apotential term appropriate for ambiguous NOEs constructor: NOEPot(instanceName, restraintList, sim1,sim2) instanceName is a user-specified identifier sim1, and sim2 are optional .Simulation specifications [they default to the current Simulation.] restraintList is an optional XPLOR-style restraint table (string). Appropriate ensemble averaging will be performed if the sim1 argument is an .EnsembleSimulation. methods addRestraints(restraintList) - add the specified XPLOR-style restraints 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 deviation() - return average deviation from the mean over ensemble. This is zero unless an with size greater than one is specified. devationSpread() - return the average devation spread over ensemble. restraints() - return a list of restraints. See the description of the 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. The following parameters can be set [defaults in square brackets] nMono - number of monomers [1] verbose - if true, sporadically spit out info [False] scale - scale factor [1] aveExp - exponential to use in sum averaging [6] dOffset - potential offset [0] hardExp - exponential in hard region of potential [2] rSwitch - distance at which to switch from hard form [0.5] softExp - exponential in soft region of potential [1] asympSlope - slope in linear asymptotic region of pot [1] threshold - threshold in violation calculation [0.5] potType - type of potential: "soft" or "hard" [hard] aveType - type of restraint averaging: "average", "center" or "sum" [sum] 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 energy function is defined as if potType=hard or potType=soft and rrSwitch: scale * (a + b / r^softExp + asympSlope * r) if popType=log: scale * log( r / cdist ) see W. Rieping, M. Habeck, and M. Nilges. Modeling errors in NOE data with a lognormal distribution improves the quality of NMR structures. J. Am. Chem. Soc., 127, 16026-16027 (2005). where b = rSwitch^(softExp+1) * (asympSlope - hardExp * rSwitch^(hardExp-1)) / softExp a = rSwitch^hardExp - b * rSwitch^(-softExp) - asympSlope * rSwitch; The distance r is related to the calcualted restraint distance d by: if d < cdist - cMinus: r = cdist - cMinus - d if d > cdist+cPlus-dOffset: r = cdist - ( d + cPlus - dOffset ) otherwise, r = 0 The restraint distance d is calculated as for aveType=average: d = [ ] ^(-1/aveExp) where q_i is the position of the i-th atom, and Nij is the number of atom pairs in the sum. sum_pairs denotes sum over all selection pairs introduced using the ASSIgn ... OR syntax. Note carefully the angle brackets: they denote ensemble average. for aveType=sum: d = [ ] ^(-1/aveExp) where q_i is the position of the i-th atom. sum_pairs denotes sum over all selection pairs introduced using the ASSIgn ... OR syntax. Note carefully the angle brackets: they denote ensemble average. for aveType=center: d = | sum_i q_i /N_1 - sum_j q_j /N_2 | where the sums are over the two selections listed in the restraint, and N_1, N_2 are the number of atoms in these selections. Center averaging ignores additional selection pairs introduced using the ASSIgn ... OR syntax: only the first pair is used in calculation of the average positions. XPLOR NOE restraint table format: ASSIgn (selection1) (selection2) ! optional comment [OR (selection1) (selection2)] ... The statement can be split across muliple lines, but the comment, if specified, should be on the same line at cPlus. The OR keyword introduces additional selection pairs. Restraint class members/methods: name() - the restraint name comment() - the restraint comment (entered after the ! in the NOE table) sel1 - an .AtomSel corresponding to the first selection in the restraint table. This member is identical to selPairs()[0].a sel2 - an .AtomSel corresponding to the second selection in the restraint table. This member is identical to selPairs()[0].a selPairs()- a list of selection pairs, accessed through members a and b. The first pair corresponds to (sel1, sel2), with additional pairs correspond to those introduced using ASSIgn ... OR assignment statements. d() - the observed radius from the restraint table dPlus() - the upper bound as listed in the restraint table dMinus() - the lower bound as listed in the restraint table dist() - the calculated average distance asString() - a string representation of the restraint. variance - variance in dist among an .EnsembleSimulation set of structures.