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()