Python: module membraneTools

membraneTools

#============================================================================ # 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), ...}