def importBBK(self, fileroot):
# replaces the core representation of the building block with the data stored in a BBK file.
xyzVals, self.blockAtomNames = fIO.loadXYZ(fileroot + '.xyz')
self.blockXYZVals = np.array([xyzVals])
inputVals = fIO.readTextFile(fileroot+'.bbk')
self.blockRefPoint = np.array([float(refVal) for refVal in inputVals[0].split()[2:]])
director = np.array([float(refVal) for refVal in inputVals[1].split()[2:]])
self.blockDirectorHat = director/np.linalg.norm(director)
self.blockConnectors = np.array([int(val) for val in inputVals[2].split()[2:]])
self.blockConnectors = np.reshape(self.blockConnectors, (self.blockConnectors/3, 3))
def generateBuildingBlock(self,
XYZFileName,
showBlockDirector=False,
visualiseEnvelope=(0, 20, 'envelope.xyz'),
envelopeList=['None'],
pointsToAvoid=[]):
self.atomNameList, self.xyzList = fIO.loadXYZ(XYZFileName)
self.numPoints = len(self.atomNameList)
minDistDummy = 0.0
return BBG.generateBuildingBlock(self,
self.numPoints,
minDistDummy,
showBlockDirector=showBlockDirector)
def generateBuildingBlockXYZ(self):
print "load spidroin coil information"
spidroinCoilSpecies1Names, spidroinCoilSpecies1XYZ = fIO.loadXYZ(
self.spidroinSpecies1FName)
spidroinCoilSpecies2Names, spidroinCoilSpecies2XYZ = fIO.loadXYZ(
self.spidroinSpecies2FName)
print "Generating spidroin sites within cluster"
spidroinPositionBB = self.SPEBBG.generateBuildingBlock(
self.numPointsInCluster, self.clusterRX, self.clusterRY,
self.clusterRZ, -90.0, 90.0, -180.0, 180.0, self.SpidroinRadius)
# compute the positions and orientations of each individual spidroin within it's cluster
spidroinPositions = spidroinPositionBB.blockXYZVals
spidroinDirectors = [spidPos for spidPos in spidroinPositions]
spidroinDirectorsHat = [
spidDir / np.linalg.norm(spidDir) for spidDir in spidroinDirectors
]
spidroinRots = [
rnd.uniform(0, 360) for _ in range(0, self.numPointsInCluster)
]
print "Generating cluster positions within the larger aggregate"
clusterPositionBB = self.VPEBBG.generateBuildingBlock(
self.numClustersInAggregate, self.aggregateRX, self.aggregateRY,
self.aggregateRZ, -90.0, 90.0, -180.0, 180.0,
(max(self.clusterRX, self.clusterRY, self.clusterRZ) +
self.species2AltitudeBoost + self.TerminalExtension))
clusterPositions = clusterPositionBB.blockXYZVals
clusterDirectors = [clustPos for clustPos in clusterPositions]
clusterDirectorsHat = [
clustDir / np.linalg.norm(clustDir)
for clustDir in clusterDirectors
]
clusterRots = [
rnd.uniform(0, 360) for _ in range(0, self.numClustersInAggregate)
]
fIO.saveXYZ(clusterPositions, 'Ne', 'aggClusterPoints.xyz')
print "Producing Cluster"
# sety up output arrays
clusterXYZ = []
clusterNames = []
spidroinNum = 0
# loop through the right number of times for the species1 data
for rotation, director, position in zip(
spidroinRots[0:self.numSpidroinSpecies1],
spidroinDirectorsHat[0:self.numSpidroinSpecies1],
spidroinPositions[0:self.numSpidroinSpecies1]):
print spidroinNum
if len(clusterXYZ) == 0:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies1XYZ[:])
clusterXYZ = xyzVals[:]
clusterNames = spidroinCoilSpecies1Names
else:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies1XYZ[:])
clusterXYZ = np.concatenate((clusterXYZ, xyzVals[:]), 0)
clusterNames = np.concatenate(
(clusterNames[:], spidroinCoilSpecies1Names), 0)
spidroinNum += 1
# loop throught the species2 data and add the species two data at a slightly higher altitude.
for rotation, director, position in zip(
spidroinRots[self.numSpidroinSpecies1:],
spidroinDirectorsHat[self.numSpidroinSpecies1:],
spidroinPositions[self.numSpidroinSpecies1:]):
print spidroinNum
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position + director * self.species2AltitudeBoost,
rotation, np.array([0.0, 0.0, 1.0]), np.array([0.0, 0.0, 0.0]),
spidroinCoilSpecies2XYZ[:])
clusterXYZ = np.concatenate((clusterXYZ, xyzVals[:]), 0)
clusterNames = np.concatenate(
(clusterNames[:], spidroinCoilSpecies2Names), 0)
spidroinNum += 1
fIO.saveXYZList(clusterXYZ, clusterNames, "cluster.xyz")
print "Producing aggregate"
# sety up output arrays
aggregateXYZ = []
aggregateNames = []
clusterNum = 0
# loop through the right number of times for the species1 data
for rotation, director, position in zip(clusterRots,
clusterDirectorsHat,
clusterPositions):
print clusterNum
if len(aggregateXYZ) == 0:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), clusterXYZ)
aggregateXYZ = xyzVals[:]
aggregateNames = clusterNames
else:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), clusterXYZ)
aggregateXYZ = np.concatenate((aggregateXYZ, xyzVals[:]), 0)
aggregateNames = np.concatenate((aggregateNames, clusterNames),
0)
clusterNum += 1
fIO.saveXYZList(aggregateXYZ, aggregateNames, "spidroinAggregate.xyz")
self.namesTemp = aggregateNames
return aggregateXYZ
import Utilities.fileIO as fIO
import Utilities.coordSystems as coords
blockNames, xyzVals = fIO.loadXYZ('species2Spidroin.hPin.xyz')
eAtomNames, ePositions, eSizes, eRs, eRotVecs = coords.convertTriplesToEllipsoids(blockNames, xyzVals, 1.0, 1.0)
fIO.saveEllipsoidXYZList(eAtomNames, ePositions, eSizes, eRs, eRotVecs, 'species2Spidroin.e.xyz')
print "example done"
def generateBuildingBlockXYZ(self):
print "load spidroin coil information"
spidroinCoilSpecies1Names, spidroinCoilSpecies1XYZ = fIO.loadXYZ(
self.spidroinSpecies1FName)
spidroinCoilSpecies2Names, spidroinCoilSpecies2XYZ = fIO.loadXYZ(
self.spidroinSpecies2FName)
print "Generating spidroin sites within cluster"
spidroinPositionBB = self.VPESCPBBG.generateBuildingBlock(
self.numPointsInCluster, self.clusterRX, self.clusterRY,
self.clusterRZ, -90.0, 90.0, -180.0, 180.0, -10.0, 10.0, -10.0,
10.0, self.monomerRadius, self.terminalSeparation, 2)
# compute the positions and orientations of each individual spidroin within it's cluster
spidroinPositionInfo = spidroinPositionBB.blockXYZVals
spidroinPositions = [
(pos + spidroinPositionInfo[2 * i + 1]) / 2.0
for i, pos in enumerate(spidroinPositionInfo[0:-1:2])
]
spidroinDirectors = [
(2.0 * float(rnd.randint(0, 1)) - 1.0) *
(spidroinPositionInfo[2 * i + 1] - pos)
for i, pos in enumerate(spidroinPositionInfo[0:-1:2])
]
spidroinDirectorsHat = [
director / np.linalg.norm(director)
for director in spidroinDirectors
]
spidroinRots = [
rnd.uniform(0.0, 360.0) for _ in range(0, self.numPointsInCluster)
]
print "Generating cluster positions within the larger aggregate"
clusterPositionBB = self.VPESCPBBG.generateBuildingBlock(
self.numClustersInAggregate, self.aggregateRX, self.aggregateRY,
self.aggregateRZ, -90.0, 90.0, -180.0, 180.0, -90.0, 90.0, -180.0,
180.0, self.clusterRY, self.clusterRX, 2)
clusterPositionInfo = clusterPositionBB.blockXYZVals
clusterPositions = [
(pos + clusterPositionInfo[2 * i + 1]) / 2.0
for i, pos in enumerate(clusterPositionInfo[0:-1:2])
]
clusterDirectors = [
(clusterPositionInfo[2 * i + 1] - pos)
for i, pos in enumerate(clusterPositionInfo[0:-1:2])
]
clusterDirectorsHat = [
clustDir / np.linalg.norm(clustDir)
for clustDir in clusterDirectors
]
clusterRots = [0.0 for _ in range(0, self.numClustersInAggregate)]
fIO.saveXYZList(spidroinPositions,
['Ca', 'O'] * self.numPointsInCluster,
'aggClusterPoints.xyz')
print "Producing Cluster"
# sety up output arrays
clusterXYZ = []
clusterNames = []
spidroinNum = 0
# loop through the right number of times for the species1 data
for rotation, director, position in zip(
spidroinRots[0:self.numSpidroinSpecies1],
spidroinDirectorsHat[0:self.numSpidroinSpecies1],
spidroinPositions[0:self.numSpidroinSpecies1]):
print spidroinNum
if len(clusterXYZ) == 0:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies1XYZ[:])
clusterXYZ = xyzVals[:]
clusterNames = spidroinCoilSpecies1Names
else:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies1XYZ[:])
clusterXYZ = np.concatenate((clusterXYZ, xyzVals[:]), 0)
clusterNames = np.concatenate(
(clusterNames[:], spidroinCoilSpecies1Names), 0)
spidroinNum += 1
# loop throught the species2 data and add the species two data at a slightly higher altitude.
for rotation, director, position in zip(
spidroinRots[self.numSpidroinSpecies1:],
spidroinDirectorsHat[self.numSpidroinSpecies1:],
spidroinPositions[self.numSpidroinSpecies1:]):
print spidroinNum
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([1.0, 0.0, 0.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies2XYZ[:])
clusterXYZ = np.concatenate((clusterXYZ, xyzVals[:]), 0)
clusterNames = np.concatenate(
(clusterNames[:], spidroinCoilSpecies2Names), 0)
spidroinNum += 1
fIO.saveXYZList(clusterXYZ, clusterNames, "cluster.xyz")
print "Producing aggregate"
# sety up output arrays
aggregateXYZ = []
aggregateNames = []
clusterNum = 0
# loop through the right number of times for the species1 data
for rotation, director, position in zip(clusterRots,
clusterDirectorsHat,
clusterPositions):
print clusterNum
if len(aggregateXYZ) == 0:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), clusterXYZ)
aggregateXYZ = xyzVals[:]
aggregateNames = clusterNames
else:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), clusterXYZ)
aggregateXYZ = np.concatenate((aggregateXYZ, xyzVals[:]), 0)
aggregateNames = np.concatenate((aggregateNames, clusterNames),
0)
clusterNum += 1
fIO.saveXYZList(aggregateXYZ, aggregateNames, "spidroinAggregate.xyz")
self.namesTemp = aggregateNames
return aggregateXYZ
from Projects.chainOfChains import chainOfChainsGenerator as CCGen
import Utilities.fileIO as fIO
filename = "chainOfChains.txt"
nameList, xyzVals = fIO.loadXYZ("species1SpidroinHPin.xyz")
# create the backbone generator object using static file parameters
chainOfChainsGen = CCGen(filename)
# generate backbone realtime parameters
minDist = 1.0
residues = [19, 15] * 93
radii = [minDist * 6] * 186
nameType = ['G', 'PQ'] * 186
pointsA = [xyzVal for xyzVal, name in zip(xyzVals, nameList) if name == 'N']
pointsB = [xyzVal for xyzVal, name in zip(xyzVals, nameList) if name == 'C']
fIO.saveXYZList(pointsA + pointsB,
['Ca'] * len(pointsA) + ['O'] * len(pointsB), "labPoints.xyz")
cOfChainsBB = chainOfChainsGen.generateBuildingBlock(
residues,
pointsA,
pointsB,
radii,
nameType,
minDist,
visualiseEnvelope=(0, 50, 'envelope.xyz'))
cOfChainsBB.exportBBK("species1Chain")
def generateBuildingBlockXYZ(self):
print "Computing standard CTerminus for export as PDB"
refPosCTerm = np.array([
-self.spidroinTerminusSeparation / 2.0, 0.0, -2.7
]) # this last 2.7 is a total hack to get pointB in the envelope
self.CTerminusAll = self.CTerminusGen.generateBuildingBlock(
backboneOnly=False,
director=self.CTermDirectorHat,
showBlockDirector=False)
self.CTerminusBackbone = self.CTerminusGen.generateBuildingBlock(
backboneOnly=True,
director=self.CTermDirectorHat,
showBlockDirector=False)
self.CTerminusAll.transformBBToLabFrame(self.spidroinDirector,
refPosCTerm, self.CTermRot)
self.CTerminusBackbone.transformBBToLabFrame(self.spidroinDirector,
refPosCTerm,
self.CTermRot)
print "Computing standard NTerminus for export as PDB"
refPosNTerm = np.array(
[self.spidroinTerminusSeparation / 2.0, 0.0, 0.0])
self.NTerminusAll = self.NTerminusGen.generateBuildingBlock(
backboneOnly=False,
director=self.NTermDirectorHat,
showBlockDirector=False)
self.NTerminusBackbone = self.NTerminusGen.generateBuildingBlock(
backboneOnly=True,
director=self.NTermDirectorHat,
showBlockDirector=False)
self.NTerminusAll.transformBBToLabFrame(self.spidroinDirector,
refPosNTerm, self.NTermRot)
self.NTerminusBackbone.transformBBToLabFrame(self.spidroinDirector,
refPosNTerm,
self.NTermRot)
print "Generating spidroin sites within cluster"
spidroinPositionBB = SPEBBG.generateBuildingBlock(
self, self.numPointsInCluster, self.clusterRX, self.clusterRY,
self.clusterRZ, -90, 90, -180, 180, self.SpidroinRadius)
# compute the positions and orientations of each individual spidroin within it's cluster
spidroinPositions = spidroinPositionBB.xyzVals
spidroinDirectors = [spidPos for spidPos in spidroinPositions]
spidroinDirectorsHat = [
spidDir / np.linalg.norm(spidDir) for spidDir in spidroinDirectors
]
spidroinRots = [
rnd.uniform(0, 360) for _ in range(0, self.numSpidroins)
]
print "Generating cluster positions with in the aggregate"
clusterPositionBB = SPEBBG.generateBuildingBlock(
self, self.numClustersInAggregate, self.aggregateRX,
self.aggregateRY, self.aggregateRZ, -90, 90, -180, 180,
max(self.clusterRX, self.clusterRY, self.clusterRZ) +
self.species2AltitudeBoost + self.TerminalExtension)
clusterPositions = clusterPositionBB.xyzVals
clusterDirectors = [clustPos for clustPos in clusterPositions]
clusterDirectorsHat = [
clustDir / np.linalg.norm(clustDir)
for clustDir in clusterDirectors
]
clusterRots = [
rnd.uniform(0, 360) for _ in range(0, self.numClustersInAggregate)
]
print "load spidroin coil information"
spidroinCoilSpecies1XYZ, spidroinCoilSpecies1Names = fIO.loadXYZ(
self.spidroinSpecies1FName)
spidroinCoilSpecies2XYZ, spidroinCoilSpecies2Names = fIO.loadXYZ(
self.spidroinSpecies2FName)
print "Producing Cluster of clusters"
# sety up output arrays
NTermPoints = []
CTermPoints = []
xyzValCoils = []
names = []
for clustDirector, clustPosition, clustRotation in zip(
clusterDirectorsHat, clusterPositions, clusterRots):
# loop through the right number of times for the species1 data
for rotation, director, position in zip(
spidroinRots[0:self.numSpidroinSpecies1],
spidroinDirectorsHat[0:self.numSpidroinSpecies1],
spidroinPositions[0:self.numSpidroinSpecies1]):
if len(NTermPoints) == 0:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0,
1.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies1XYZ[:])
xyzVals = coords.transformFromBlockFrameToLabFrame(
clustDirector, clustPosition, clustRotation, director,
position, xyzVals)
NTermPoints = xyzVals[0]
NTermPoints = xyzVals[-1]
xyzValCoils = xyzVals
names = spidroinCoilSpecies1Names
else:
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position, rotation, np.array([0.0, 0.0,
1.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies1XYZ[:])
xyzVals = coords.transformFromBlockFrameToLabFrame(
clustDirector, clustPosition, clustRotation, director,
position, xyzVals)
NTermPoints = np.concatenate((NTermPoints, xyzVals[0]), 0)
CTermPoints = np.concatenate((CTermPoints, xyzVals[0]), 0)
xyzValCoils = np.concatenate((xyzValCoils, xyzVals), 0)
names = np.concatenate((names, spidroinCoilSpecies1Names),
0)
# loop throught the species2 data and add the species two data at a slightly higher altitude.
for rotation, director, position in zip(
spidroinRots[self.numSpidroinSpecies1:],
spidroinDirectorsHat[self.numSpidroinSpecies1:],
spidroinPositions[self.numSpidroinSpecies1:]):
xyzVals = coords.transformFromBlockFrameToLabFrame(
director, position + director * self.species2AltitudeBoost,
rotation, np.array([0.0, 0.0, 1.0]),
np.array([0.0, 0.0, 0.0]), spidroinCoilSpecies2XYZ[:])
xyzVals = coords.transformFromBlockFrameToLabFrame(
clustDirector, clustPosition, clustRotation, director,
position, xyzVals)
NTermPoints = np.concatenate((NTermPoints, xyzVals[0]), 0)
CTermPoints = np.concatenate((CTermPoints, xyzVals[0]), 0)
xyzValCoils = np.concatenate((xyzValCoils, xyzVals), 0)
names = np.concatenate((names, spidroinCoilSpecies2Names), 0)
self.namesTemp = names
return xyzValCoils