cstMagPot |
index |
potential term to refine against chemical shift tensor magnitudes.
This term is normally constructed using the helper function
cstMagTools.create_CSTMagPot.
constructor: CSTMagPot(instanceName,
angle1Vals,
angle2Vals,
surf1Vals,
surf2Vals,
surf3Vals,
simulation=0)
instanceName is a user-specified identifier
angle1Vals and angle2Vals are sequences of angle values defining a grid
on which three tensor magnitudes s11, s22 and s33 are specified.
surf1Vals, surf2Vals and surf3Vals are these surface values in
cdsMatrix.CDSMatrix_double objects.
simulation is an optional simulation.Simulation specification
[it defaults to the current Simulation.]
methods
addRestraints(restraintString) - add the specified restraints specified in
the given string. See below for restraint
assignment syntax.
calcEnergy() - calc energy, returns the energy value.
calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value.
rms() - return the restraint rms violation
numRestraints() - return the numbder of restraints defined for this term.
violations() - return number of violations
restraints() - return a list of restraints. See the description of the
CSTMag_Restraint class below.
info() - current info about the state of this instance
showRestraints(violated) - return info on restraints. Argument violated is
boolean specifying whether to return only
violated restraints.
showViolations() - return string containing pretty-printed info
on all violated restraints.
simulation() - return the associated simulation.
The following parameters can be set [defaults in square brackets]
verbose - if true, sporadically spit out info [False]
scale - scale factor [1]
cstOffset - offset added to all surfaces [0]
cstScale - scale factor applied to all surfaces [1]
cstWeights - weighting in the energy calculation of each surface contribution
[ (1,1,1) ]
threshold - threshold in violation calculation [0.5]
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]
the above quantities may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
The following raw members can be accessed:
angle1Vals - values of angles on the grid
angle2Vals returned as a list.
surf1 - the three surfaces representations corresponding to
surf2 s11, s22 and s33.
surf3 These are spline.Spline2D objects.
The energy function for each restraint is defined as
scale * (w1 * (s11-s11_obs)^2 +
w2 * (s22-s22_obs)^2 +
w3 * (s33-s33_obs)^2 )
where w1-3 are weights specified by cstWeights. s11, s22 and s33 are
calculated from the two associated dihedral phi1 and phi2 angles via
s11 = cstScale * surf1(phi1,phi2) + cstOffset
surf1 is interpolated from the input surface grid values.
The restraint table format consists of pairs of specifications.
NAME <string>
ASSIgn (selection1A) (selection1B) (selection1C) (selection1D)
(selection2A) (selection2B) (selection2C) (selection2D)
<s11_obs> <s22_obs> <s33_obs> ! optional comment
The name statement specifies the name for the following assignment. If
it is omitted, a numerical name is generated.
The two sets of four atom selections in the ASSIgn statement specify
two dihedral angles. This statement can be split across muliple lines,
but the comment, if specified, should be on the same line as s33_obs.
CSTMag_Restraint class
methods:
name() - the restraint name
comment() - the restraint comment (entered after the ! in the ASSIgn
statement)
energy() - the energy associated with this restraint.
raw members:
phi1 - dihedral.Dihedral objects representing the two
phi2 dihedral angles
vphi1 - values of these angles from the most recent energy calculation
vphi2
calcd1 - calculated surface values
calcd2
calcd3
obs1 - observed surface values as input via the ASSIgn statement
obs2 in the restraint table.
obs3
# 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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