eefxPotTools
index
/home/schwitrs/xplor/python/eefxPotTools.py


 
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 *'
keys(self)
list(self, *args, **kwargs) -> 'CDSList< rc_Pot >'
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_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'
setThreshold(self, *args, **kwargs) -> 'void'
setUseSimEnsWeights(self, *args, **kwargs) -> 'void'
showReport(self, *args, **kwargs) -> 'String'
simulation(self, *args) -> 'EnsembleSimulation 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