Tools to help create, manipulate and analyze eefxPot.EEFxPot objects
which implements an implicit solvent energy for solution and membrane
environments, based on
 
 Lazaridis & Karplus Proteins 35, 133 (1999).
 Lazaridis  Proteins 52, 176 (2003).

Classes
		potList.PotList(potList.rc_Pot) EEFx_PotList   class EEFx_PotList(potList.PotList)     EEFx_PotList(*args)   Object type returned if the asList argument is True in create_EEFxPot above.     Method resolution order: EEFx_PotList potList.PotList potList.rc_Pot builtins.object Methods defined here: __getattr__(self, name) __init__(self, *args) Initialize self.  See help(type(self)) for accurate signature. Methods inherited from potList.PotList: __deref__(self, *args, **kwargs) -> 'PotList *' __getitem__(self, cnt) __getslice__(self, *args, **kwargs) -> 'PotList' __len__(self, *args, **kwargs) -> 'int' __oldinit__ = __init__(self, *args, **kwargs) __ref__(self, *args, **kwargs) -> 'PotList &' __repr__ = _swig_repr(self) add(self, pot) addEnergyReport(self, *args, **kwargs) -> 'void' addEnsWeights(self, *args, **kwargs) -> 'void' append(self, pot) byName(self, *args, **kwargs) -> 'rc_Pot' calcWDerivs(self, *args, **kwargs) -> 'bool const' clearEnergyReports(self, *args, **kwargs) -> 'void' clearEnsWeights(self, *args, **kwargs) -> 'void' copy(self, potList) decrRefCnt(self, *args, **kwargs) -> 'void' energyMaybeDerivs0(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs1(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs2(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs3(self, *args, **kwargs) -> 'float_type' energyMaybeDerivs4(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPost(self, *args, **kwargs) -> 'float_type' energyMaybeDerivsPre(self, *args, **kwargs) -> 'float_type' energyReports(self, *args, **kwargs) -> 'CDSList< EnergyReport >' ensWeight(self, *args, **kwargs) -> 'float_type' ensWeights(self, *args, **kwargs) -> 'CDSList< float_type >' ensWeightsInfo(self, *args, **kwargs) -> 'String' getEnsWeights(self, *args, **kwargs) -> 'CDSList< VarEnsWeights > &' getitem_int(self, *args, **kwargs) -> 'rc_Pot' getitem_string(self, *args, **kwargs) -> 'rc_Pot' incrRefCnt(self, *args, **kwargs) -> 'void' instanceData(self, *args, **kwargs) -> 'PyObject *' isParallel(self, *args, **kwargs) -> 'bool const' keys(self) list(self, *args, **kwargs) -> 'CDSList< rc_Pot >' makeCopy(self, *args) numRestraints(self, *args, **kwargs) -> 'int' pyXplorHelp(self, *args, **kwargs) -> 'String' refCnt(self, *args, **kwargs) -> 'int' registerInstanceData(self, *args, **kwargs) -> 'void' registerTo(self, *args, **kwargs) -> 'void' remove(self, name) removeAll(self, *args, **kwargs) -> 'void' renamed_add(self, *args, **kwargs) -> 'void' renamed_makeCopy(self, *args, **kwargs) -> 'rc_DerivedPot< PotList >' renamed_remove(self, *args, **kwargs) -> 'void' resetInstanceName(self, *args, **kwargs) -> 'void' resetPotName(self, *args, **kwargs) -> 'void' rms(self, *args, **kwargs) -> 'float_type' setCalcWDerivs(self, *args, **kwargs) -> 'void' setEnsWeights(self, *args, **kwargs) -> 'void' setIsParallel(self, *args, **kwargs) -> 'void' setThreshold(self, *args, **kwargs) -> 'void' setUseSimEnsWeights(self, *args, **kwargs) -> 'void' showReport(self, *args, **kwargs) -> 'String' simulation(self, *args) -> 'EnsembleSimulationBase const *' size(self, *args, **kwargs) -> 'int' threshold(self, *args, **kwargs) -> 'float_type const' unRegister(self, *args, **kwargs) -> 'void' updateDelta(self, *args, **kwargs) -> 'void' updateEnsWeights(self, *args, **kwargs) -> 'void' updateValues(self, *args, **kwargs) -> 'void' useSimEnsWeights(self, *args, **kwargs) -> 'bool const' violations(self, *args, **kwargs) -> 'float_type' Static methods inherited from potList.PotList: __swig_destroy__ = delete_PotList(...) Data descriptors inherited from potList.PotList: instanceDataCleanup   instanceDataCreate   instanceData_   modified   registeredSimulations   thisown   The membership flag Data and other attributes inherited from potList.PotList: noViolationStats = True Methods inherited from potList.rc_Pot: calcEnergy(self, *args, **kwargs) -> 'float_type' calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type' instanceName(self, *args, **kwargs) -> 'String' potName(self, *args, **kwargs) -> 'String' scale(self, *args, **kwargs) -> 'float_type' setScale(self, *args, **kwargs) -> 'void' Data descriptors inherited from potList.rc_Pot: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined)

Functions
		EEFx_Shadow__getattr__(self, name) analyze(potList) perform analysis of EEFxPot terms and return nicely formatted summary. create_EEFxBoundaryPot(name='EEFxWall', Xsize=None, Ysize=None, Zsize=None, radius=0) Create a boundary potential term to restrain atoms from flying off.   If radius>0 a spherical boundary will be created. Otherwise, planeDistPot plane-distance potentials will be created at +/- values given in the Xsize, Ysize, and Zsize arguments. Any of these set to None will cause no potential in that direction. create_EEFxPot(name, selection='not PSEUDO', immx=False, thickness=20, profileN=10, a=0.85, paramSet=None, moveTol=0.5, temperature=298.15, cutoffDist=None, potList=None, selPairs=[], asList=False, verbose=False) Create an instance of eefxPot.EEFxPot, with moveTol and temperature settings as specified in the argument list.   paramSet specifies a solvation parameter set to use. If it is not specified, a value is deduced from the XPLOR variable protein_par_vers specified in the parameter file. If set explicitly, valid values in this module are:      param_LK36    param_LK    param_LK19    param_LK22    param_LK22_LIPID    param_MOPED   This value depends on the XPLOR protein_par_vers variable, which should be  set in the .par parameter file. If protein_par_vers has a value of eef-1.1, eef-1.2, eef-2.0, or contains the string "charmm22" paramsSet is set to param_LK22. Otherwise, it is set to param_LK.   If the potList argument is given, separate terms will be added to the specified potList for electrostatic, solvation, and VdW terms. In this case, the returned potential term should not be appended to this potList.   The selPairs argument is an optional sequence of pairs of atomSel.AtomSel objects or strings selection strings which specify particular pairs of atoms to compute interactions between.   If asList is specified, a PotList object will be returned containing entries for the electrostatic, solvation, and VdW terms.   Setting immx to True enables IMMx membrane mode, where set following parameters are also set and have meaning:        thickness - membrane thickness      profileN  - membrane profile parameter      a         - membrane dielectric screening parameter eefxAtomEnergy(pot='', output='') Needs to be documented appropriate. eefxAtomInfo(pot='', sel='') Needs to be documented appropriate. eefxResEnergy(pot='', sel='', output='') Needs to be documented appropriate. initEEFx(topparSet=None, weak_omega=False, verbose=False) Initialize topology and parameters for use with the EEFx implicit solvent force field. If present, topparSet specifies a two membered tuple containing the names of topology and parameter files.     Finally, if topparSet is not specified and the EEFX_TOPPAR environment variable is present, it is interpreted as either a special name, or the topology and parameter names separated by the colon character.   Alternately, topparSet can be one of the special names: "default" or "charmm22".   If the parameter file sets the XPLOR variable protein_par_vers to a string containing "charmm22", the module-local variable useTorsionDB is set to False. Otherwise, this value takes the value True.   The weak_omega and verbose arguments are passed to protocol.initParams.

Data
		param_LK = {'C': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.0, 0.0, 0.0), 'C3S6': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C3S7': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C3S8': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C3S9': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C5': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 1.8, -1.35, -2.13), 'C5W': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 1.8, -1.35, -2.13), 'CF': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 1.8, -1.35, -2.13), 'CH1E': (23.7, -0.187, -0.25, 0.876, 0.0, 3.5, 2.275, -0.645, -0.86), 'CH2E': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.175, -0.72, -1.01), ...} param_LK19 = {'C': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.1, 0.0, 0.0), 'C5': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 2.1, -1.35, -2.13), 'C5W': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 2.1, -1.35, -2.13), 'CF': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 2.1, -1.35, -2.13), 'CH1E': (23.7, -0.187, -0.25, 0.876, 0.0, 3.5, 2.365, -0.645, -0.86), 'CH2E': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.235, -0.72, -1.01), 'CH2G': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.235, -0.72, -1.01), 'CH2P': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.235, -0.72, -1.01), 'CH3E': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.165, -0.665, -0.92), 'CM': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.1, 0.0, 0.0), ...} param_LK22 = {'C': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.0, 0.0, 0.0), 'C3S6': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C3S7': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C3S8': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'C3S9': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'CA': (18.4, 0.057, 0.08, -0.973, 6.9, 3.5, 1.9924, -0.41, -0.57), 'CC': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.0, 0.0, 0.0), 'CP1': (23.7, -0.187, -0.25, 0.876, 0.0, 3.5, 2.275, -0.645, -0.86), 'CP2': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.175, -0.72, -1.01), 'CP3': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.175, -0.72, -1.01), ...} param_LK22_LIPID = {'CL': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.0, 0.0, 0.0), 'CTL1': (23.7, -0.187, -0.25, 0.876, 0.0, 3.5, 2.275, -0.645, -0.86), 'CTL2': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.175, -0.72, -1.01), 'CTL3': (30.0, 1.089, 1.5, -1.779, 35.6, 3.5, 2.06, -0.665, -0.92), 'NH3L': (11.2, -20.0, -20.0, -25.0, -18.0, 6.0, 1.85, -1.145, -1.15), 'NTL': (11.2, -13.0, -26.0, -25.0, -18.0, 6.0, 1.85, -1.145, -1.15), 'O2L': (10.8, -10.0, 0.0, -12.0, -9.4, 6.0, 1.7, -0.9, -0.9), 'OBL': (10.8, -5.33, -5.85, -5.787, -8.8, 3.5, 1.7, -1.27, -1.39), 'OHL': (10.8, -5.92, -6.7, -9.264, -11.2, 3.5, 1.77, -0.96, -1.09), 'OSL': (10.8, -5.92, -6.7, -9.264, -11.2, 3.5, 1.77, -0.96, -1.09), ...} param_LK36 = {'C': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.0, 0.0, 0.0), 'CA': (18.4, 0.057, 0.08, -0.973, 6.9, 3.5, 1.992, -0.41, -0.57), 'CC': (14.7, 0.0, 0.0, 0.0, 0.0, 3.5, 2.0, 0.0, 0.0), 'CP1': (23.7, -0.187, -0.25, 0.876, 0.0, 3.5, 2.275, -0.645, -0.86), 'CP2': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.175, -0.72, -1.01), 'CP3': (22.4, 0.372, 0.52, -0.61, 18.6, 3.5, 2.175, -0.72, -1.01), 'CPH1': (18.4, 0.057, 0.08, -0.973, 6.9, 3.5, 1.8, -0.41, -0.57), 'CPH2': (18.4, 0.057, 0.08, -0.973, 6.9, 3.5, 1.8, -0.41, -0.57), 'CPT': (18.4, 0.057, 0.08, -0.973, 6.9, 3.5, 1.8, -0.41, -0.57), 'CT1': (23.7, -0.187, -0.25, 0.876, 0.0, 3.5, 2.275, -0.645, -0.86), ...} param_MOPED = {'C': (15.4, 0.0, 0.0, 0.0, 0.0, 3.5, 2.1, 0.0, 0.0), 'CH1E': (25.8, -0.187, -0.09, 0.876, 0.0, 4.62, 2.265, -0.645, -0.31), 'CH2E': (17.8, 0.372, 4.52, -0.61, 18.6, 4.86, 2.635, -0.72, -8.75), 'CH3E': (30.0, 1.089, 3.05, -1.779, 35.6, 3.31, 2.574, -0.665, -1.86), 'CR': (8.3, -0.89, -1.4, 2.22, 6.9, 3.5, 2.15, -1.35, -2.12), 'CR1E': (25.8, 0.057, -1.44, -0.973, 6.9, 3.16, 2.0, -0.41, 10.37), 'H': (0.0, 0.0, 0.0, 0.0, 0.0, 3.5, 0.8, 0.0, 0.0), 'N': (0.0, -1.0, -1.45, -1.25, 8.8, 2.62, 1.55, -1.145, -1.66), 'NC2': (10.4, -10.0, -8.99, -12.0, -7.0, 3.59, 1.1, -0.2, -0.18), 'NH1': (6.5, -5.95, -8.34, -9.059, -8.8, 2.97, 1.5, -1.145, -1.61), ...} useTorsionDB = True