def initialiseParameters(self):
BBG.initialiseParameters(self)
self.numResiduesAlphaHelix = self.getParam('numResiduesAlphaHelix')
self.lengthPerResidueAlpha = self.getParam('lengthPerResidueAlpha')
self.lengthPerResidueBeta = self.getParam('lengthPerResidueBeta')
self.terminiSeparation = self.getParam('terminiSeparation')
self.numBetaSheets = self.getParam('numBetaSheets')
self.numBetaStrands = self.getParam('numBetaStrands')
self.betaStrandLength = self.getParam('betaStrandLength')
self.betaSheetRx = self.getParam('betaSheetRx')
self.betaSheetRy = self.getParam('betaSheetRy')
self.betaSheetRz = self.getParam('betaSheetRz')
self.alphaBetaSeparation = self.getParam('alphaBetaSeparation')
self.alphaHelixAtomName = self.getParam('alphaHelixAtomName')
self.betaStrandAtomName = self.getParam('betaStrandAtomName')
self.coilAtomName = self.getParam('coilAtomName')
self.BSG = BSG(self.paramFilename)
self.AHG = PBG(self.paramFilename)
self.PHG = PHG(self.paramFilename)
self.USP = NBB(self.paramFilename)
self.SPEBBG = SPEBBG(self.paramFilename)
if self.noLoadErrors == False:
print "Critical Parameters are undefined for Spidroin Object"
sys.exit()
def initialiseParameters(self):
BBG.initialiseParameters(self)
# N terminal PDB information and directors
self.NTerminalFilename = self.getParam('NTerminalFilename')
NTerminalDirector = self.getParam('NTerminalDirector')
NTerminalDirector = np.array(
[component for component in NTerminalDirector[0]])
self.NTermDirectorHat = NTerminalDirector / np.linalg.norm(
NTerminalDirector)
self.NTermRot = self.getParam('NTermRot') * np.pi / 180
# C terminal PDB information and directors
self.CTerminalFilename = self.getParam('CTerminalFilename')
CTerminalDirector = self.getParam('CTerminalDirector')
CTerminalDirector = np.array(
[component for component in CTerminalDirector[0]])
self.CTermDirectorHat = CTerminalDirector / np.linalg.norm(
CTerminalDirector)
self.CTermRot = self.getParam('CTermRot') * np.pi / 180
# Over all parameters used to describe the shape and size of the spidroin packing envelope.
self.spidroinTerminusSeparation = self.getParam(
'spidroinTerminusSeparation')
self.SpidroinFrustumMaxRadius = self.getParam(
'SpidroinFrustumMaxRadius')
self.SpidroinFrustumMinRadius = self.getParam(
'SpidroinFrustumMinRadius')
self.SpidroinFrustumZ1 = 0.0
self.SpidroinFrustumZ2 = self.getParam('SpidroinFrustumZ2')
self.ellipseRX = self.getParam('ellipseRX')
self.ellipseRY = self.getParam('ellipseRY')
self.ellipseRZ = self.getParam('ellipseRZ')
self.CNbondLength = self.getParam('CNbondLength')
self.CCbondLength = self.getParam('CCbondLength')
self.omega = self.getParam('omega')
self.angleN = self.getParam('angleN')
self.psi = self.getParam('psi')
self.angleC = self.getParam('angleC')
self.phi = self.getParam('phi')
self.angleC = self.getParam('angleC')
self.dumpInterimFiles = self.getParam('dumpInterimFiles')
self.verbose = self.getParam('verbose')
# for colouring regions distinct colours in blender:
self.NTerminalAtomName = self.getParam('NTerminalAtomName')
self.CTerminalAtomName = self.getParam('CTerminalAtomName')
self.spidroinHairpinAtomName = self.getParam('spidroinHairpinAtomName')
self.spidroinAtomName = self.getParam('spidroinAtomName')
# create instances of all the building block generators that we will need.
self.SpidroinCoilGen = SHGen(self.paramFilename)
self.CTerminusGen = PDBGen(self.CTerminalFilename)
self.NTerminusGen = PDBGen(self.NTerminalFilename)
if self.noLoadErrors == False:
print "Critical Parameters are undefined for Spidroin Object"
sys.exit()
def initialiseParameters(self):
# ensure parent initialisation takes place and core values are initialised
BBG.initialiseParameters(self)
self.maxNumPackMoves = self.getParam("maxNumPackMoves")
self.packT = self.getParam("packT")
self.verbose = self.getParam("verbose")
if self.noLoadErrors == False:
print "Critical Parameters are undefined for SpacePack object"
sys.exit()
def initialiseParameters(self):
BBG.initialiseParameters(self)
self.spidroinSpecies1FName = self.getParam('spidroinSpecies1.xyz')
self.spidroinSpecies2FName = self.getParam('spidroinSpecies2.xyz')
self.ellipsoidPack = SPEBBG(self.paramFilename)
self.species2AltitudeBoost = self.getParam('species2AltitudeBoost')
if self.noLoadErrors == False:
print "Critical Parameters are undefined for Spidroin Object"
sys.exit()
def initialiseParameters(self):
# ensure parent initialisation takes place and core values are initialised
BBG.initialiseParameters(self)
self.particleName = self.getParam('particleName')
self.CPPBBG = CPPBBG(self.paramFilename)
self.VPCBBG = VPCBBG(self.paramFilename)
if self.noLoadErrors == False:
print("Critical Parameters are undefined for constrained polymer object")
sys.exit()
def initialiseParameters(self):
# ensure parent initialisation takes place and core values are initialised
BBG.initialiseParameters(self)
self.particleName = self.getParam('particleName')
self.foldingTemp = self.getParam('foldingTemp')
self.maxNumFoldingMoves = self.getParam('maxNumFoldingMoves')
self.dumpInterimFiles = self.getParam('dumpInterimFiles')
if self.noLoadErrors == False:
print "Critical Parameters are undefined for constrained polymer object"
sys.exit()
def initialiseParameters(self):
# ensure parent initialisation takes place and core values are initialised
BBG.initialiseParameters(self)
self.particleName = self.getParam('particleName')
self.numCrankShaftMoves = self.getParam('numCrankShaftMoves')
self.stubbornGroupLife = self.getParam('stubbornGroupLife')
self.stubbornCranks = self.getParam('stubbornCranks')
if self.noLoadErrors == False:
print "Critical Parameters are undefined for constrained polymer object"
sys.exit()
def initialiseParameters(self):
# ensure parent initialisation takes place and core values are initialised
BBG.initialiseParameters(self)
self.compressionScaleFactor = self.getParam('compressionScaleFactor')
self.maxNumAttempts = self.getParam('maxNumAttempts')
self.maxLivesPerNewNode = self.getParam('maxLivesPerNewNode')
self.maxLivesPerTwoNodes = self.getParam('maxLivesPerTwoNodes')
self.particleName = self.getParam('particleName')
if self.noLoadErrors == False:
print "Critical Parameters are undefined for constrained polymer object"
sys.exit()
def initialiseParameters(self):
# ensure parent initialisation takes place and core values are initialised
BBG.initialiseParameters(self)
self.particleName = self.getParam('particleName')
self.foldingTemp = self.getParam('foldingTemp')
self.maxNumFoldingMoves = self.getParam('maxNumFoldingMoves')
self.dumpInterimFiles = self.getParam('dumpInterimFiles')
self.distEpsilon = self.getParam("distEpsilon")
self.distanceScale = self.getParam("distanceScale")
self.maxNumConnectingMoves = self.getParam("maxNumConnectingMoves")
self.springConstant = self.getParam("springConstant")
self.connectingTemp = self.getParam("connectingTemp")
self.beta = self.getParam("beta") * np.pi / 180.0
self.alpha = self.getParam("alpha") * np.pi / 180.0
if self.noLoadErrors == False:
print(
"Critical Parameters are undefined for constrained polymer object"
)
sys.exit()
def initialiseParameters(self):
BBG.initialiseParameters(self)
# Over all parameters used to describe the shape and size of the spidroin packing envelope.
self.spidroinSpecies1FName = self.getParam('spidroinSpecies1Filename')
self.spidroinSpecies2FName = self.getParam('spidroinSpecies2Filename')
self.terminalSeparation = self.getParam('terminalSeparation')
self.monomerRadius = self.getParam('monomerRadius')
self.clusterRX = self.getParam('clusterRX')
self.clusterRY = self.getParam('clusterRY')
self.clusterRZ = self.getParam('clusterRZ')
self.aggregateRX = self.getParam('aggregateRX')
self.aggregateRY = self.getParam('aggregateRY')
self.aggregateRZ = self.getParam('aggregateRZ')
self.minDist = self.getParam('minDist')
self.SPEBBG = SPEBBG(self.paramFilename)
self.VPESCPBBG = VPESCPBBG(self.paramFilename)
if self.noLoadErrors == False:
print "Critical Parameters are undefined for Spidroin Object"
sys.exit()
def initialiseParameters(self):
BBG.initialiseParameters(self)
# get the C Terminal information about dimers and monomers
self.CTermDiFilename = self.getParam('CTerminalFilenameDimer')
CTermDiCI = self.getParam('CTermDimerConnectorIndices')
self.CTermDiConnectorIndices = [[
CTermDiCI[0], CTermDiCI[1], CTermDiCI[2]
], [CTermDiCI[3], CTermDiCI[4], CTermDiCI[5]]]
self.CTermMonFilename = self.getParam('CTerminalFilenameMonomer')
CTermMonCI = self.getParam('CTermMonomerConnectorIndices')
self.CTermMonConnectorIndices = [[
CTermMonCI[0], CTermMonCI[1], CTermMonCI[2]
]]
# get the C Terminal information about dimers and monomers
self.NTermDiFilename = self.getParam('NTerminalFilenameDimer')
NTermDiCI = self.getParam('NTermDimerConnectorIndices')
self.NTermDiConnectorIndices = [[
NTermDiCI[0], NTermDiCI[1], NTermDiCI[2]
], [NTermDiCI[3], NTermDiCI[4], NTermDiCI[5]]]
# get the monomer information
self.NTermMonFilename = self.getParam('NTerminalFilenameMonomer')
NTermMonCI = self.getParam('NTermMonomerConnectorIndices')
self.NTermMonConnectorIndices = [[
NTermMonCI[0], NTermMonCI[1], NTermMonCI[2]
]]
self.NTermMonGen = PDBGen(self.NTermMonFilename)
self.NTermDiGen = PDBGen(self.NTermDiFilename)
self.CTermMonGen = PDBGen(self.CTermMonFilename)
self.CTermDiGen = PDBGen(self.CTermDiFilename)
if self.noLoadErrors == False:
print "Critical Parameters are undefined for Spidroin Object"
sys.exit()