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
 
  
 
 
 
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.

 
Classes
       
__builtin__.object
AtomProb
AtomProbPtr
AtomProb_GridValues
AtomProb_GridValuesPtr
Grid
GridPtr

 
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)

 
getGrid(*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 = 3
GAUSSIAN = 1
NORMALIZE = 2
OFF = 4
QUARTIC = 0
__dict__ = <dictproxy object at 0x263cde0>

 
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)

 
getGrid(*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 = 3
GAUSSIAN = 1
NORMALIZE = 2
OFF = 4
QUARTIC = 0
__dict__ = <dictproxy object at 0x263cde0>

 
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 0x263cd00>

 
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 0x263cef8>

 
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 Grid(__builtin__.object)
   
 

 
  Methods defined here:
CopyData(*args)

 
__call__(*args)

 
__del__(self, destroy=<built-in function delete_Grid>)

 
__getattr__ lambda self, name

 
__iadd__(*args)

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
dataSum(*args)

 
get(*args)

 
getGridCoords(*args)

 
maxPos(*args)

 
maxVal(*args)

 
scale(*args)

 
toGrid(*args)

 
toGridX(*args)

 
toGridY(*args)

 
toGridZ(*args)

 
toPoint(*args)

 
writeEDM(*args)

 
zero(*args)

 

Properties defined here:
Edata

 
get = Grid_Edata_get(...)

 
set = Grid_Edata_set(...)

 
alen

 
get = Grid_alen_get(...)

 
set = Grid_alen_set(...)

 
amin

 
get = Grid_amin_get(...)

 
set = Grid_amin_set(...)

 
bmin

 
get = Grid_bmin_get(...)

 
set = Grid_bmin_set(...)

 
cmin

 
get = Grid_cmin_get(...)

 
set = Grid_cmin_set(...)

 
data

 
get = Grid_data_get(...)

 
set = Grid_data_set(...)

 
gridCoords

 
get = Grid_gridCoords_get(...)

 
set = Grid_gridCoords_set(...)

 
grid_pmeter

 
get = Grid_grid_pmeter_get(...)

 
set = Grid_grid_pmeter_set(...)

 
xdelta

 
get = Grid_xdelta_get(...)

 
set = Grid_xdelta_set(...)

 
xnum

 
get = Grid_xnum_get(...)

 
set = Grid_xnum_set(...)

 
ydelta

 
get = Grid_ydelta_get(...)

 
set = Grid_ydelta_set(...)

 
ynum

 
get = Grid_ynum_get(...)

 
set = Grid_ynum_set(...)

 
zdelta

 
get = Grid_zdelta_get(...)

 
set = Grid_zdelta_set(...)

 
znum

 
get = Grid_znum_get(...)

 
set = Grid_znum_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x264c788>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'Edata': <built-in function Grid_Edata_get>, 'alen': <built-in function Grid_alen_get>, 'amin': <built-in function Grid_amin_get>, 'bmin': <built-in function Grid_bmin_get>, 'cmin': <built-in function Grid_cmin_get>, 'data': <built-in function Grid_data_get>, 'gridCoords': <built-in function Grid_gridCoords_get>, 'grid_pmeter': <built-in function Grid_grid_pmeter_get>, 'xdelta': <built-in function Grid_xdelta_get>, 'xnum': <built-in function Grid_xnum_get>, ...}
__swig_setmethods__ = {'Edata': <built-in function Grid_Edata_set>, 'alen': <built-in function Grid_alen_set>, 'amin': <built-in function Grid_amin_set>, 'bmin': <built-in function Grid_bmin_set>, 'cmin': <built-in function Grid_cmin_set>, 'data': <built-in function Grid_data_set>, 'gridCoords': <built-in function Grid_gridCoords_set>, 'grid_pmeter': <built-in function Grid_grid_pmeter_set>, 'xdelta': <built-in function Grid_xdelta_set>, 'xnum': <built-in function Grid_xnum_set>, ...}
__weakref__ = <attribute '__weakref__' of 'Grid' objects>

 
list of weak references to the object (if defined)

 
class GridPtr(Grid)
   
 

 
 
Method resolution order:
GridPtr
Grid
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from Grid:
CopyData(*args)

 
__call__(*args)

 
__del__(self, destroy=<built-in function delete_Grid>)

 
__getattr__ lambda self, name

 
__iadd__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
dataSum(*args)

 
get(*args)

 
getGridCoords(*args)

 
maxPos(*args)

 
maxVal(*args)

 
scale(*args)

 
toGrid(*args)

 
toGridX(*args)

 
toGridY(*args)

 
toGridZ(*args)

 
toPoint(*args)

 
writeEDM(*args)

 
zero(*args)

 

Properties inherited from Grid:
Edata

 
get = Grid_Edata_get(...)

 
set = Grid_Edata_set(...)

 
alen

 
get = Grid_alen_get(...)

 
set = Grid_alen_set(...)

 
amin

 
get = Grid_amin_get(...)

 
set = Grid_amin_set(...)

 
bmin

 
get = Grid_bmin_get(...)

 
set = Grid_bmin_set(...)

 
cmin

 
get = Grid_cmin_get(...)

 
set = Grid_cmin_set(...)

 
data

 
get = Grid_data_get(...)

 
set = Grid_data_set(...)

 
gridCoords

 
get = Grid_gridCoords_get(...)

 
set = Grid_gridCoords_set(...)

 
grid_pmeter

 
get = Grid_grid_pmeter_get(...)

 
set = Grid_grid_pmeter_set(...)

 
xdelta

 
get = Grid_xdelta_get(...)

 
set = Grid_xdelta_set(...)

 
xnum

 
get = Grid_xnum_get(...)

 
set = Grid_xnum_set(...)

 
ydelta

 
get = Grid_ydelta_get(...)

 
set = Grid_ydelta_set(...)

 
ynum

 
get = Grid_ynum_get(...)

 
set = Grid_ynum_set(...)

 
zdelta

 
get = Grid_zdelta_get(...)

 
set = Grid_zdelta_set(...)

 
znum

 
get = Grid_znum_get(...)

 
set = Grid_znum_set(...)

 

Data and other attributes inherited from Grid:
__dict__ = <dictproxy object at 0x264b478>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'Edata': <built-in function Grid_Edata_get>, 'alen': <built-in function Grid_alen_get>, 'amin': <built-in function Grid_amin_get>, 'bmin': <built-in function Grid_bmin_get>, 'cmin': <built-in function Grid_cmin_get>, 'data': <built-in function Grid_data_get>, 'gridCoords': <built-in function Grid_gridCoords_get>, 'grid_pmeter': <built-in function Grid_grid_pmeter_get>, 'xdelta': <built-in function Grid_xdelta_get>, 'xnum': <built-in function Grid_xnum_get>, ...}
__swig_setmethods__ = {'Edata': <built-in function Grid_Edata_set>, 'alen': <built-in function Grid_alen_set>, 'amin': <built-in function Grid_amin_set>, 'bmin': <built-in function Grid_bmin_set>, 'cmin': <built-in function Grid_cmin_set>, 'data': <built-in function Grid_data_set>, 'gridCoords': <built-in function Grid_gridCoords_set>, 'grid_pmeter': <built-in function Grid_grid_pmeter_set>, 'xdelta': <built-in function Grid_xdelta_set>, 'xnum': <built-in function Grid_xnum_set>, ...}
__weakref__ = <attribute '__weakref__' of 'Grid' objects>

 
list of weak references to the object (if defined)

 
Functions
       
help(...)

 

 
Data
        __package__ = None
pyXplorHelp = Type help() for interactive help, or help(object) for help about object.