represent ensemble of structures as a density map.
C.D. Schwieters and G.M. Clore, ``G.M. Reweighted atomic densities
to represent ensembles of NMR structures,'' J. Biomol. NMR 23, 221-225
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.
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,
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
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
distribution - FIX: ??
weights - a list of per structure weights which must be
the same length as atomPosList. These weights
isProjection - if True, generate a 2D projection in a map which has znum=1.
mapType - one of "density", "projection", or "height"
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.
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
d_dR - for projections and height maps, after calcGradient is called,
this is filled with the gradient with respect to the
# 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.