| atomProbMask |
index |
Before a projection is computed the molcular coordinate are rotated into the appropriate frame using the rotation R: where Rpseudo is the rotation matrix associated with pseudo-atoms, Rmask is the rotation matrix defined by atomic selections used to place the system into a defining reference frame, and Rorient is a user defined rotation (mapOrientation below) used to rotate from the defining reference frame to the mask frame.
The AtomProbMask Class
The mask contains a mask image and an optional definition of rotation matrices to place a molecule in the appropriate reference from for the mask.
Constructor:
AtomProbMask(grid,
molOrientationSels,
molPlaneSel,
molCenterSel,
zDirSels,
mapCenter,
mapOrientation)
grid - a densityGrid.DensityGrid object containing
the mask image.
molOrientationSels - a sequence of two atomSel.AtomSel
objects which specify map direction (within the
map plane).
zDirSels - a sequence of two atomSel.AtomSel used to
disambiguate the sign of the plane normal vector.
molPlaneSel - an atomSel.AtomSel specifying atoms defining
the mask plane.
molCenterSel - selection specifying the molecular center of
rotation.
mapCenter - a vec3.Vec3 specifying the mask center.
mapOrientation - a mat3.Mat3 specifying the mask orientation.
Read-only Accessors:
These methods return values specified in the constructor:
grid()
molOrientationSels()
molPlaneSel()
zDirSels()
mapCenter()
mapOrientation()
One of these values can be modified after mask creation:
setZDirSels( val )
The following accessors return computed values:
molPlaneCentroid() - centroid of molPlaneSel
molPlanePos() - molPlaneSel's coordinates after subtraction by
molPlaneCentroid
planeVals() - eigenvalues of matrix molPlanePos molPlanePos^T
planeVecs() - corresponding eigenvectors.
zDir() - direction of zDirSels[1] - zDirSels[0]
normal() - normal to plane (eigenvector corresponding to the
smallest eigenvalue) with sign corrected s.t.
dot(zDir, normal) > 1.
maskRot() - the rotation matrix formed by
/ u0^T \
maskR = | u1^T |
\ n^T /
where n is normal()
u0 = unitVec(molOrientation - dot(molOrientation,u2) u2)
u1 = unitVec( u2 X u0 )
normal - plane normal direction.
zRef - vector defining the positive z direction of the
plane normal. i.e. the sign of normal is chosen
s.t. dot(zRef, normal) > 0.
molCenterSel()- return rotation center selection
molCenterAve()- return rotation center position.
Methods:
swapZdir() - swap zDirSels selections, to reverse the sign of the plane
normal.
update() - compute all derived quantities. If molOrientationSels
contains an empty AtomSel, mapCenter and
molPlaneCentroid are set to the origin and maskR is set
to the dentity matrix.
apply(data,
R,t ) - Mask data given orientation R and translation t,
which default to the identity matrix and zero vector,
respectively. No value is returned, but the passed
grid is modified (masked). This involves interpolation of
the mask.
applyInFrame(data) - apply massk to data in the mask frame.
placeInFrame(atomProb) - update the orientation and translation of
the passed atomProb.AtomProb object to be
in the mask frame.
# 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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