| tagPairDist |
index |
TagPairDist- A class used for computing a pairwise distance distribution
arising from a pair of sidechain rotamer tags. This is used in the
deerPot and tagPairPot modules.
Constructor:
TagPairDist(tagEnvironment,
rVals,
atomSel1,
atomSel2)
tagEnvironment is a TagEnvironment object (described below), rVals
is a sequence of distance values (in Angstroms) to compute a Pr(r).
atomSel1 and atomSel2 define two sets of tag rotamers between which
the Pr is computed.
Members
comment - optional comment string.
tagRadii1 - arrays containing radii for each rotamer corresponding to atoms
tagRadii2 in atomSel1 and atomSel2.
Methods
iWeights1()/setIWeights1(val) - return/set the intrinsic weights of
iWeights2()/setIWeights2(val) - each rotamer in the two tags.
distanceWeights1() - return the weights computed from overlap of tag atom
distanceWeights2() identified in atomSel1/2 with tagEnvironment's
nonTagSel.
distanceWeight for each tag atom is the product of
w_d = 1 * w_1 * w_2 * ... w_N
where N = min(env.numClosestAtoms,num neighbors).
The weight w_i corresponding to overlap between the tag atom and
neighbor i is given by a piecewise continuous function depending
on distance d_i = |q_tag - q_i|:
/ L(d_i-r_tag-r_i) , for d_i < r_tag+r_i
w_i = | P(d_i-r_tag-r_i) , for d_i >= r_tag+r_i,
| d_i < r_tag+r_i+r_c
\ 1 , for d_i >= r_tag+r_i+r_c
where r_i is the radius of neighbor i and r_tag is the tag radius,
r_c is distanceSigmoidWidth, L(r) the logistic curve, and P(r) a
fifth order polynomial:
L(r) = (1 + exp(-A_c r))^(-1)
P(r) = (1.+r*(1/5*r^4 -2/3*r_c^2*r^2 + r_c^4)/N_P) / 2
with A_c = 15/4/r_c, and N_P = 8/15*r_c^5.
removeTagAtoms1(sel) - remove the atoms in atomSel1 as specified in the
atomSel.AtomSel sel argument.
removeTagAtoms2(sel) - remove the atoms in atomSel2 as specified in the
atomSel.AtomSel sel argument.
tagEnv() - return the TagEnvironment object.
pairDist() - the pairDist.PairDist object used to compute the Pr(r).
The weights used in pairDist's computation of Pr(r) are
(normalized) values of iWeights1 * distanceWeights1 and
iWeights2 * distanceWeights2.
Associated short-cut methods, returning methods from pairDist():
rVals() - return the r,Pr values associated with
Pr() - the distance probability distribution.
atomSel1() - AtomSel objects describing the two sets of rotamers.
atomSel2()
class TagEnvironment describes rotamer tags and the environment with which
they interact. This class is instantiated in deerPot.DEERPot and
tagPairPot.TagPairPot.
Members:
radii - array of radii, one for each atom in simulation()
Methods:
nonTagSelection() - return atomSel.AtomSel corresponding to the
nonTagSel argument given when the object was created.
printNeighborList() - print neighbors of all tagAtoms. These neighbors will
be come from nonTagSelection, specified
rValues(minR=-1, - return an array of distances starting at minR, ending
maxR=-1, at maxR, with spacing of deltaR. If a negative value
deltaR=-1) is given, the object default values (below) are used.
maxRadius() - the maximum of tagRadii and radii
simulation() - the simulation.Simulation of nonTagSelection()
addTagAtoms(sel) - add the atoms specified as a atomSel.AtomSel in
the argument as tag atoms. This requries that
setTagRadii has been called previously for all atom
in sel.
tagAtoms() - return a list of all atoms added via addTagAtoms().
setRadii(radii) - set radii, one for each atom in simulation()
setTagRadii(resname, - set the radius for one tag atom specified by residue
atomName, name resname and atomName to val.
val)
tagRadius(resname, - return the the radius set for the atom specified by
atomName) resname and AtomName.
Accessors:
The quantities below may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
moveTol - threshold triggering regeneration of neighbors of
tagAtoms: if any atom moves more (in Agstroms) than
moveTol, neighbors are recomputed.
distanceSigmoidWidth - width used to control how quickly distance weights
change from 1 to 0 when there is overlap between
tagAtom and nonTagSelection [3 Angstrom].
absoluteWeights - force all product weights to be positive [True].
numClosestAtoms - number of atoms to use in computation of distance
weight [3].
minR - default values (in Angstroms) for [15]
maxR creation of [100]
deltaR the distance array. [0.5]
verbose - toggle verbose output [False]
Static Functions:
distanceWeight(dist, - return the distance weight function
radius1, with the given parameters
radius2,
distanceSigmoidWidth)
d_distanceWeight(dist, - return the derivative of the
radius1, distanceWeight function.
radius2,
distanceSigmoidWidth)
# 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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