def generateBuildingBlockXYZ(self):
# create the first residue in the BB
if self.seedResidue == None:
strand = self.startResidue()
else:
strand = self.seedResidue
# tally the number of residues we added to strand
numResidues = 1
# loop until we've added the right number of residues
while numResidues < self.numResidues:
# create new residue from the last three points
residue = self.generateResidue(strand[-3:])
# add the new Residues to the strandVec list
[strand.append(monomer) for monomer in residue]
numResidues += 1
# perform final orientation depending on whether or not a seed residue was provided.
# If seed was provided then don't fiddle with orientation at all.
# if seed wasn't provided then return the strand with it's centre of mass
# at the origin and it's helical axis pointing along the z-axis
if self.seedResidue == None and self.numResidues > 3:
# This structure was created in such a way that the first two atoms are
# aligned with Z vector. We want the structure to be returned so it is at it's
# centre of mass and also with the helical axis pointing up the z axis.
# We will use the transformation from Lab to Block to achieve this,
# with a little bit of hacking of the member variables.
# find the helix axis and the centre of mass of the construct
# as it is right now.
currentDirector = coords.axisFromHelix(strand)
currentDirectorHat = currentDirector / np.linalg.norm(
currentDirector)
currentCOM = cart.getCentreOfMass(strand)
# Now specify the orientation and position that we want to map to.
# store the refPoint as a member variable.
targetRefPoint = np.array([0.0, 0.0, 0.0])
targetDirectorHat = np.array([0.0, 0.0, 1.0])
# modify the strand accordingly with the universal transformation function
strand = coords.transformFromBlockFrameToLabFrame(
targetDirectorHat, targetRefPoint, 0.0, currentDirectorHat,
currentCOM, strand)
return list(
np.around(strand, 12)
) # round the positions to 12.dp - cleans up machine precision noise on zeroes
def generateBuildingBlockRefPoint(self):
# TODO overload this function defining a principal reference point in the backbone
return cart.getCentreOfMass(self.buildingBlockXYZ)
def generateBuildingBlockRefPoint(self):
return cart.getCentreOfMass(self.buildingBlockXYZ)
def getCOM(self):
return cart.getCentreOfMass(self.blockXYZVals)