atomDensity
index
atomDensity.py

generates a density map of a given protein structure.
 
See
   The class is similar to atomProb class atomProb. The major differences 
   are: 
      atomDensity class is only capable of handling single structure whereas
      atomProb class can generate maps from an ensemble.
      atomDensity class does not have any normalization method for scaling
      the density data values.  
      The map created by atomProb belongs to grid class whereas map 
      generated by atomDensity belongs to DensityGrid class. 
   
constructor:
  AtomDensity(atomSel)-  
    atomSel is a string or atomSel.AtomSel
   
 
methods:
  calc()               - calculate density map. Need to call Incalc() before 
                         calling this method.
 
  Incalc(DensityGrid)  - Generates a new grid same as the passed grid & also 
                         set the rotation matrix and trans vectors same as 
                         the passed grid.
  
  ecalc(DensityGrid)   - Generate a density map. If DensiytGrid=0, a new map is
                         created.  
 
  writeEDM(filename)   - write map to specified file in xplor edm format
 
  calcDerv()           - calculates the derivative of the density function.
  
 
  accessor pairs:
  
  atomRadius/setAtomRadius
  verbose/setVerbose        - boolean
  distType/setDistType      - one of "quartic","gaussian"
 
 
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
AtomDensity
AtomDensityPtr
AtomDensity_GridValues
AtomDensity_GridValuesPtr
DGridhelp
DGridhelpPtr
DensityGrid
DensityGridPtr

 
class AtomDensity(__builtin__.object)
   
 

 
  Methods defined here:
InGrid(*args)

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

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
atomRadius(*args)

 
calc(*args)

 
calcDerv(*args)

 
distType(*args)

 
ecalc(*args)

 
getGrid(*args)

 
help(*args)

 
modified(*args)

 
setAtomRadius(*args)

 
setDistType(*args)

 
setVerbose(*args)

 
updateValues(*args)

 
verbose(*args)

 
writeEDM(*args)

 

Properties defined here:
grid

 
get = AtomDensity_grid_get(...)

 
set = AtomDensity_grid_set(...)

 
gridVals

 
get = AtomDensity_gridVals_get(...)

 
set = AtomDensity_gridVals_set(...)

 
nAtoms

 
get = AtomDensity_nAtoms_get(...)

 
set = AtomDensity_nAtoms_set(...)

 

Data and other attributes defined here:
CROSS_CORRELATION = 1
DIFF = 0
GAUSSIAN = 1
QUARTIC = 0
__dict__ = <dictproxy object at 0x26ce6a8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'grid': <built-in function AtomDensity_grid_get>, 'gridVals': <built-in function AtomDensity_gridVals_get>, 'nAtoms': <built-in function AtomDensity_nAtoms_get>}
__swig_setmethods__ = {'grid': <built-in function AtomDensity_grid_set>, 'gridVals': <built-in function AtomDensity_gridVals_set>, 'nAtoms': <built-in function AtomDensity_nAtoms_set>}
__weakref__ = <attribute '__weakref__' of 'AtomDensity' objects>

 
list of weak references to the object (if defined)

 
class AtomDensityPtr(AtomDensity)
   
 

 
 
Method resolution order:
AtomDensityPtr
AtomDensity
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from AtomDensity:
InGrid(*args)

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

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
atomRadius(*args)

 
calc(*args)

 
calcDerv(*args)

 
distType(*args)

 
ecalc(*args)

 
getGrid(*args)

 
help(*args)

 
modified(*args)

 
setAtomRadius(*args)

 
setDistType(*args)

 
setVerbose(*args)

 
updateValues(*args)

 
verbose(*args)

 
writeEDM(*args)

 

Properties inherited from AtomDensity:
grid

 
get = AtomDensity_grid_get(...)

 
set = AtomDensity_grid_set(...)

 
gridVals

 
get = AtomDensity_gridVals_get(...)

 
set = AtomDensity_gridVals_set(...)

 
nAtoms

 
get = AtomDensity_nAtoms_get(...)

 
set = AtomDensity_nAtoms_set(...)

 

Data and other attributes inherited from AtomDensity:
CROSS_CORRELATION = 1
DIFF = 0
GAUSSIAN = 1
QUARTIC = 0
__dict__ = <dictproxy object at 0x26cea28>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'grid': <built-in function AtomDensity_grid_get>, 'gridVals': <built-in function AtomDensity_gridVals_get>, 'nAtoms': <built-in function AtomDensity_nAtoms_get>}
__swig_setmethods__ = {'grid': <built-in function AtomDensity_grid_set>, 'gridVals': <built-in function AtomDensity_gridVals_set>, 'nAtoms': <built-in function AtomDensity_nAtoms_set>}
__weakref__ = <attribute '__weakref__' of 'AtomDensity' objects>

 
list of weak references to the object (if defined)

 
class AtomDensity_GridValues(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_AtomDensity_GridValues>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 

Properties defined here:
cushion

 
get = AtomDensity_GridValues_cushion_get(...)

 
set = AtomDensity_GridValues_cushion_set(...)

 
xdelta

 
get = AtomDensity_GridValues_xdelta_get(...)

 
set = AtomDensity_GridValues_xdelta_set(...)

 
xmax

 
get = AtomDensity_GridValues_xmax_get(...)

 
set = AtomDensity_GridValues_xmax_set(...)

 
xmin

 
get = AtomDensity_GridValues_xmin_get(...)

 
set = AtomDensity_GridValues_xmin_set(...)

 
ydelta

 
get = AtomDensity_GridValues_ydelta_get(...)

 
set = AtomDensity_GridValues_ydelta_set(...)

 
ymax

 
get = AtomDensity_GridValues_ymax_get(...)

 
set = AtomDensity_GridValues_ymax_set(...)

 
ymin

 
get = AtomDensity_GridValues_ymin_get(...)

 
set = AtomDensity_GridValues_ymin_set(...)

 
zdelta

 
get = AtomDensity_GridValues_zdelta_get(...)

 
set = AtomDensity_GridValues_zdelta_set(...)

 
zmax

 
get = AtomDensity_GridValues_zmax_get(...)

 
set = AtomDensity_GridValues_zmax_set(...)

 
zmin

 
get = AtomDensity_GridValues_zmin_get(...)

 
set = AtomDensity_GridValues_zmin_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x26cea28>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'cushion': <built-in function AtomDensity_GridValues_cushion_get>, 'xdelta': <built-in function AtomDensity_GridValues_xdelta_get>, 'xmax': <built-in function AtomDensity_GridValues_xmax_get>, 'xmin': <built-in function AtomDensity_GridValues_xmin_get>, 'ydelta': <built-in function AtomDensity_GridValues_ydelta_get>, 'ymax': <built-in function AtomDensity_GridValues_ymax_get>, 'ymin': <built-in function AtomDensity_GridValues_ymin_get>, 'zdelta': <built-in function AtomDensity_GridValues_zdelta_get>, 'zmax': <built-in function AtomDensity_GridValues_zmax_get>, 'zmin': <built-in function AtomDensity_GridValues_zmin_get>}
__swig_setmethods__ = {'cushion': <built-in function AtomDensity_GridValues_cushion_set>, 'xdelta': <built-in function AtomDensity_GridValues_xdelta_set>, 'xmax': <built-in function AtomDensity_GridValues_xmax_set>, 'xmin': <built-in function AtomDensity_GridValues_xmin_set>, 'ydelta': <built-in function AtomDensity_GridValues_ydelta_set>, 'ymax': <built-in function AtomDensity_GridValues_ymax_set>, 'ymin': <built-in function AtomDensity_GridValues_ymin_set>, 'zdelta': <built-in function AtomDensity_GridValues_zdelta_set>, 'zmax': <built-in function AtomDensity_GridValues_zmax_set>, 'zmin': <built-in function AtomDensity_GridValues_zmin_set>}
__weakref__ = <attribute '__weakref__' of 'AtomDensity_GridValues' objects>

 
list of weak references to the object (if defined)

 
class AtomDensity_GridValuesPtr(AtomDensity_GridValues)
   
 

 
 
Method resolution order:
AtomDensity_GridValuesPtr
AtomDensity_GridValues
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from AtomDensity_GridValues:
__del__(self, destroy=<built-in function delete_AtomDensity_GridValues>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 

Properties inherited from AtomDensity_GridValues:
cushion

 
get = AtomDensity_GridValues_cushion_get(...)

 
set = AtomDensity_GridValues_cushion_set(...)

 
xdelta

 
get = AtomDensity_GridValues_xdelta_get(...)

 
set = AtomDensity_GridValues_xdelta_set(...)

 
xmax

 
get = AtomDensity_GridValues_xmax_get(...)

 
set = AtomDensity_GridValues_xmax_set(...)

 
xmin

 
get = AtomDensity_GridValues_xmin_get(...)

 
set = AtomDensity_GridValues_xmin_set(...)

 
ydelta

 
get = AtomDensity_GridValues_ydelta_get(...)

 
set = AtomDensity_GridValues_ydelta_set(...)

 
ymax

 
get = AtomDensity_GridValues_ymax_get(...)

 
set = AtomDensity_GridValues_ymax_set(...)

 
ymin

 
get = AtomDensity_GridValues_ymin_get(...)

 
set = AtomDensity_GridValues_ymin_set(...)

 
zdelta

 
get = AtomDensity_GridValues_zdelta_get(...)

 
set = AtomDensity_GridValues_zdelta_set(...)

 
zmax

 
get = AtomDensity_GridValues_zmax_get(...)

 
set = AtomDensity_GridValues_zmax_set(...)

 
zmin

 
get = AtomDensity_GridValues_zmin_get(...)

 
set = AtomDensity_GridValues_zmin_set(...)

 

Data and other attributes inherited from AtomDensity_GridValues:
__dict__ = <dictproxy object at 0x26ce9f0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'cushion': <built-in function AtomDensity_GridValues_cushion_get>, 'xdelta': <built-in function AtomDensity_GridValues_xdelta_get>, 'xmax': <built-in function AtomDensity_GridValues_xmax_get>, 'xmin': <built-in function AtomDensity_GridValues_xmin_get>, 'ydelta': <built-in function AtomDensity_GridValues_ydelta_get>, 'ymax': <built-in function AtomDensity_GridValues_ymax_get>, 'ymin': <built-in function AtomDensity_GridValues_ymin_get>, 'zdelta': <built-in function AtomDensity_GridValues_zdelta_get>, 'zmax': <built-in function AtomDensity_GridValues_zmax_get>, 'zmin': <built-in function AtomDensity_GridValues_zmin_get>}
__swig_setmethods__ = {'cushion': <built-in function AtomDensity_GridValues_cushion_set>, 'xdelta': <built-in function AtomDensity_GridValues_xdelta_set>, 'xmax': <built-in function AtomDensity_GridValues_xmax_set>, 'xmin': <built-in function AtomDensity_GridValues_xmin_set>, 'ydelta': <built-in function AtomDensity_GridValues_ydelta_set>, 'ymax': <built-in function AtomDensity_GridValues_ymax_set>, 'ymin': <built-in function AtomDensity_GridValues_ymin_set>, 'zdelta': <built-in function AtomDensity_GridValues_zdelta_set>, 'zmax': <built-in function AtomDensity_GridValues_zmax_set>, 'zmin': <built-in function AtomDensity_GridValues_zmin_set>}
__weakref__ = <attribute '__weakref__' of 'AtomDensity_GridValues' objects>

 
list of weak references to the object (if defined)

 
class DGridhelp(__builtin__.object)
   
 

 
  Methods defined here:
__del__(self, destroy=<built-in function delete_DGridhelp>)

 
__getattr__ lambda self, name

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
atomProb2atomDensity(*args)

 

Properties defined here:
grid

 
get = DGridhelp_grid_get(...)

 
set = DGridhelp_grid_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x26ce6a8>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'grid': <built-in function DGridhelp_grid_get>}
__swig_setmethods__ = {'grid': <built-in function DGridhelp_grid_set>}
__weakref__ = <attribute '__weakref__' of 'DGridhelp' objects>

 
list of weak references to the object (if defined)

 
class DGridhelpPtr(DGridhelp)
   
 

 
 
Method resolution order:
DGridhelpPtr
DGridhelp
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from DGridhelp:
__del__(self, destroy=<built-in function delete_DGridhelp>)

 
__getattr__ lambda self, name

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
atomProb2atomDensity(*args)

 

Properties inherited from DGridhelp:
grid

 
get = DGridhelp_grid_get(...)

 
set = DGridhelp_grid_set(...)

 

Data and other attributes inherited from DGridhelp:
__dict__ = <dictproxy object at 0x26ce910>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'grid': <built-in function DGridhelp_grid_get>}
__swig_setmethods__ = {'grid': <built-in function DGridhelp_grid_set>}
__weakref__ = <attribute '__weakref__' of 'DGridhelp' objects>

 
list of weak references to the object (if defined)

 
class DensityGrid(__builtin__.object)
   
 

 
  Methods defined here:
CData(*args)

 
CalcCentroid(*args)

 
CopyData(*args)

 
EvalEnergy(*args)

 
GridParameters(*args)

 
GridTest(*args)

 
MaxEnergy(*args)

 
WriteData(*args)

 
__call__(*args)

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

 
__getattr__ lambda self, name

 
__iadd__(*args)

 
__init__(self, *args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
centroid(*args)

 
dataSum(*args)

 
getData(*args)

 
getEData(*args)

 
getGridCoords(*args)

 
maxPos(*args)

 
maxVal(*args)

 
rotMat(*args)

 
rotMatT(*args)

 
scale(*args)

 
setCentroid(*args)

 
setRotMat(*args)

 
setRotMatT(*args)

 
setTransVec(*args)

 
toGrid(*args)

 
toGridX(*args)

 
toGridY(*args)

 
toGridZ(*args)

 
toPoint(*args)

 
transVec(*args)

 
writeEDM(*args)

 
zero(*args)

 

Properties defined here:
Edata

 
get = DensityGrid_Edata_get(...)

 
set = DensityGrid_Edata_set(...)

 
alen

 
get = DensityGrid_alen_get(...)

 
set = DensityGrid_alen_set(...)

 
amin

 
get = DensityGrid_amin_get(...)

 
set = DensityGrid_amin_set(...)

 
bmin

 
get = DensityGrid_bmin_get(...)

 
set = DensityGrid_bmin_set(...)

 
cmin

 
get = DensityGrid_cmin_get(...)

 
set = DensityGrid_cmin_set(...)

 
data

 
get = DensityGrid_data_get(...)

 
set = DensityGrid_data_set(...)

 
gridCoords

 
get = DensityGrid_gridCoords_get(...)

 
set = DensityGrid_gridCoords_set(...)

 
grid_pmeter

 
get = DensityGrid_grid_pmeter_get(...)

 
set = DensityGrid_grid_pmeter_set(...)

 
xdelta

 
get = DensityGrid_xdelta_get(...)

 
set = DensityGrid_xdelta_set(...)

 
xnum

 
get = DensityGrid_xnum_get(...)

 
set = DensityGrid_xnum_set(...)

 
ydelta

 
get = DensityGrid_ydelta_get(...)

 
set = DensityGrid_ydelta_set(...)

 
ynum

 
get = DensityGrid_ynum_get(...)

 
set = DensityGrid_ynum_set(...)

 
zdelta

 
get = DensityGrid_zdelta_get(...)

 
set = DensityGrid_zdelta_set(...)

 
znum

 
get = DensityGrid_znum_get(...)

 
set = DensityGrid_znum_set(...)

 

Data and other attributes defined here:
__dict__ = <dictproxy object at 0x26ce948>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'Edata': <built-in function DensityGrid_Edata_get>, 'alen': <built-in function DensityGrid_alen_get>, 'amin': <built-in function DensityGrid_amin_get>, 'bmin': <built-in function DensityGrid_bmin_get>, 'cmin': <built-in function DensityGrid_cmin_get>, 'data': <built-in function DensityGrid_data_get>, 'gridCoords': <built-in function DensityGrid_gridCoords_get>, 'grid_pmeter': <built-in function DensityGrid_grid_pmeter_get>, 'xdelta': <built-in function DensityGrid_xdelta_get>, 'xnum': <built-in function DensityGrid_xnum_get>, ...}
__swig_setmethods__ = {'Edata': <built-in function DensityGrid_Edata_set>, 'alen': <built-in function DensityGrid_alen_set>, 'amin': <built-in function DensityGrid_amin_set>, 'bmin': <built-in function DensityGrid_bmin_set>, 'cmin': <built-in function DensityGrid_cmin_set>, 'data': <built-in function DensityGrid_data_set>, 'gridCoords': <built-in function DensityGrid_gridCoords_set>, 'grid_pmeter': <built-in function DensityGrid_grid_pmeter_set>, 'xdelta': <built-in function DensityGrid_xdelta_set>, 'xnum': <built-in function DensityGrid_xnum_set>, ...}
__weakref__ = <attribute '__weakref__' of 'DensityGrid' objects>

 
list of weak references to the object (if defined)

 
class DensityGridPtr(DensityGrid)
   
 

 
 
Method resolution order:
DensityGridPtr
DensityGrid
__builtin__.object

Methods defined here:
__init__(self, this)

 

Methods inherited from DensityGrid:
CData(*args)

 
CalcCentroid(*args)

 
CopyData(*args)

 
EvalEnergy(*args)

 
GridParameters(*args)

 
GridTest(*args)

 
MaxEnergy(*args)

 
WriteData(*args)

 
__call__(*args)

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

 
__getattr__ lambda self, name

 
__iadd__(*args)

 
__repr__(self)

 
__setattr__ lambda self, name, value

 
centroid(*args)

 
dataSum(*args)

 
getData(*args)

 
getEData(*args)

 
getGridCoords(*args)

 
maxPos(*args)

 
maxVal(*args)

 
rotMat(*args)

 
rotMatT(*args)

 
scale(*args)

 
setCentroid(*args)

 
setRotMat(*args)

 
setRotMatT(*args)

 
setTransVec(*args)

 
toGrid(*args)

 
toGridX(*args)

 
toGridY(*args)

 
toGridZ(*args)

 
toPoint(*args)

 
transVec(*args)

 
writeEDM(*args)

 
zero(*args)

 

Properties inherited from DensityGrid:
Edata

 
get = DensityGrid_Edata_get(...)

 
set = DensityGrid_Edata_set(...)

 
alen

 
get = DensityGrid_alen_get(...)

 
set = DensityGrid_alen_set(...)

 
amin

 
get = DensityGrid_amin_get(...)

 
set = DensityGrid_amin_set(...)

 
bmin

 
get = DensityGrid_bmin_get(...)

 
set = DensityGrid_bmin_set(...)

 
cmin

 
get = DensityGrid_cmin_get(...)

 
set = DensityGrid_cmin_set(...)

 
data

 
get = DensityGrid_data_get(...)

 
set = DensityGrid_data_set(...)

 
gridCoords

 
get = DensityGrid_gridCoords_get(...)

 
set = DensityGrid_gridCoords_set(...)

 
grid_pmeter

 
get = DensityGrid_grid_pmeter_get(...)

 
set = DensityGrid_grid_pmeter_set(...)

 
xdelta

 
get = DensityGrid_xdelta_get(...)

 
set = DensityGrid_xdelta_set(...)

 
xnum

 
get = DensityGrid_xnum_get(...)

 
set = DensityGrid_xnum_set(...)

 
ydelta

 
get = DensityGrid_ydelta_get(...)

 
set = DensityGrid_ydelta_set(...)

 
ynum

 
get = DensityGrid_ynum_get(...)

 
set = DensityGrid_ynum_set(...)

 
zdelta

 
get = DensityGrid_zdelta_get(...)

 
set = DensityGrid_zdelta_set(...)

 
znum

 
get = DensityGrid_znum_get(...)

 
set = DensityGrid_znum_set(...)

 

Data and other attributes inherited from DensityGrid:
__dict__ = <dictproxy object at 0x26ce8a0>

 
dictionary for instance variables (if defined)
__swig_getmethods__ = {'Edata': <built-in function DensityGrid_Edata_get>, 'alen': <built-in function DensityGrid_alen_get>, 'amin': <built-in function DensityGrid_amin_get>, 'bmin': <built-in function DensityGrid_bmin_get>, 'cmin': <built-in function DensityGrid_cmin_get>, 'data': <built-in function DensityGrid_data_get>, 'gridCoords': <built-in function DensityGrid_gridCoords_get>, 'grid_pmeter': <built-in function DensityGrid_grid_pmeter_get>, 'xdelta': <built-in function DensityGrid_xdelta_get>, 'xnum': <built-in function DensityGrid_xnum_get>, ...}
__swig_setmethods__ = {'Edata': <built-in function DensityGrid_Edata_set>, 'alen': <built-in function DensityGrid_alen_set>, 'amin': <built-in function DensityGrid_amin_set>, 'bmin': <built-in function DensityGrid_bmin_set>, 'cmin': <built-in function DensityGrid_cmin_set>, 'data': <built-in function DensityGrid_data_set>, 'gridCoords': <built-in function DensityGrid_gridCoords_set>, 'grid_pmeter': <built-in function DensityGrid_grid_pmeter_set>, 'xdelta': <built-in function DensityGrid_xdelta_set>, 'xnum': <built-in function DensityGrid_xnum_set>, ...}
__weakref__ = <attribute '__weakref__' of 'DensityGrid' objects>

 
list of weak references to the object (if defined)

 
Functions
       
help(...)

 

 
Data
        __package__ = None
cvar = <Global variables>
pyXplorHelp = Type help() for interactive help, or help(object) for help about object.