atomProb
index
atomProb.py

represent ensemble of structures as a density map.
 
See 
   C.D. Schwieters and G.M. Clore, ``G.M. Reweighted atomic densities 
   to represent ensembles of NMR structures,'' J. Biomol. NMR 23, 221-225
   (2002).
 
 
constructor:
  AtomProb(atomSel,
           atomPosList) - 
    atomSel is a string or atomSel.AtomSel
    atomPosList is a list of atomic coordinates for the structures which
      will make up the map.
 
 
methods:
  calc()             - calculate density map
  writeEDM(filename) - write map to specified file in xplor edm format
 
  accessor pairs:
  
  atomRadius/setAtomRadius
  verbose/setVerbose        - boolean
  fullMap/setFullMap        - boolean. Specify whether to calculate map due
                              to all atoms, rather than only those in the
                              selection.
  distType/setDistType      - one of "quartic","gaussian"
  scaleType/setScaleType    - one of "amplitude","distribution","flat"
 
 
members:
  gridVals - with members: 
        xdelta, ydelta, zdelta
        xmin, ymin, zmin
        xmax, ymax, zmax        - grid parameters
        cushion                 - space around molecule for auto-grid 
                                  generation
 
  
 

 
Classes
       
__builtin__.object
AtomProb
AtomProbPtr
AtomProb_GridValues
AtomProb_GridValuesPtr

 
class AtomProb(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_AtomProb>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value
atomRadius(*args)
calc(*args)
distType(*args)
fullMap(*args)
help(*args)
modified(*args)
scaleType(*args)
setAtomRadius(*args)
setDistType(*args)
setFullMap(*args)
setScaleType(*args)
setVerbose(*args)
updateValues(*args)
verbose(*args)
writeEDM(*args)

Properties defined here:
gridVals
get = AtomProb_gridVals_get(...)
set = AtomProb_gridVals_set(...)

Data and other attributes defined here:
AMPLITUDE = 0
DISTRIBUTION = 1
FLAT = 2
GAUSSIAN = 1
QUARTIC = 0
__dict__ = <dictproxy object at 0x12c41a0>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'gridVals': <built-in function AtomProb_gridVals_get>}
__swig_setmethods__ = {'gridVals': <built-in function AtomProb_gridVals_set>}
__weakref__ = <attribute '__weakref__' of 'AtomProb' objects>
list of weak references to the object (if defined)

 
class AtomProbPtr(AtomProb)
    
Method resolution order:
AtomProbPtr
AtomProb
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from AtomProb:
__del__(self, destroy=<built-in function delete_AtomProb>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value
atomRadius(*args)
calc(*args)
distType(*args)
fullMap(*args)
help(*args)
modified(*args)
scaleType(*args)
setAtomRadius(*args)
setDistType(*args)
setFullMap(*args)
setScaleType(*args)
setVerbose(*args)
updateValues(*args)
verbose(*args)
writeEDM(*args)

Properties inherited from AtomProb:
gridVals
get = AtomProb_gridVals_get(...)
set = AtomProb_gridVals_set(...)

Data and other attributes inherited from AtomProb:
AMPLITUDE = 0
DISTRIBUTION = 1
FLAT = 2
GAUSSIAN = 1
QUARTIC = 0
__dict__ = <dictproxy object at 0x12c60f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'gridVals': <built-in function AtomProb_gridVals_get>}
__swig_setmethods__ = {'gridVals': <built-in function AtomProb_gridVals_set>}
__weakref__ = <attribute '__weakref__' of 'AtomProb' objects>
list of weak references to the object (if defined)

 
class AtomProb_GridValues(__builtin__.object)
     Methods defined here:
__del__(self, destroy=<built-in function delete_AtomProb_GridValues>)
__getattr__ lambda self, name
__init__(self, *args)
__repr__(self)
__setattr__ lambda self, name, value

Properties defined here:
cushion
get = AtomProb_GridValues_cushion_get(...)
set = AtomProb_GridValues_cushion_set(...)
xdelta
get = AtomProb_GridValues_xdelta_get(...)
set = AtomProb_GridValues_xdelta_set(...)
xmax
get = AtomProb_GridValues_xmax_get(...)
set = AtomProb_GridValues_xmax_set(...)
xmin
get = AtomProb_GridValues_xmin_get(...)
set = AtomProb_GridValues_xmin_set(...)
ydelta
get = AtomProb_GridValues_ydelta_get(...)
set = AtomProb_GridValues_ydelta_set(...)
ymax
get = AtomProb_GridValues_ymax_get(...)
set = AtomProb_GridValues_ymax_set(...)
ymin
get = AtomProb_GridValues_ymin_get(...)
set = AtomProb_GridValues_ymin_set(...)
zdelta
get = AtomProb_GridValues_zdelta_get(...)
set = AtomProb_GridValues_zdelta_set(...)
zmax
get = AtomProb_GridValues_zmax_get(...)
set = AtomProb_GridValues_zmax_set(...)
zmin
get = AtomProb_GridValues_zmin_get(...)
set = AtomProb_GridValues_zmin_set(...)

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x12c40f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'cushion': <built-in function AtomProb_GridValues_cushion_get>, 'xdelta': <built-in function AtomProb_GridValues_xdelta_get>, 'xmax': <built-in function AtomProb_GridValues_xmax_get>, 'xmin': <built-in function AtomProb_GridValues_xmin_get>, 'ydelta': <built-in function AtomProb_GridValues_ydelta_get>, 'ymax': <built-in function AtomProb_GridValues_ymax_get>, 'ymin': <built-in function AtomProb_GridValues_ymin_get>, 'zdelta': <built-in function AtomProb_GridValues_zdelta_get>, 'zmax': <built-in function AtomProb_GridValues_zmax_get>, 'zmin': <built-in function AtomProb_GridValues_zmin_get>}
__swig_setmethods__ = {'cushion': <built-in function AtomProb_GridValues_cushion_set>, 'xdelta': <built-in function AtomProb_GridValues_xdelta_set>, 'xmax': <built-in function AtomProb_GridValues_xmax_set>, 'xmin': <built-in function AtomProb_GridValues_xmin_set>, 'ydelta': <built-in function AtomProb_GridValues_ydelta_set>, 'ymax': <built-in function AtomProb_GridValues_ymax_set>, 'ymin': <built-in function AtomProb_GridValues_ymin_set>, 'zdelta': <built-in function AtomProb_GridValues_zdelta_set>, 'zmax': <built-in function AtomProb_GridValues_zmax_set>, 'zmin': <built-in function AtomProb_GridValues_zmin_set>}
__weakref__ = <attribute '__weakref__' of 'AtomProb_GridValues' objects>
list of weak references to the object (if defined)

 
class AtomProb_GridValuesPtr(AtomProb_GridValues)
    
Method resolution order:
AtomProb_GridValuesPtr
AtomProb_GridValues
__builtin__.object

Methods defined here:
__init__(self, this)

Methods inherited from AtomProb_GridValues:
__del__(self, destroy=<built-in function delete_AtomProb_GridValues>)
__getattr__ lambda self, name
__repr__(self)
__setattr__ lambda self, name, value

Properties inherited from AtomProb_GridValues:
cushion
get = AtomProb_GridValues_cushion_get(...)
set = AtomProb_GridValues_cushion_set(...)
xdelta
get = AtomProb_GridValues_xdelta_get(...)
set = AtomProb_GridValues_xdelta_set(...)
xmax
get = AtomProb_GridValues_xmax_get(...)
set = AtomProb_GridValues_xmax_set(...)
xmin
get = AtomProb_GridValues_xmin_get(...)
set = AtomProb_GridValues_xmin_set(...)
ydelta
get = AtomProb_GridValues_ydelta_get(...)
set = AtomProb_GridValues_ydelta_set(...)
ymax
get = AtomProb_GridValues_ymax_get(...)
set = AtomProb_GridValues_ymax_set(...)
ymin
get = AtomProb_GridValues_ymin_get(...)
set = AtomProb_GridValues_ymin_set(...)
zdelta
get = AtomProb_GridValues_zdelta_get(...)
set = AtomProb_GridValues_zdelta_set(...)
zmax
get = AtomProb_GridValues_zmax_get(...)
set = AtomProb_GridValues_zmax_set(...)
zmin
get = AtomProb_GridValues_zmin_get(...)
set = AtomProb_GridValues_zmin_set(...)

Data and other attributes inherited from AtomProb_GridValues:
__dict__ = <dictproxy object at 0x12c70f8>
dictionary for instance variables (if defined)
__swig_getmethods__ = {'cushion': <built-in function AtomProb_GridValues_cushion_get>, 'xdelta': <built-in function AtomProb_GridValues_xdelta_get>, 'xmax': <built-in function AtomProb_GridValues_xmax_get>, 'xmin': <built-in function AtomProb_GridValues_xmin_get>, 'ydelta': <built-in function AtomProb_GridValues_ydelta_get>, 'ymax': <built-in function AtomProb_GridValues_ymax_get>, 'ymin': <built-in function AtomProb_GridValues_ymin_get>, 'zdelta': <built-in function AtomProb_GridValues_zdelta_get>, 'zmax': <built-in function AtomProb_GridValues_zmax_get>, 'zmin': <built-in function AtomProb_GridValues_zmin_get>}
__swig_setmethods__ = {'cushion': <built-in function AtomProb_GridValues_cushion_set>, 'xdelta': <built-in function AtomProb_GridValues_xdelta_set>, 'xmax': <built-in function AtomProb_GridValues_xmax_set>, 'xmin': <built-in function AtomProb_GridValues_xmin_set>, 'ydelta': <built-in function AtomProb_GridValues_ydelta_set>, 'ymax': <built-in function AtomProb_GridValues_ymax_set>, 'ymin': <built-in function AtomProb_GridValues_ymin_set>, 'zdelta': <built-in function AtomProb_GridValues_zdelta_set>, 'zmax': <built-in function AtomProb_GridValues_zmax_set>, 'zmin': <built-in function AtomProb_GridValues_zmin_set>}
__weakref__ = <attribute '__weakref__' of 'AtomProb_GridValues' objects>
list of weak references to the object (if defined)

 
Functions
       
help(...)