surfaceArea
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/surfaceArea.py

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'