| atomProb |
index |
represent ensemble of structures as a density map. The evenly-weighted atom density at point q is
defined as where Ns is the number of structures in the ensemble,
Na the number of atoms in each structure, qkl the
position (after application of rotation R and translation
t) of atom l in
structure k. ρa(q) is a normalized
distribution for a
single atom. By default this density is a piecewise function, whose
nonzero region is a quartic polynomial: where a[1 − √(2) ⁄ 2]1 ⁄ 2 is the distance at which the density
is one-half its maximum value. This distance is given by the radii()
method. For "amplitude" scaleType, the density is reweighted such that the
maximum is the same for each atom: where
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
corresponding to the current coordinates and
settings - generated by calc().
getGridRaw() - same as above, but immediately returns the
DensityGrid object without first updating.
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 Angstrom.
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. This corresponds to ρeven
below.
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 t
for centering a projection.
orientation - Rotation matrix R
defining orientation for projection.
This transformation is given by:
q → R(q − qc) + qc + t
where qc
is the selection centroid:
qc = 1 ⁄ Ns∑iqi
where Ns
is the number of atoms in the selection.
qc - center of rotation. The defaults to the average position
of atomSel.
centroidSel - selection used to define qc.
mapResolution - resolution (Gaussian width) of the experimental map which
is fit to, used for Gaussian blurring. This is
currently only used by AtomProbProjections, and
defaults to 0 (no blurring).
mask - an optional atomProbMask.AtomProbMask object to mask the map
computed by atomProb(). Using the accessor setMask has the
side-effect that centroidSel is reset to mask.molPlaneSel.
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.
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