atomProb
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/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. If it is omitted, coordinates will be take from
      the coordinates assocated with the atomSel argument.
 
 
methods:
  calc()             - calculate density map
  writeEDM(filename) - write map to specified file in xplor edm format
 
  getGrid()            - return the densityGrid.DensityGrid object
                         generated by calc().
  selection()          - return atomSel given during construction.
  setAtomRadius(val)   - set default atomic radius
  calc()               - compute atomic probability 
 
  calcGradient(derivList,  - given a derivList.DerivList, and dFdRho_ijk,
               dFdRho    )   compute the gradient of dFdq_l
  radiusGradient(dFdRho)   - return a vector with the value of dFdr_l,
                             given dFdRho_ijk.
accessor pairs:
  
  verbose        - boolean
  radii          - vector of atomic radii- one per atom in selection's
                   simulation. Default value is 1 Anstrom.
  atomWeights    - vector of per-atom weights- one per atom in selection's
                   simulation, and distinct from the weights member for
                   per-structure weights. This defaults to 1,
  generateGrid   - boolean. If true, calc() will regenerate the grid
                   extent based on the gridVals member.
  distType      - one of "quartic","gaussian"
  scaleType    - one of "amplitude", "distribution", "normalize",
                 "flat", "volume" or "off". This specifies the normalization
                 of an atom's contribution to the distribution:
                     off and flat  -specify that no normalization be applied:
                                    for each atom contribution in the
                                    supplied atomPosList array a normalized
                                    distribution will be contributed to the
                                    grid.
                     amplitude     -contribution from each atom will be
                                    normalized by the maximum contribution
                                    from that atom.
                     normalize     -same as amplitude, but the prefactor
                                    is divided by an additional
                                    factor proportional to volume.
                     volume        -a normalized distribution is multiplied
                                    by the associated volume. With this
                                    scaleType, all atoms contribute constant
                                    density.
                     distribution  - FIX: ??
                     
  weights        - a list of per structure weights which must be
                              the same length as atomPosList. These weights
                              are normalized.
  isProjection   - if True, generate a 2D projection in a map which has znum=1.
  mapType        - one of "density", "projection", or "height"
                   [default: "density"]
 
  translation    - translation vector for centering a projection.
  orientation    - Rotation matrix defining orientation for projection.
 
  mapResolution  - resolution of the experimental map which is fit-to. This
                   is currently only used by AtomProbProjections.
 
 
members:
 
  gridVals    - a densityGrid.DensityGrid_Params object used to
                generate grid extents if generateGrid is True.
 
  d_dt        - for projections and height maps, after calcGradient is
                called, this is filled with the gradient with respect to the
                translation vector.
 
  d_dR        - for projections and height maps, after calcGradient is called,
                this is filled with the gradient with respect to the
                orientation matrix.
 
 
 
 
# 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
AtomProb
CDSVector_float_type

 
class AtomProb(builtins.object)
    AtomProb(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
atomRadius(self, *args, **kwargs) -> 'double'
atomWeights(self, *args, **kwargs) -> 'CDSVector< float_type > const'
calc(self, *args, **kwargs) -> 'void'
calcGradient(self, *args, **kwargs) -> 'void'
copyGrid(self, *args, **kwargs) -> 'void'
distType(self, *args, **kwargs) -> 'AtomProb::DistType'
gamma(self, *args, **kwargs) -> 'float_type const'
generateGrid(self, *args, **kwargs) -> 'bool const'
getGrid(self, *args, **kwargs) -> 'DensityGrid *'
mapResolution(self, *args, **kwargs) -> 'float_type const'
mapType(self, *args, **kwargs) -> 'AtomProb::MapType'
maxType(self, *args, **kwargs) -> 'AtomProb::MaxType'
minZ(self, *args, **kwargs) -> 'float_type'
modified(self, *args, **kwargs) -> 'bool'
orientation(self, *args, **kwargs) -> 'Mat3 const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
radii(self, *args, **kwargs) -> 'CDSVector< float_type > const'
radiusGradient(self, *args, **kwargs) -> 'CDSVector< float_type >'
scaleType(self, *args, **kwargs) -> 'AtomProb::ScaleType'
selection(self, *args, **kwargs) -> 'AtomSel'
setAtomRadius(self, *args, **kwargs) -> 'void'
setAtomWeights(self, *args, **kwargs) -> 'void'
setDistType(self, *args, **kwargs) -> 'void'
setGamma(self, *args, **kwargs) -> 'void'
setGenerateGrid(self, *args, **kwargs) -> 'void'
setIsProjection(s, isProjection)
backwards compatibility
setMapResolution(self, *args, **kwargs) -> 'void'
setMapType(self, *args, **kwargs) -> 'void'
setMaxType(self, *args, **kwargs) -> 'void'
setOrientation(self, *args, **kwargs) -> 'void'
setRadii(self, *args, **kwargs) -> 'void'
setScaleType(self, *args, **kwargs) -> 'void'
setSigma(self, *args, **kwargs) -> 'void'
setTranslation(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setWeights(self, *args, **kwargs) -> 'void'
sigma(self, *args, **kwargs) -> 'float_type const'
softMinZ(self, *args, **kwargs) -> 'float_type'
translation(self, *args, **kwargs) -> 'Vec3 const'
updateValues(self, *args, **kwargs) -> 'void'
val(self, *args, **kwargs) -> 'double'
verbose(self, *args, **kwargs) -> 'bool const'
weights(self, *args, **kwargs) -> 'CDSVector< float_type >'
writeEDM(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_AtomProb(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
d_dR

 
d_dt

 
gridVals

 
thisown

 
The membership flag

Data and other attributes defined here:
AMPLITUDE = 0
DENSITY = 0
DISTRIBUTION = 1
FLAT = 3
GAUSSIAN = 1
HARD = 0
HEIGHT = 2
LOGSUMEXP = 1
NORMALIZE = 2
OFF = 4
PROJECTION = 1
QUARTIC = 0
QUARTICSPREAD = 2
VOLUME = 5

 
class CDSVector_float_type(builtins.object)
    CDSVector_float_type(*args)
 

 
  Methods defined here:
__add__(self, *args) -> 'CDSVector< float_type >'
__getitem__(self, *args, **kwargs)
__getslice__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__iadd__(self, *args) -> 'CDSVector< float_type >'
__imul__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__isub__(self, *args) -> 'CDSVector< float_type >'
__itruediv__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__len__(self, *args, **kwargs) -> 'int'
__mul__(self, *args) -> 'CDSVector< float_type >'
__neg__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__pow__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__radd__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__repr__ = _swig_repr(self)
__rmul__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__rsub__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__rtruediv__(self, *args, **kwargs) -> 'CDSVector< float_type >'
__setitem__(self, *args, **kwargs) -> 'void'
__str__(self, *args, **kwargs) -> 'String'
Return str(self).
__sub__(self, *args) -> 'CDSVector< float_type >'
__truediv__(self, *args) -> 'CDSVector< float_type >'
fromList(s, l)
get(self, *args, **kwargs) -> 'float_type'
help(self, *args, **kwargs) -> 'String'
resize(self, *args, **kwargs) -> 'void'
scale(self, *args, **kwargs) -> 'void'
set(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_CDSVector_float_type(...)

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

 
Functions
       
cat(*args, **kwargs) -> 'CDSVector< float_type >'
cat3(*args, **kwargs) -> 'CDSVector< float_type >'
cat4(*args, **kwargs) -> 'CDSVector< float_type >'
max(*args, **kwargs) -> 'float_type'
min(*args, **kwargs) -> 'float_type'
pyXplorHelp(*args) -> 'String'
sum(*args, **kwargs) -> 'float_type'