centrePos = np.array([0, 0, 0])
director = np.array([0, 0, 1])
rotation = 0
xRadius = 100
yRadius = 100
zRadius = 100
minDist = 1
theta1 = -90.0
theta2 = 90.0
phi1 = 45.0
phi2 = 90.0
envelopeList = ['None']
envelopeList = ['innersphere 60', 'outersphere 80']
# generate the building block
EllipsoidPackBB = EllipsoidPackBBG.generateBuildingBlock(
numPoints,
xRadius,
yRadius,
zRadius,
theta1,
theta2,
phi1,
phi2,
minDist,
envelopeList=envelopeList,
defaultBlockRefPoint=centrePos)
EllipsoidPackBB.transformBBToLabFrame(director, centrePos, rotation)
EllipsoidPackBB.blockAtomNames[0] = 'P'
EllipsoidPackBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
names = ['N', 'C', 'C'] * self.numResidues
if (self.polarity == "CN"):
names = ['C', 'C', 'N'] * self.numResidues
return names
if __name__ == "__main__":
# get the file name from the command line
filename = sys.argv[1]
# create the backbone generator object.
hairPinGen = peptideHairpinGenerator(filename)
# generate a backbone
numResidues = 5
bondLength = 3.5
pointA = np.array([3, 0, 0])
pointB = np.array([-3, 0, 0])
pointC = pointA + bondLength * np.array([0.77, 0.77, 0.0])
pointD = pointC + bondLength * np.array([0.0, 1.0, 0.0])
pointE = pointD + bondLength * np.array([0.0, 1.0, 1.0])
minDist = 3
polarity = 'NC'
fIO.saveXYZ([pointA, pointB, pointC, pointD, pointE], 'Ca', 'externalPoint.xyz')
# build building block and dump to file
hairpinBuildingBlock = hairPinGen.generateBuildingBlock(numResidues, pointA, pointB, pointC, pointD, pointE, minDist, bondLength, polarity)
hairpinBuildingBlock.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print "hairpin done"
# generate backbone realtime parameters
numPoints = 100
pointA = 11.0 * np.array(
[1.0 / np.sqrt(3.0), 1.0 / np.sqrt(3.0), 1.0 / np.sqrt(3)])
pointB = 11.0 * np.array(
[-1.0 / np.sqrt(3.0), -1.0 / np.sqrt(3.0), -1.0 / np.sqrt(3)])
minDist = 1.0
bondLength = 1.5
crankMoves = 20
spherePointGenerator = EPBBG('../../Library/EllipsoidPacking.txt')
spherePoints = spherePointGenerator.generateBuildingBlock(
30, 11, 11, 11, -90, 90, -180, 180, 4)
pointsToAvoid = spherePoints.getAtomsXYZ()
fIO.saveXYZList([pointA, pointB], ['Ca', 'O'], 'labPoints.xyz')
fIO.saveXYZ(pointsToAvoid, 'Na', 'labPointsToAvoid.xyz')
# generate a curve between the speicifed points
ConstrainedPolymerPackBB = ConstrainedPolymerPackGBB.generateBuildingBlock(
numPoints,
pointA,
pointB,
minDist,
bondLength,
crankMoves,
envelopeList=["outersphere 12.0", "innersphere 10.0"],
pointsToAvoid=pointsToAvoid)
ConstrainedPolymerPackGBB.checkBondLengths()
ConstrainedPolymerPackBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print "constrainedPolymer Done"
# get the file name from the command line
filename = sys.argv[1]
# create the NPack object.
SpacePackBBG = SpacePackBBG(filename)
numPoints = 1000
centrePos = np.array([0.0, 0.0, 0.0])
director = np.array([0.0, 0.0, 1.0])
rotation = 0
xR = [-20, 20]
yR = [-20, 20]
zR = [0, 30]
minDist = .2
envelopeList = ['endsphere 20.0 10.0']
envelopeList.append('frustum 20.0 10.0 -10.0 0.0')
# generate the building block
SpacePackBB = SpacePackBBG.generateBuildingBlock(numPoints,
xR,
yR,
zR,
minDist,
envelopeList=envelopeList,
pointsToAvoid=[])
SpacePackBB.transformBBToLabFrame(director, centrePos, rotation)
# dump the list of values to file
SpacePackBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print "Space Pack Done"
def getParams(self):
return self.params
if __name__ == '__main__':
# get the file name from the command line
filename = sys.argv[1]
# create the NPack object.
CylinderBBG = SurfacePackCylinderBBG(filename)
numPoints = 300
centerPos = np.array([-0, -0, 0])
director = np.array([0, 0, 1])
rotation = 0
rx = 15
ry = 10
z1 = 0
z2 = 40
phi1 = -135
phi2 = 135
minDist = 2
# generate the XYZVals in the packed spaced
CylinderBB = CylinderBBG.generateBuildingBlock(numPoints, rx, ry, z1, z2,
phi1, phi2, minDist)
CylinderBB.transformBBToLabFrame(director, centerPos, rotation)
CylinderBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
return np.array([0.0, 0.0, 0.0])
def generateBuildingBlockNames(self):
spidroinNames = self.NTermMonBB.atomNames
spidroinNames += self.CTermMonBB.atomNames
return spidroinNames
if __name__ == "__main__":
noErrors = True
filename = sys.argv[1]
# generating an individual spidroin
spidroinTerminalGenerator = spidroinTerminalGenerator(filename)
startPoint = np.array([0.0, -0.0, 0.0])
direction = np.array([-0.0, 0.0, 1.0])
rotation = 0
SpidroinBB = spidroinTerminalGenerator.generateBuildingBlock(
startPoint,
direction,
rotation,
alignDirectors=False,
showDirector=False,
nameByBuildingBlockType=True)
SpidroinBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print("Done.")
# create the generator
RandomPolymerPackBBG = RandomPolymerPackBBG(filename)
# generate backbone realtime parameters
numPoints = 70
pointA = np.array([0.0, 0.0, 0.0])
minDist = 1.0
bondLength = 1.5
alpha1 = 45 # 45.0
alpha2 = 65 # 75.0
beta1 = 110.0
beta2 = 140.0
envelopeList = ['frustum 40 15 0 5']
# generate a curve between the specifed points
RandomPolymerPackBB = RandomPolymerPackBBG.generateBuildingBlock(
numPoints,
pointA,
alpha1,
alpha2,
beta1,
beta2,
minDist,
bondLength,
envelopeList=envelopeList,
visualiseEnvelope=(100000, 100))
RandomPolymerPackBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print("RandomPolymer Done")
for n, pointToTest in enumerate(xyzVals):
# perform spatial test
pointGood = self.checkPointInBounds(pointToTest)
# if the point is bad then add the index to the array of bad points
if not pointGood:
badPoints.append(n)
return badPoints
if __name__ == "__main__":
# specify filename
filename = "buildingBlockGeneratorExample.txt"
# create the backbone generator object using static file parameters
BBG = BuildingBlockGenerator(filename)
# generate building block realtime parameters
numPos = 30
startPos = np.array([0.0, 0.0, 0.0])
director = np.array([0.0, 0.0, 1.0])
rotation = 45 * np.pi / 180
minDist = 1.0
testBuildBlock = BBG.generateBuildingBlock(numPos, minDist)
testBuildBlock.transformBBToLabFrame(director, startPos, rotation)
testBuildBlock.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print("building block done")
# get the file name from the command line
filename = "alphahelix.txt"
# create the backbone generator object using static file parameters
backboneObject = peptideBackboneGenerator(filename)
# generate backbone realtime parameters
numResidues = 16
startPos = np.array([0.0, 0.0, 0.0])
director = np.array([0.0, 0.0, 1.0])
rotation = 0 * np.pi / 180
backBoneBuildingBlock = backboneObject.generateBuildingBlock(
numResidues, showBlockDirector=False)
backBoneBuildingBlock.transformBBToLabFrame(director, startPos, rotation)
backBoneBuildingBlock.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
filename = "betastrand.txt"
# create the backbone generator object using static file parameters
backboneObject = peptideBackboneGenerator(filename)
# generate backbone realtime parameters
numResidues = 15
startPos = np.array([0.0, 0.0, 0.0])
director = np.array([0.0, 0.0, 1.0])
rotation = 0 * np.pi / 180
backBoneBuildingBlock = backboneObject.generateBuildingBlock(numResidues)
backBoneBuildingBlock.transformBBToLabFrame(director, startPos, rotation)
backBoneBuildingBlock.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
return directorHat
def generateBuildingBlockConnectors(self):
return [
np.array([2, 1, 0]),
np.array(
[self.numPoints - 3, self.numPoints - 2, self.numPoints - 1])
]
if __name__ == "__main__":
filename = "spidroinBackbone.txt"
# create the backbone generator object using static file parameters
backboneObject = spidroinBackboneGenerator(filename)
# generate backbone realtime parameters
startPos = np.array([0.0, 0.0, 0.0])
director = np.array([0.0, 0.0, 1.0])
rotation = 0 * np.pi / 180
SP1BuildingBlock = backboneObject.generateBuildingBlock('SP1')
SP1BuildingBlock.transformBBToLabFrame(director, startPos, rotation)
SP1BuildingBlock.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
SP2BuildingBlock = backboneObject.generateBuildingBlock('SP2')
SP2BuildingBlock.transformBBToLabFrame(director, startPos, rotation)
SP2BuildingBlock.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print "spidroin backbone done"
return
def atomsToCOM(self):
'''sets an atoms array to its centre of mass. Returns the COM and the new array'''
newAtoms = []
COM = np.array([0.0, 0.0, 0.0])
for atom in self.atoms:
COM += np.array([atom[7], atom[8], atom[9]])
COM /= len(self.atoms)
for atom in self.atoms:
newAtom = [item for item in atom]
newAtom[7] -= COM[0]
newAtom[8] -= COM[1]
newAtom[9] -= COM[2]
newAtoms.append(newAtom)
self.Com = COM
return newAtoms
if __name__ == "__main__":
pdbfilename = 'dargo##' #sys.argv[1]
# create instance of PDB object
pdbObject = PDB(pdbfilename)
infile = fIO.fileRootFromInfile(pdbfilename, "pdb")
pdbObject.makeXYZForBlenderFromPDB(infile + ".xyz", backBoneOnly=True)
print("Done")
def extractBackBoneIndices(self):
# Extracts the index numbers of the backbone atoms
return [
atomIndex for atomIndex, atom in enumerate(self.pdb.atoms)
if atom[1] in ['N', 'CA', 'C']
]
def exportPDBWithNewCoords(self, newXYZVals, filename):
self.pdb.replacePdbAtoms(newXYZVals, filename)
if __name__ == "__main__":
# get the file name from the command line
filename = sys.argv[1]
# create the pdb object generator
pdbObject = pdbPeptideBackboneGenerator(filename)
# generate backbone realtime parameters
refPos = np.array([0.0, 0.0, 0.0])
director = np.array([0.0, 0.0, 1.0])
rotation = 0 * np.pi / 180
pdbBuildingBlock = pdbObject.generateBuildingBlock(showBlockDirector=True)
pdbBuildingBlock.transformBBToLabFrame(director, refPos, rotation)
pdbBuildingBlock.exportBBK(fIO.fileRootFromInfile(
filename, 'pdb')) # adds the xyz extension automatically
print "pdb building block done"
if __name__ == '__main__':
# get the file name from the command line
filename = sys.argv[1]
# create the NPack object.
CuboidPackSCBBG = VolumePackCuboidSCParticlesBBG(filename)
numPoints = 80
centrePos = np.array([0, 0, 0])
director = np.array([0, 0, 1])
rotation = 0
xSize = 10.0
ySize = 10.0
zSize = 10.0
thetad1 = -75.0
thetad2 = -65.0
phid1 = -10.0
phid2 = 10.0
minDist = 2.0
pLength = 10.0
numSpheresPerParticle = 30
# generate the building block
CuboidPackSCBB = CuboidPackSCBBG.generateBuildingBlock(
numPoints, xSize, ySize, zSize, thetad1, thetad2, phid1, phid2,
minDist, pLength, numSpheresPerParticle)
CuboidPackSCBB.transformBBToLabFrame(director, centrePos, rotation)
CuboidPackSCBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
# create the backbone generator object using static file parameters
betasheetGenerator = betasheetGen(filename)
# generate backbone realtime parameters
numStrands = 4
lengthStrand = 7
numLoopResidues = 0
minDist = 1.0
inStrandDirector = np.array([0.0, 0.0, 1.0])
crossStrandDirector = np.array([1.0, 0.0, 0.0])
offset = np.array([0.0, 0.0, 0.0])
betasheetBB = betasheetGenerator.generateBuildingBlock(numStrands,
lengthStrand,
numLoopResidues,
minDist,
inStrandDirector,
crossStrandDirector,
offset,
parallel=True)
# global positioning
startPos = np.array([0.0, 0.0, 0.0])
globalDirector = np.array([0.0, 0.0, 1.0])
rotation = 0 * np.pi / 180
betasheetBB.transformBBToLabFrame(globalDirector, startPos, rotation)
betasheetBB.exportBBK(fIO.fileRootFromInfile(filename, 'txt'))
print "betasheet done"
startPoint,
direction,
rotation,
rx,
ry,
rz,
theta1,
theta2,
phi1,
phi2,
alignDirectors=True,
showDirector=False,
nameByBuildingBlockType=True)
spidAggBBSpherical.exportBBK(
fIO.fileRootFromInfile(sphericalFilename, 'txt'))
# generating elliptical structures
spidroinAggregateGeneratorElliptical = spidroinAggregateGenerator(
ellipticalFilename)
# changed parameters
rx = 135
ry = 180
rz = 70
spidAggBBElliptical = spidroinAggregateGeneratorElliptical.generateBuildingBlock(
numSpids,
startPoint,
direction,
rotation,
