is the N terminus of interest
# generate TNB frames at either connector
TNBA = coords.constructTNBFrame(connectorA[0], connectorA[1],
connectorA[2])
TNBB = coords.constructTNBFrame(connectorB[0], connectorB[1],
connectorB[2])
# C terminus is CCN triad (new atom will be an N).
betaA = self.angleC
alphaA = self.phi
# N Terminus is CNC triad. (new atom will be a C).
betaB = self.angleN
alphaB = self.psi
# compute the coil start and end points
pointA = connectorA[2] + self.CNbondLength * coords.generateTNBVecXYZ(
TNBA, betaA, alphaA)
pointB = connectorB[2] + self.CNbondLength * coords.generateTNBVecXYZ(
TNBB, betaB, alphaB)
if self.dumpInterimFiles:
fIO.saveXYZList([pointA, connectorA[2], pointB, connectorB[2]],
['Ca', 'S', 'O', 'S'], 'connectionDetails.xyz')
fIO.saveXYZ(pointsToAvoid, 'K', 'pointsToAvoid.xyz')
numCrankMoves = 0
if self.parallel:
iSphereR = 0.4 * self.strandLength * 3.5
else:
iSphereR = 0.9 * self.betaStrandSeparation / 2.0
# create the loop building Blockss
return loopGen.generateBuildingBlock(
self.numLoopResidues,
pointA,
pointB,
self.minDist,
numCrankMoves,
pointsToAvoid=pointsToAvoid,
envelopeList=["innersphere " + str(iSphereR)])
def residueToAtoms(self, S0, S1, S2, S3, alpha0, b1, beta1, b2, beta2, b3, beta3):
# Positioning M0 correctly in the S0, S1, S2 TNB frame
# allows for alpha0, b1 and beta1 to be set correctly.
TNB_S0_S1_S2 = coords.constructTNBFrame(S0, S1, S2)
M0 = S2 + b1 * coords.generateTNBVecXYZ(TNB_S0_S1_S2, beta1, alpha0)
TNB_S1_S2_M0 = coords.constructTNBFrame(S1, S2, M0)
# Can position M1 such that b2, and beta2 are correct, but that leaves b3 and beta3 and only one
# parameter - alpha2 - which is dihedral about s2 to m0 axis. So find the alpha which
# minimises the difference between b3 and linalg.norm(M1 - S3).
results = minimize(coords.computeDistBetweenM1AndS3, [-60 *np.pi/180], (TNB_S1_S2_M0, beta2, S3, b3))
alpha2 = results['x']
# compute position of M1 with b2, beta2 and alpha2. We don't care what the last angle is.
M1 = M0 + b2 * coords.generateTNBVecXYZ(TNB_S1_S2_M0, beta2, alpha2)
return M0, M1
def generateResidue(self, prevRes):
# given a list of 3 xyz positions for the previous residue
# construct the next set of three positions with appropriate bond angles
# and dihedral angles.
# construct the first TNB from the previous residue
TNB1 = coords.constructTNBFrame(prevRes[0], prevRes[1], prevRes[2])
NPos = prevRes[2] + self.CNbondLength * coords.generateTNBVecXYZ(
TNB1, self.angleC, self.phi)
TNB2 = coords.constructTNBFrame(prevRes[-2], prevRes[-1], NPos)
CAPos = NPos + self.CNbondLength * coords.generateTNBVecXYZ(
TNB2, self.angleN, self.omega)
TNB3 = coords.constructTNBFrame(prevRes[-1], NPos, CAPos)
CPos = CAPos + self.CCbondLength * coords.generateTNBVecXYZ(
TNB3, self.angleCA, self.psi)
return [NPos, CAPos, CPos]
def generateGPQUnit(self, prevGPQ):
# given a list of 6 xyz positions for the previous G-PQ Unit
# construct the next G-PQ unit with appropriate bond angles
# and dihedral angles.
# construct the first G Unit from the previous G-PQ unit
TNB1 = coords.constructTNBFrame(prevGPQ[2], prevGPQ[3], prevGPQ[5])
NPosG = prevGPQ[5] + self.CNbondLength * coords.generateTNBVecXYZ(
TNB1, self.angleC, self.PGPsi)
TNB2 = coords.constructTNBFrame(prevGPQ[3], prevGPQ[5], NPosG)
dirHat = coords.generateTNBVecXYZ(TNB2, self.angleN, self.PGPhi)
if self.species == 'SP1':
FPosG = NPosG + self.GG1bondLength / 2.0 * dirHat
CPosG = FPosG + self.GG1bondLength / 2.0 * dirHat
else:
FPosG = NPosG + self.GG2bondLength / 2.0 * dirHat
CPosG = FPosG + self.GG2bondLength / 2.0 * dirHat
TNB3 = coords.constructTNBFrame(prevGPQ[5], NPosG, CPosG)
# now construct the P or Q unit
if self.species == 'SP1':
dirHat = coords.generateTNBVecXYZ(TNB3, self.angleN, self.GPPsi)
NPosP = CPosG + self.CNbondLength * dirHat
TNB4 = coords.constructTNBFrame(NPosG, CPosG, NPosP)
dirHat = coords.generateTNBVecXYZ(TNB4, self.angleN, self.GPPhi)
FPosP = NPosP + self.PPbondLength / 2.0 * dirHat
CPosP = FPosP + self.PPbondLength / 2.0 * dirHat
G_PQUnit = [NPosG, FPosG, CPosG, NPosP, FPosP, CPosP]
else:
dirHat = coords.generateTNBVecXYZ(TNB3, self.angleC, self.GQPsi)
NPosQ = CPosG + self.CNbondLength * dirHat
TNB4 = coords.constructTNBFrame(NPosG, CPosG, NPosQ)
dirHat = coords.generateTNBVecXYZ(TNB4, self.angleN, self.GQPhi)
FPosQ = NPosQ + self.QQbondLength / 2.0 * dirHat
CPosQ = FPosQ + self.QQbondLength / 2.0 * dirHat
G_PQUnit = [NPosG, FPosG, CPosG, NPosQ, FPosQ, CPosQ]
return G_PQUnit
def findLastPoint(self, startPoints, endPoints, pointsToAvoid):
# construct a TNB frame
TNB = coords.constructTNBFrame(startPoints[-2],
startPoints[-1],
endPoints[-1])
# Compute position in TB plane of last point
TComponent = np.linalg.norm(startPoints[-1] - endPoints[-1])/2
BComponent = np.sqrt(self.bondLength**2 - TComponent**2)
newPoint = startPoints[-1] + BComponent*TNB[2] + TComponent*TNB[0]
# perform a whizz Check
return self.whizzCheck(startPoints, endPoints, pointsToAvoid, newPoint)
def findLastTwoPointsFit(self, startPoints, endPoints, distanceBetweenPoints):
# This function figures out the coordinates of the last
# one or two points in a polymer chain such that they are
# bondLength distance apart. It stops worrying about bond angles.
# This is a many dimensional problem and there
# are many ways to solve it. varies all four angles simultaneously
# and calculates the resulting distance
# between the particles. THe function minimises this distance - bondLength.
# construct TNB frames
TNBA = coords.constructTNBFrame(startPoints[-3],
startPoints[-2],
startPoints[-1])
TNBB = coords.constructTNBFrame(endPoints[-3],
endPoints[-2],
endPoints[-1])
# pick bond angles at random from the acceptable range
betaA = rnd.uniform(self.beta1, self.beta2)
betaB = rnd.uniform(self.beta1, self.beta2)
alphaA = rnd.uniform(self.alpha1, self.alpha2)
alphaB = rnd.uniform(self.alpha1, self.alpha2)
# optimise the angles for the given function.
finalAngles = minimize(coords.computeDistBetweenPoints,
[alphaA, alphaB],
args=(startPoints[-1], endPoints[-1], TNBA, TNBB, betaA, betaB, self.bondLength, distanceBetweenPoints))
pointA = startPoints[-1] + self.bondLength * coords.generateTNBVecXYZ(TNBA, betaA, finalAngles['x'][0])
pointB = endPoints[-1] + self.bondLength * coords.generateTNBVecXYZ(TNBB, betaB, finalAngles['x'][1])
# true if the optimisation exited successfully (it gave a result!)
listsAreGood = finalAngles['success']
return pointA, pointB, listsAreGood
def startResidue(self):
# generates the first residue of the backbone
# set first NPos to be at origin.
NPos = np.array([0.0, 0.0, 0.0])
# Assume CAPos is along director axis from NPos - bad assumption - we'll correct it later
CAPos = NPos + self.CNbondLength * self.directorHat
# generate a third dummy vector
DummyPos = NPos + np.array([1.0, 0.0, 0.0])
# compute the final CPos for the initial residue
TNB3 = coords.constructTNBFrame(DummyPos, NPos, CAPos)
CPos = CAPos + self.CCbondLength * coords.generateTNBVecXYZ(
TNB3, self.angleCA, self.psi)
return [NPos, CAPos, CPos]
def generateSpaceCurve(self):
# generates a space curve with a specified bond angle, dihedrals and bondlength
b = self.bondLength
n = self.numPoints
# generate 3 points a distance b apart one of which is pointA
s2 = self.pointA - b * self.blockDirectorHat
s1Dir = np.array([
rnd.uniform(0.0, 1.0),
rnd.uniform(0.0, 1.0),
rnd.uniform(0.0, 1.0)
])
s1 = s2 - b * s1Dir / np.linalg.norm(s1Dir)
spaceCurve = [s1, s2, self.pointA]
# have first point so add a further n-1 points
for _ in range(n - 1):
# construct TNB frame from last three points of the space curve
tnb = coords.constructTNBFrame(spaceCurve[-3], spaceCurve[-2],
spaceCurve[-1])
if self.angularRange[0] == 'None':
# compute a new direction based on beta and alpha
alpha = self.alpha
beta = self.beta
else:
# if the angular range is set then pick a random direction. (hope it's not too madly self intersecting. Got a bit chill about that later on.
# careful narrow choices of ranges can give good results without checking for intersections.
alpha = rnd.uniform(self.angularRange[0], self.angularRange[1])
beta = rnd.uniform(self.angularRange[2], self.angularRange[3])
dirn = coords.generateTNBVecXYZ(tnb, beta, alpha)
# construct next space curve point
spaceCurve.append(spaceCurve[-1] + b * dirn / np.linalg.norm(dirn))
currentAxis = coords.axisFromHelix(spaceCurve[2:])
currentRefPoint = self.pointA
spaceCurve = coords.transformFromBlockFrameToLabFrame(
self.blockDirectorHat, self.pointA, 0.0, currentAxis,
currentRefPoint, spaceCurve[2:])
return spaceCurve
def generateSpaceCurve(self):
# generates a space curve with specified bondLength but with bond angles and dihedrals
# chosen from a range
b = self.bondLength
n = self.numPoints
# generate 3 points a distance b apart one of which is pointA
s2 = self.pointA - b * self.blockDirectorHat
s1Dir = np.array([
rnd.uniform(0.0, 1.0),
rnd.uniform(0.0, 1.0),
rnd.uniform(0.0, 1.0)
])
s1 = s2 - b * s1Dir / np.linalg.norm(s1Dir)
spaceCurve = [s1, s2, self.pointA]
# have first point so add a further n-1 points
for _ in range(n - 1):
# construct TNB frame from last three points of the space curve
tnb = coords.constructTNBFrame(spaceCurve[-3], spaceCurve[-2],
spaceCurve[-1])
beta = rnd.uniform(self.beta1, self.beta2)
alpha = rnd.uniform(self.alpha1, self.alpha2)
# compute a new direction based on beta and alpha
dirn = coords.generateTNBVecXYZ(tnb, beta, alpha)
# construct next space curve point
spaceCurve.append(spaceCurve[-1] + b * dirn / np.linalg.norm(dirn))
# chop the starting points off
spaceCurve = spaceCurve[2:]
if self.SpaceCurveTransform == True:
currentAxis = coords.axisFromHelix(spaceCurve)
currentRefPoint = self.pointA
spaceCurve = coords.transformFromBlockFrameToLabFrame(
self.blockDirectorHat, self.pointA, 0.0, currentAxis,
currentRefPoint, spaceCurve)
return spaceCurve
def pickRandomPointInDefinedSpace(self):
# Takes the last three points of the nList and picks a new point in XYZ which
# is inside the given angular ranges. No need to check the ranges, because the points are only selected inside those zones.
# construct the TNB vectors from the last three points of the nList.
TNB = coords.constructTNBFrame(self.nList[-3], self.nList[-2], self.nList[-1])
# compute a directional vector in XYZ coords from the last point on the list to the new point, within the given angular range constraints.
newCoordXYZRel = coords.pickRandomTNBDirectionInAngRangeXYZ(TNB,
self.beta1,
self.beta2,
self.alpha1,
self.alpha2)
# should be a unit vector already but just in case
newCoordXYZRelHat = newCoordXYZRel/np.linalg.norm(newCoordXYZRel)
# scale the vector by the bondlength and add it to the last point in the list to give new position vector
return self.nList[-1] + self.bondLength * newCoordXYZRelHat
def correctBondLengths(self, xyzVals):
# whip through the xyz vals and subtly adjust the positions of the atoms
# so they are all exactly bondlength apart.
for i, pos in enumerate(xyzVals):
if i > 0 and i < len(xyzVals) - 1:
# if the bondLengths
b1 = np.linalg.norm(pos - xyzVals[i - 1])
b2 = np.linalg.norm(pos - xyzVals[i + 1])
if (np.abs(b1 - self.bondLength) >
0.01) or (np.abs(b2 - self.bondLength) > 0.01):
tnb = coords.constructTNBFrame(pos, xyzVals[i - 1],
xyzVals[i + 1])
midPoint = (xyzVals[i - 1] + xyzVals[i + 1]) / 2
l = np.linalg.norm(xyzVals[i - 1] - xyzVals[i + 1]) / 2
r = np.sqrt(self.bondLength**2 - l**2)
xyzVals[i] = midPoint + tnb[2] * r
return xyzVals
def pickRandomPointInDefinedSpace(self, p1, p2, p3):
# Takes the given three points and picks a new point in XYZ which
# is bondLength distance from p3, but inside the given angular ranges
# as defined by the bond angle p2 - p3 - newPoint and dihedral p1-p2-p3-new point.
# No need to check againt angle ranges once point is selected because angles
# are picked inside those ranges already.
# construct the TNB vectors from the last three points of the nList.
TNB = coords.constructTNBFrame(p1, p2, p3)
# compute a directional vector in XYZ coords from the last point on the list to the new point, within the given angular range constraints.
newCoordXYZRel = coords.pickRandomTNBDirectionInAngRangeXYZ(TNB,
self.betaMin,
self.betaMax,
self.alphaMin,
self.alphaMax)
# should be a unit vector already but just in case
newCoordXYZRelHat = newCoordXYZRel/np.linalg.norm(newCoordXYZRel)
# scale the vector by the bondlength and add it to the last point in the list to give new position vector
return p3 + self.bondLength * newCoordXYZRelHat
def generateBuildingBlockXYZ(self):
# create a strand and loop generator
strandGen = PBG(self.paramFilename)
loopGen = PHG(self.paramFilename)
loopPoints = []
sphereCentrePoints = []
dummyConnector = [[2, 1, 0]]
# construct the base line for the strand start points
baseLine = [
self.startPos +
n * self.betaStrandSeparation * self.crossStrandDirectorHat
for n in range(self.numStrands)
]
# construct a prototype beta strand building Block in the defined polarity
strandA_BB = strandGen.generateBuildingBlock(self.numPoints,
self.polarity,
dummyConnector)
# assume loop length needs to be long enough to stretch a whole beta strand.
loopLength = int(np.ceil(1.5 * self.strandLength))
# In a not parallel situation construct the antiparallel strand - StrandB
# also add the offset to every other strand starting on the first or second strand depending on the polarity
# also compute the alternative strand building block
if not self.parallel:
loopLength = 2 # in a parallel situation the loop is always 2 (residues) long. I just said so.
if self.polarity == 'NC':
baseLine = [
basePoint + self.offsetXYZ if (n % 2) == 0 else basePoint
for n, basePoint in enumerate(baseLine)
]
strandB_BB = strandGen.generateBuildingBlock(
self.numPoints, 'CN', dummyConnector)
else:
baseLine = [
basePoint + self.offsetXYZ if (n % 2) == 1 else basePoint
for n, basePoint in enumerate(baseLine)
]
strandB_BB = strandGen.generateBuildingBlock(
self.numPoints, 'NC', dummyConnector)
# compute the relative vector from the end of the first chain to the next atom in the hairpin.
TNB = coords.constructTNBFrame(strandA_BB.xyzVals[-3],
strandA_BB.xyzVals[-2],
strandA_BB.xyzVals[-1])
if self.polarity == 'NC':
# if polarity is NC then the last three values are an NCC triad.
beta = self.angleC
alpha = self.phi
bondLength = self.CNbondLength
else:
# if polarity is CN then the last three values are CCN triad.
beta = self.angleN
alpha = self.psi
bondLength = self.CNbondLength
# the vector from the end of the first strand to its hairpin is defined as the positive connectorVector.
ConnectorVectorPos = bondLength * coords.generateTNBVecXYZ(
TNB, beta, alpha)
# -ve connector vector is the reciprocal of that
ConnectorVectorNeg = -1 * ConnectorVectorPos
# for parallel all CVs are always the Positive from end of strand to hairpin
# and from hairpin to end of strand
connectorVectorStrandToHairpin = ConnectorVectorPos
connectorVectorHairpinToStrand = ConnectorVectorPos
# for parallel strands are always the same set of xyz vals
curStrandXYZ = strandA_BB.xyzVals
# now the preparatory stuff is complete begin constructing the beta sheet
# copy across the first strand to get the structure going.
buildingBlockXYZ = [baseLine[0] + xyz for xyz in strandA_BB.xyzVals]
innerRadiusParallel = 0.75 * self.strandLength * 3 * bondLength / 2
outerRadiusParallel = 40 * self.strandLength * 3 * bondLength / 2
innerRadiusAntiParallel = 0.9 * self.betaStrandSeparation / 2
outerRadiusAntiParallel = 40 * self.betaStrandSeparation
print "Radii: ", innerRadiusParallel, outerRadiusParallel, innerRadiusAntiParallel, outerRadiusAntiParallel
print "Diameter: ", 2 * innerRadiusParallel, 2 * outerRadiusParallel, 2 * innerRadiusAntiParallel, 2 * outerRadiusAntiParallel
# contruct the remaining strands following this procedure
curStrand = 1
while curStrand < self.numStrands:
# if parallel, strands and connectorvectors are always the same so do nothing
# to them.
# if not parallel work out the connectorVectors for attaching hairpin between
# the previous strand and the current strand.
if not self.parallel:
if (curStrand % 2) == 0:
connectorVectorStrandToHairpin = ConnectorVectorNeg
connectorVectorHairpinToStrand = ConnectorVectorPos
curStrandXYZ = strandA_BB.xyzVals
if (curStrand % 2) == 1:
connectorVectorStrandToHairpin = ConnectorVectorPos
connectorVectorHairpinToStrand = ConnectorVectorNeg
curStrandXYZ = list(reversed(strandB_BB.xyzVals))
# loop start is end of building block + connectorvector
loopStartPoint = buildingBlockXYZ[
-1] + connectorVectorStrandToHairpin
loopPoints.append(loopStartPoint)
# compute values for new strand
newStrand = [baseLine[curStrand] + xyz for xyz in curStrandXYZ]
# loop end point is start of next strand - connector vector.
loopEndPoint = newStrand[0] - connectorVectorHairpinToStrand
loopPoints.append(loopEndPoint)
sphereCentrePoint = (loopEndPoint + loopStartPoint) / 2
sphereCentrePoints.append(sphereCentrePoint)
print "loopPointdist: ", np.linalg.norm(loopEndPoint -
loopStartPoint)
# now we have the length of the loop and the start and end points
# makes and attempt to stop the hairpin from entering
# a sphere at the mid point of the start and end points
if self.loopEnds:
if self.parallel:
loop = loopGen.generateBuildingBlock(
loopLength * 3, loopStartPoint, loopEndPoint, 0, -180,
180, beta * 180 / np.pi - 40, beta * 180 / np.pi + 40,
0.9 * bondLength, bondLength, innerRadiusParallel,
outerRadiusParallel, sphereCentrePoint, self.polarity)
else:
loop = loopGen.generateBuildingBlock(
loopLength * 3, loopStartPoint, loopEndPoint, 0, -180,
180, beta * 180 / np.pi - 40, beta * 180 / np.pi + 40,
0.9 * bondLength, bondLength, innerRadiusAntiParallel,
outerRadiusAntiParallel, sphereCentrePoint,
self.polarity)
# append the loop to the array
buildingBlockXYZ = buildingBlockXYZ + loop.xyzVals
# append each vector to the current output array
buildingBlockXYZ = buildingBlockXYZ + newStrand
#next strand
curStrand += 1
#buildingBlockXYZ = buildingBlockXYZ + loopPoints
#buildingBlockXYZ = buildingBlockXYZ + sphereCentrePoints
self.numPoints = len(buildingBlockXYZ)
return buildingBlockXYZ
def startGPQUnit(self):
# generates the first G-PQ unit of the spidroin Backbone
# A G or PQ unit has three nodes: the NPos, the FPos and the CPos.
# The NPos is the N terminal of the unit, The FPos is the force centre and the CPos is the C terminal.
# Together these three things define an ellipsoid and a central repulsive/attractive field.
if self.species == 'SP2':
# First Unit in SP2 is a P-Unit
# set up a dummy pos to sort out first dihedral
DPos = np.array([1.0, 0.0, 0.0])
# set first NPos to be at origin.
NPosP1 = np.array([0.0, 0.0, 0.0])
# Assume FPos is along director axis from NPos - bad assumption - we'll correct it later
FPosP1 = NPosP1 + self.PPbondLength / 2.0 * self.directorHat
# Make the CPos at the end of the GUnit
CPosP1 = NPosP1 + self.PPbondLength / 2.0 * self.directorHat
# set up the TNB frame to define the alpha and betas for the first part of the P to G Unit
TNB1 = coords.constructTNBFrame(DPos, NPosP1, CPosP1)
NPosG = CPosP1 + self.CNbondLength * coords.generateTNBVecXYZ(
TNB1, self.angleC, self.PGPsi)
# set up the TNB frame to define the alpha and betas for the second part of the P to G Unit
TNB2 = coords.constructTNBFrame(NPosP1, CPosP1, NPosG)
# set up FPosG and CPosG
dirHat = coords.generateTNBVecXYZ(TNB2, self.angleN, self.PGPhi)
FPosG = NPosG + self.GG2bondLength / 2.0 * dirHat
CPosG = FPosG + self.GG2bondLength / 2.0 * dirHat
# now generate NPosP2, FPosP2, CPosP2
# set up the TNB frame to define the alpha and betas for the first part of the G to P Unit
TNB3 = coords.constructTNBFrame(CPosP1, NPosG, CPosG)
NPosP2 = CPosG + self.CNbondLength * coords.generateTNBVecXYZ(
TNB3, self.angleC, self.GPPsi)
# set up the TNB frame to define the alpha and betas for the second part of the G to P Unit
TNB2 = coords.constructTNBFrame(NPosG, CPosG, NPosP2)
dirHat = coords.generateTNBVecXYZ(TNB3, self.angleN, self.GPPhi)
# Assume FPos is along director axis from NPos - bad assumption - we'll correct it later
FPosP2 = NPosP2 + self.PPbondLength / 2.0 * dirHat
# Make the CPos at the end of the GUnit
CPosP2 = NPosP1 + self.PPbondLength / 2.0 * dirHat
GPQUnit = [
NPosP1, FPosP1, CPosP1, NPosG, FPosG, CPosG, NPosP2, FPosP2,
CPosP2
]
# In SP1 we start with a G-Q, in SP2 we start with a P-G-P
if self.species == 'SP1':
# First unit in SP1 is a G-Q unit.
# set up a dummy pos to sort out first dihedral
DPos = np.array([1.0, 0.0, 0.0])
# set first NPos to be at origin.
NPosG = np.array([0.0, 0.0, 0.0])
# Assume FPos is along director axis from NPos - bad assumption - we'll correct it later
FPosG = NPosG + self.GG1bondLength / 2.0 * self.directorHat
# Make the CPos at the end of the GUnit
CPosG = FPosG + self.GG1bondLength / 2.0 * self.directorHat
# set up the TNB frame to define the alpha and betas for the first part of the G to P Unit
TNB1 = coords.constructTNBFrame(DPos, NPosG, CPosG)
NPosQ = CPosG + self.CNbondLength * coords.generateTNBVecXYZ(
TNB1, self.angleC, self.GQPsi)
# set up the TNB frame to define the alpha and betas for the second part of the G to Q Unit
TNB2 = coords.constructTNBFrame(NPosG, CPosG, NPosQ)
# set up FPosPQ and CPosPQ
dirHat = coords.generateTNBVecXYZ(TNB2, self.angleN, self.GQPhi)
FPosQ = NPosQ + self.QQbondLength / 2.0 * dirHat
CPosQ = FPosQ + self.QQbondLength / 2.0 * dirHat
GPQUnit = [NPosG, FPosG, CPosG, NPosQ, FPosQ, CPosQ]
return GPQUnit
def makeConnection(self, selfConnector, newBB, newBBConnector, displacement, alpha1, beta1, alpha2, beta2, alpha3):
# Returns a copy of the newBB that is correctly positioned relative to self, as defined
# by the six parameters provided. Six degrees of freedom are necessary to specify the global
# position and orientation of the mobile block. These are specified in terms of the dihedral and bond angles
# formed by the juxtaposition of the two connectors used to connect the blocks. Input angles are in Radians.
#
# Six atoms are used to connect the blocks which are specified using 2 arrays of 3 indices that refer to the atoms in
# both of the building blocks. There are three atoms from each block: called 0s, 1s, 2s and 0m, 1m, 2m where m stands for
# mobile and s for static.
#
# It is envisaged that 2m and 2s are the two atoms that form the connecting "bond" between the blocks so 2 is
# at the surface of a structure and 1, and 0 are increasingly deeper into the structures with m and s specifying which
# block they come from.
#
# The algorithm never moves the static block and proceeds by first establishing the correct position for 2m in the
# mobile block, then 1m and then 0m. This is performed by a translation and three rotations.
# Alpha1 is the dihedral angle formed by the atoms referenced by connector indices 0s 1s 2s 2m
# beta1 is the bond angle formed by the atoms 1s, 2s and 2m.
# displacement is the distance between 2s and 2m which form the connector points.
# Together displacement, alpha1 and beta1 define where atom 2m goes in the static TNB frame formed
# from 0s, 1s and 2s, when this frame is positioned at 2s.
#
# Thus the first translation places the mobile block so that atom 2m is at the location specified.
#
# Alpha2, beta2 and alpha3 then define the re-orientation of the entire second block.
#
# Beta2 is set first and is the the bond angle that should exist between the 2s 2m and 1m atoms.
# This angle is set by first measuring the existing bond angle so formed after the translation.
# The second block is then rotated by the necessary angle about an axis through 2m which is Normal
# to the plane formed by 2s, 2m and 1m. (this is the N vector of the TNBframe define by the points
# 2s, 2m, 1m).
#
# Alpha2 is set next and is the dihedral angle formed by the point 1s 2s 2m 1m.
# The existing angle is measured and the mobile block is then
# rotated by the appropriate angle about a vector through 2m which is parallel to 2m - 2s.
#
# point 1m is now positioned correctly.
#
# THe final dihedral that must be set is the one defined by 2s, 2m, 1m and 0m, which is a rotation about the 2m to 1m axis.
# The dihedral is measured and adjusted accordingly.
# Only moves point 0m and that means that the second block is now correctly positioned.
# first create a copy of the new BB so as not to modify the original building block.
# mBB = mobile Building Block
mBB = cp.copy(newBB)
# extract the connection points for the two building blocks (self and mobile).
selfConnectXYZ = self.getConnectionAtoms(selfConnector)
mobileConnectXYZ = mBB.getConnectionAtoms(newBBConnector)
# construct a TNB frame from 0s, 1s and 2s.
TNB1 = coord.constructTNBFrame(selfConnectXYZ[0], selfConnectXYZ[1], selfConnectXYZ[2])
# Compute the displacement of the mobileBlock so that the mobile BB's connection point 2m
# is at the right place in the TNB frame of the first connector when it is position with it's origin on the
# third point. The vector in this frame is defined by displacement, alpha1 and beta1.
displacementVec = selfConnectXYZ[2] + displacement * coord.generateTNBVecXYZ(TNB1, beta1, alpha1) - mobileConnectXYZ[2]
# translate the mobile block so it's in the right place
mBB.translateBB(displacementVec)
##### Rot 1: Set alpha 2 - dihedral about 2s to 2m axis ######
# get the new repositioned mobile connector block
mobileConnectXYZ = mBB.getConnectionAtoms(newBBConnector)
# measure the dihedral between s1, s2, m2 and m1, keep order the same to maintain signs.
alpha2Meas = coord.Dihedral(selfConnectXYZ[1], selfConnectXYZ[2], mobileConnectXYZ[2], mobileConnectXYZ[1])
if alpha2Meas==None:
alpha2Meas = alpha2
# compute the alpha2rotation axis (unti vector from 2s to 2m)
alpha2RotAxis = mobileConnectXYZ[2] - selfConnectXYZ[2]
alpha2RotAxisHat = alpha2RotAxis/np.linalg.norm(alpha2RotAxis)
# rotate the second block by an angle (alpha2 - alpha2Meas) about a vector through the point 2m which is parallel to the 2s 2m axis
# Only 1m and 0m should move from the static and mobile connector sets.
mBB.rotateBBArbitraryAxis(mobileConnectXYZ[2], alpha2RotAxisHat, alpha2 - alpha2Meas)
##### Rot 2: Set Beta2- bond angle from point m2 ######
# get the new repositioned mobile connector block
mobileConnectXYZ = mBB.getConnectionAtoms(newBBConnector)
# measure the bondangle between s2, m2 and m1
beta2Meas = coord.bondAngle(selfConnectXYZ[2], mobileConnectXYZ[2], mobileConnectXYZ[1])
# construct a TNB frame from s2, m2 and m1
TNB2 = coord.constructTNBFrame(selfConnectXYZ[2], mobileConnectXYZ[2], mobileConnectXYZ[1])
# rotate mobile connector by angle (beta2 - beta2Meas) about a vector through the point 2m which is parallel with TNB2 frame N-axis
# i.e. normal to plane of s2, m2 and m1 - the way normal is defined versus measurements of angle means to put a minus sign in there.
mBB.rotateBBArbitraryAxis(mobileConnectXYZ[2], TNB2[1], -(beta2 - beta2Meas))
###### rot3: set alpha3 - dihedral ab out 2m to 1m axis.
# extract the new mobile connectors
mobileConnectXYZ = mBB.getConnectionAtoms(newBBConnector)
# construct rot3Axis from 2m to 1m.
rot3Axis = mobileConnectXYZ[1] - mobileConnectXYZ[2]
rot3AxisHat = rot3Axis/np.linalg.norm(rot3Axis)
# measure the dihedral betwee s2, m2, m1 and m0.
alpha3Meas = coord.Dihedral(selfConnectXYZ[2], mobileConnectXYZ[2], mobileConnectXYZ[1], mobileConnectXYZ[0])
# rotate the second block by an angle (alpha3 - alpha3Meas) about a vector through the point 2m which is parallel to the 2m 1m axis
# Only 0m should move to it's final place from the static and mobile connector sets.
mBB.rotateBBArbitraryAxis(mobileConnectXYZ[2], rot3AxisHat, alpha3 - alpha3Meas)
# return the rotated Building Block
return mBB
