Python: module surfaceArea

surfaceArea

surface area calculator SurfaceArea objects are usually created using the create_SurfaceArea function from the surfaceTools module. constructor: SurfaceArea(radii, atomSel) radii is list of length numAtoms containing atomic radii. These are effective radii- any solvent radius should be pre-added. atomSelection is selection used in the surface area calculation. singleAtom(atom, altRadius=-1., saveData =0) calculate and return exposed solvent accessible surface area for the specified atom. Only those neighboring atoms included in selection are included in this calculation. An alternative radius for this one atom can be optionally specified. also information from a previous calc can be passed in as saveData - this will speed things up if the atoms haven't moved too much. singleAtomDerivs(DerivList&); calculate derivatives wrt surface area info. This must be called after singleAtom, and before atoms have moved. saveData() return the SaveData info corresponding to the most recent singleAtom() call. radius(Atom) setRadius(Atom, num) get/set the effective radius of the specified atom. selection() setSelection(atomSel); get/set atoms to include in surface area calc. simulation() get the simulation associated with selection() verbose() setVerbose(val) get/set the verbosity level (0-4) [default:0] useConvexHull() setUseConvexHull(val) get/set the value of useConvexHull. This specifies whether the Convex Hull neighbor culling algorithm is used. See Fraczkiewicz and Braun, J. Comp. Chem 19, 319 (1998) for more details. [default:0(off)] useSphereMetric() setUseSphereMetric(boolVal) sphereGridSize() setSphereGridSize(intVal) sphere metric approximation: divide sphere evenly (by surface are) into grids. For each neighbor find the closest grid and calculate a metric based on how much surface of cAtom is occluded. For each grid point retain only that atom which has the maximum metric. thus, the number of neighbors is reduced. [off by default] moveTol() setMoveTol(floatVal) how much movement to allow before recalcing neighbor identity [default: 0.] setModified() notify object that atom positions have changed. updateTouchingList() update the array of lists of touching atoms. # This file was automatically generated by SWIG (http://www.swig.org). # Version 4.0.2 # # Do not make changes to this file unless you know what you are doing--modify # the SWIG interface file instead.

Classes

builtins.object

CDSList_CDSList_SA_Arc
CDSList_SA_Arc
CDSList_rc_Neighbor
SA_Arc
SA_ArcDerivInfo
SA_Neighbor
SA_TouchingList
SA_Vertex
SurfaceArea
SurfaceAreaSaveData
rc_ptr_SA_ArcDerivInfo
rc_ptr_SA_Neighbor
rc_ptr_SA_Vertex
rc_ptr_SurfaceAreaSaveData

class CDSList_CDSList_SA_Arc(builtins.object)

CDSList_CDSList_SA_Arc(*args)

Methods defined here:

__delitem__(self, *args, **kwargs) -> 'void'

__getitem__(self, *args) -> 'CDSList< CDSList< SA_Arc,10 > >'

__getslice__(self, *args, **kwargs) -> 'CDSList< CDSList< SA_Arc,10 > >'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__len__(self, *args, **kwargs) -> 'int'

__repr__ = _swig_repr(self)

__setitem__(self, *args, **kwargs) -> 'void'

append(self, *args, **kwargs) -> 'void'

help(self, *args, **kwargs) -> 'String'

remove(self, *args, **kwargs) -> 'void'

removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_CDSList_CDSList_SA_Arc(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class CDSList_SA_Arc(builtins.object)

CDSList_SA_Arc(*args)

Methods defined here:

__delitem__(self, *args, **kwargs) -> 'void'

__getitem__(self, *args) -> 'CDSList< SA_Arc >'

__getslice__(self, *args, **kwargs) -> 'CDSList< SA_Arc >'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__len__(self, *args, **kwargs) -> 'int'

__repr__ = _swig_repr(self)

__setitem__(self, *args, **kwargs) -> 'void'

append(self, *args, **kwargs) -> 'void'

help(self, *args, **kwargs) -> 'String'

remove(self, *args, **kwargs) -> 'void'

removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_CDSList_SA_Arc(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class CDSList_rc_Neighbor(builtins.object)

CDSList_rc_Neighbor(*args)

Methods defined here:

__delitem__(self, *args, **kwargs) -> 'void'

__getitem__(self, *args) -> 'CDSList< CDS::rc_ptr< SA_Neighbor > >'

__getslice__(self, *args, **kwargs) -> 'CDSList< CDS::rc_ptr< SA_Neighbor > >'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__len__(self, *args, **kwargs) -> 'int'

__repr__ = _swig_repr(self)

__setitem__(self, *args, **kwargs) -> 'void'

append(self, *args, **kwargs) -> 'void'

help(self, *args, **kwargs) -> 'String'

remove(self, *args, **kwargs) -> 'void'

removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_CDSList_rc_Neighbor(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class SA_Arc(builtins.object)

SA_Arc(*args)

Methods defined here:

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

ni(self, *args, **kwargs) -> 'SA_Neighbor const *'

nj(self, *args, **kwargs) -> 'SA_Neighbor const *'

nk(self, *args, **kwargs) -> 'SA_Neighbor const *'

Static methods defined here:

__swig_destroy__ = delete_SA_Arc(...)

Data descriptors defined here:

Omega

Phi

S

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

cosTheta

derivInfo

m

n

thisown: The membership flag

v0

v1

vertexIndex

class SA_ArcDerivInfo(builtins.object)

SA_ArcDerivInfo(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

Static methods defined here:

__swig_destroy__ = delete_SA_ArcDerivInfo(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

dP

dPhi

dPhiNext

dPhiPrev

dQ

dg

du

thisown: The membership flag

class SA_Neighbor(builtins.object)

SA_Neighbor(*args, **kwargs)

Methods defined here:

__eq__(self, *args, **kwargs) -> 'bool': Return self==value.

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

pos(self, *args, **kwargs) -> 'Vec3'

radius(self, *args, **kwargs) -> 'float_type'

update(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_SA_Neighbor(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

a

atom

d

g

index

pos_

r

thisown: The membership flag

u

Data and other attributes defined here:

__hash__ = None

class SA_TouchingList(builtins.object)

SA_TouchingList(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

update(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_SA_TouchingList(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

engulfed

posCache

thisown: The membership flag

class SA_Vertex(builtins.object)

SA_Vertex(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

swapNeighbors(self, *args, **kwargs) -> 'void'

update(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_SA_Vertex(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

cosPhi

eta

gamma

n0

n1

omega

pos

sinPhi

tau0

tau1

thisown: The membership flag

class SurfaceArea(builtins.object)

SurfaceArea(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

moveTol(self, *args, **kwargs) -> 'float_type const'

pyXplorHelp(self, *args, **kwargs) -> 'String'

radius(self, *args, **kwargs) -> 'float_type'

saveData(self, *args, **kwargs) -> 'SurfaceArea::SaveData_p'

selection(self, *args, **kwargs) -> 'AtomSel const &'

setMoveTol(self, *args, **kwargs) -> 'void'

setRadius(self, *args, **kwargs) -> 'void'

setSelection(self, *args, **kwargs) -> 'void'

setSphereGridSize(self, *args, **kwargs) -> 'void'

setUseConvexHull(self, *args, **kwargs) -> 'void'

setUseSphereMetric(self, *args, **kwargs) -> 'void'

setVerbose(self, *args, **kwargs) -> 'void'

simulation(self, *args, **kwargs) -> 'Simulation const *'

singleAtom(self, *args, **kwargs) -> 'float_type'

singleAtomDerivs(self, *args, **kwargs) -> 'void'

sphereGridSize(self, *args, **kwargs) -> 'int const'

useConvexHull(self, *args, **kwargs) -> 'bool const'

useSphereMetric(self, *args, **kwargs) -> 'bool const'

verbose(self, *args, **kwargs) -> 'int const'

Static methods defined here:

__swig_destroy__ = delete_SurfaceArea(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

thisown: The membership flag

class SurfaceAreaSaveData(builtins.object)

SurfaceAreaSaveData(*args, **kwargs)

Methods defined here:

__init__(self, *args, **kwargs): Initialize self. See help(type(self)) for accurate signature.

__repr__ = _swig_repr(self)

Static methods defined here:

__swig_destroy__ = delete_SurfaceAreaSaveData(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

cAtomPos

isoContrib

isolated

paths

thisown: The membership flag

class rc_ptr_SA_ArcDerivInfo(builtins.object)

rc_ptr_SA_ArcDerivInfo(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'SA_ArcDerivInfo *'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__ref__(self, *args, **kwargs) -> 'SA_ArcDerivInfo &'

__repr__ = _swig_repr(self)

count(self, *args, **kwargs) -> 'int'

decr(self, *args, **kwargs) -> 'void'

forceDelete(self, *args, **kwargs) -> 'void'

incr(self, *args, **kwargs) -> 'void'

ptr(self, *args, **kwargs) -> 'SA_ArcDerivInfo *'

release(self, *args, **kwargs) -> 'SA_ArcDerivInfo *'

reset(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_SA_ArcDerivInfo(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

dP

dPhi

dPhiNext

dPhiPrev

dQ

dg

du

thisown: The membership flag

class rc_ptr_SA_Neighbor(builtins.object)

rc_ptr_SA_Neighbor(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'SA_Neighbor *'

__eq__(self, *args, **kwargs) -> 'bool': Return self==value.

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__ref__(self, *args, **kwargs) -> 'SA_Neighbor &'

__repr__ = _swig_repr(self)

count(self, *args, **kwargs) -> 'int'

decr(self, *args, **kwargs) -> 'void'

forceDelete(self, *args, **kwargs) -> 'void'

incr(self, *args, **kwargs) -> 'void'

pos(self, *args, **kwargs) -> 'Vec3'

ptr(self, *args, **kwargs) -> 'SA_Neighbor *'

radius(self, *args, **kwargs) -> 'float_type'

release(self, *args, **kwargs) -> 'SA_Neighbor *'

reset(self, *args, **kwargs) -> 'void'

update(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_SA_Neighbor(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

a

atom

d

g

index

pos_

r

thisown: The membership flag

u

Data and other attributes defined here:

__hash__ = None

class rc_ptr_SA_Vertex(builtins.object)

rc_ptr_SA_Vertex(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'SA_Vertex *'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__ref__(self, *args, **kwargs) -> 'SA_Vertex &'

__repr__ = _swig_repr(self)

count(self, *args, **kwargs) -> 'int'

decr(self, *args, **kwargs) -> 'void'

forceDelete(self, *args, **kwargs) -> 'void'

incr(self, *args, **kwargs) -> 'void'

ptr(self, *args, **kwargs) -> 'SA_Vertex *'

release(self, *args, **kwargs) -> 'SA_Vertex *'

reset(self, *args, **kwargs) -> 'void'

swapNeighbors(self, *args, **kwargs) -> 'void'

update(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_SA_Vertex(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

cosPhi

eta

gamma

n0

n1

omega

pos

sinPhi

tau0

tau1

thisown: The membership flag

class rc_ptr_SurfaceAreaSaveData(builtins.object)

rc_ptr_SurfaceAreaSaveData(*args)

Methods defined here:

__deref__(self, *args, **kwargs) -> 'SurfaceAreaSaveData *'

__init__(self, *args): Initialize self. See help(type(self)) for accurate signature.

__ref__(self, *args, **kwargs) -> 'SurfaceAreaSaveData &'

__repr__ = _swig_repr(self)

count(self, *args, **kwargs) -> 'int'

decr(self, *args, **kwargs) -> 'void'

forceDelete(self, *args, **kwargs) -> 'void'

incr(self, *args, **kwargs) -> 'void'

ptr(self, *args, **kwargs) -> 'SurfaceAreaSaveData *'

release(self, *args, **kwargs) -> 'SurfaceAreaSaveData *'

reset(self, *args, **kwargs) -> 'void'

Static methods defined here:

__swig_destroy__ = delete_rc_ptr_SurfaceAreaSaveData(...)

Data descriptors defined here:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

cAtomPos

isoContrib

isolated

paths

thisown: The membership flag

Functions
		pyXplorHelp(*args) -> 'String'