| distSymmPot |
index |
Potential term restraining distances expected to be symmetric. This is
approximately the same functionality as that of the XPLOR NOE SYMMetry
routine. The primary difference is that this term will correctly treat
<n ensembleSimulation>.EnsembleSimulation averaging.
Constructor:
It is suggested that this potential term be created using the helper
function distSymmTools.create_DistSymmPot().
DistSymmPot(instanceName, - creates a potential term with the given name.
simulation ) The simulation argument is optional- it omitted
simulation.defaultSimulation() will be used.
Methods:
addRestraint(listOfTuples) - list of two-membered tuples of atom
selections, each of which specifies a
distance which should be
restrained. E.g. for a dimer, the list
should contain two sets of distances.
rms() - returns a measure of RMSD of distance
symmetry violation (see below).
violations() - returns number of violated distance
symmetry restraints
numRestraints() - return the number of restraints
info() - current info about the state of this instance
showViolations() - return string containing pretty-printed info
on all violated restraints.
restraints() - return a list of restraints. See the description
of the Restraint class below.
ensWeigth(index) - return the ensemble weight associated with the
specified member.
setEnsWeights(vals) - use the specified ensemble weights instead of those
in the underlying EnsembleSimulation.
Read-Write accessors:
scale - scale factor (force constant) for the potential term.
ensembleAveType - "none" or "average" - controls whether to enforce
symmetry restraints on each ensemble member- or to
enforce only overall ensemble symmetry (see below).
threshold - amount of violation of restraint greater than which
the restraint is considered violated [0.2 angstrom]
showAllRestraints - boolean which changes the behavior of showViolations. If
this parameter is set to True, the behavior of
showViolations is modified such that all restraints are
printed. Violated restraints are indicated by an
asterisk in the first column. [False]
useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
or to use those of the underlying EnsembleSimulation.
the above quantities may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
class DistSymmPot_Restraint:
methods:
public:
energy() - return current energy
name() - restraint name (String)
raw members:
tol - error tolerance for this restraint
distAtom1 - list of lists of atoms. These contain atoms specified by
distAtom2 addRestraints.
contrib - array containing the contribution to energy from each ensemble
member
aveDistIntra - ave. dist. within an ensemble member
deltaIntra
aveDistInter - distance between atom1 in different ensemble members
deltaInter1
aveDistInter2 - distance between atom2 in different ensemble members
deltaInter2
The potential term is defined as
E = scale() * sum_r E_r
with
E_r being the contribution from each restraint.
For ensembleAveType="none", each restraint's energy is a sum over
contributions from each ensemble member i:
E_r = sum_i w_i ( ca_i + sum_i' w_i' (cr1_ii' + cr2_ii') ),
with w_i being the ensemble member's weight,
ca_i = < d_i^2 >_j - < d_i >_j^2 (averaged over all distances)
with d_ij = |q1_ij - q2_ij|
and q1_ij, the position of the atom corresponding to the first
selection of the jth entry in the restraint's distAtom1 in ensemble
member i.
cr1_ii' = < dr1_ii'^2 >_j - < dr1_ii' >_j^2
cr2_ii' = < dr2_ii'^2 >_j - < dr2_ii' >_j^2
with dr1_ii'j = |q1_ij - q2_i'j|
for ensembleAveType="average", distances are calculated using
ensemble-averaged positions:
E_r = ( <d^2>_k - <d>_k^2 - tol )
for <d^2>_k - <d>_k^2 > tol and zero otherwise.
The average distance is
<d>_k = 1/Nk sum_k |<q1_k>_e - <q2_k>_e|
and variance is
<d^2>_k = 1/Nk sum_k |<q1_k>_e - <q2_k>_e|^2
where the k-sums are over the restraint's distances, and <>_e denotes
ensemble average.
The RMSD is calculated as
sqrt( sum_r E_r / N_r )
where N_r is the number of restraints.
# 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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