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


 
#============================================================================
# Ez potential for quick embedding of transmembrane domains.
# Reference: 
#   Senes, A.; Chadi, D. C.; Law, P. B.; Walters, R. F. S.; Nanda, V.; DeGrado, W. F. J. Mol. Biol. 2007, 366, 436-448.

 
Classes
       
pyPot.PyPot(builtins.object)
EzPot

 
class EzPot(pyPot.PyPot)
    EzPot(name, sel='')
 

 
 
Method resolution order:
EzPot
pyPot.PyPot
builtins.object

Methods defined here:
__init__(self, name, sel='')
Initialize self.  See help(type(self)) for accurate signature.
calcEnergy(self)
calcEnergyAndDerivList(self, derivs)
calcXYCenter(self)
resEzDerive(self, z, resitype)
resEzEnergy(self, z, resitype)
setLipid(self, Type)
setPara(self, type, E0, Zmid, n)
setScale(self, scale)
setThickness(self, T)
setWall(self, wall)
setXYCenter(self, s)

Methods inherited from pyPot.PyPot:
__deref__(self, *args, **kwargs) -> 'PyPot *'
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'PyPot &'
__repr__ = _swig_repr(self)
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
pythonPot(self, *args, **kwargs) -> 'PyObject *'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

Static methods inherited from pyPot.PyPot:
__swig_destroy__ = delete_PyPot(...)

Data descriptors inherited from pyPot.PyPot:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
Functions
       
calcTiltAngle(zMin=0, zMax=0, res='')
calcTiltAngleNH(res='')
exp(x, /)
Return e raised to the power of x.
fabs(x, /)
Return the absolute value of the float x.
fitTiltAngleIH(pdb='', alphaSel='')
flipAll(Axis='X', theta=180)
Needs to be documented and moved somewhere more appropriate.
pow(x, y, /)
Return x**y (x to the power of y).
setCenter(selection='not PSEUDO', zshift=0)
Translate the coordinates of all atoms such that the centroid of the
specified atomSel.AtomSel is set to the origin. The zshift argument
specifies an offset for the z component of the centroid.
setCenterXY(selection='not PSEUDO')
Translate the coordinates of all atoms such that the x- and y- components
of the centroid of the specified atomSel.AtomSel are set to the origin.
The z-coordinates are not translated.

 
Data
        idealHelixModel = '\nATOM 1 N ALA 1 -0.802 -1.224 ...1.297 1.273 16.875 1.00 0.00 ALPH\nEND \n'
lipidType = {'16,22PC': (38.3, 25.2, 27.4), 'DGDG': (38.8, 14.4, 22.5), 'DGDG|POPE': (38.9, 15.1, 25.0, 1.0), 'DGDG|SOPC': (38.9, 18.3, 25.1, 0.8), 'DLPC': (31.6, 27.4, 18.9), 'DMPC-27': (35.7, 26.5, 23.1), 'DMPE': (40.4, 22.7, 28.8), 'DOPC': (35.9, 28.1, 25.4), 'DOPE|DOPC': (37.7, 19.4, 28.6, 3.0), 'DOPS': (39.6, 13.9, 26.2), ...}