Tools to aid in reporting on and analyzing pot.Pot terms

Classes
		builtins.tuple(builtins.object) TermEntry   AnalyzeTermEntry = class TermEntry(builtins.tuple)     AnalyzeTermEntry(func, title, prefix, moduleName, doc)   TermEntry(func, title, prefix, moduleName, doc)     Method resolution order: TermEntry builtins.tuple builtins.object Methods defined here: __getnewargs__(self) Return self as a plain tuple.  Used by copy and pickle. __repr__(self) Return a nicely formatted representation string _asdict(self) Return a new dict which maps field names to their values. _replace(self, /, **kwds) Return a new TermEntry object replacing specified fields with new values Class methods defined here: _make(iterable) from builtins.type Make a new TermEntry object from a sequence or iterable Static methods defined here: __new__(_cls, func, title, prefix, moduleName, doc) Create new instance of TermEntry(func, title, prefix, moduleName, doc) Data descriptors defined here: func   Alias for field number 0 title   Alias for field number 1 prefix   Alias for field number 2 moduleName   Alias for field number 3 doc   Alias for field number 4 Data and other attributes defined here: __match_args__ = ('func', 'title', 'prefix', 'moduleName', 'doc') _field_defaults = {} _fields = ('func', 'title', 'prefix', 'moduleName', 'doc') Methods inherited from builtins.tuple: __add__(self, value, /) Return self+value. __contains__(self, key, /) Return key in self. __eq__(self, value, /) Return self==value. __ge__(self, value, /) Return self>=value. __getattribute__(self, name, /) Return getattr(self, name). __getitem__(self, key, /) Return self[key]. __gt__(self, value, /) Return self>value. __hash__(self, /) Return hash(self). __iter__(self, /) Implement iter(self). __le__(self, value, /) Return self<=value. __len__(self, /) Return len(self). __lt__(self, value, /) Return self<value. __mul__(self, value, /) Return self*value. __ne__(self, value, /) Return self!=value. __rmul__(self, value, /) Return value*self. count(self, value, /) Return number of occurrences of value. index(self, value, start=0, stop=9223372036854775807, /) Return first index of value.   Raises ValueError if the value is not present. Class methods inherited from builtins.tuple: __class_getitem__(...) from builtins.type See PEP 585

Functions
		analyze(potList, extraTerms=<potList.PotList; proxy of <Swig Object of type 'rc_DerivedPot< PotList > *' at 0x7f4947b26940> >, outFilename=0) pretty print appropriate terms from the given PotList and return them in a remarks string. The optional extraTerms is a PotList of terms which do not contribute to the total energy, but which should be analyzed all the same- use this for cross-validated potential terms. The potList and extraTerms arguments can have type of Pot, PotList, list or tuple.   If outFilename is specified, the verbose violations info is written to the specified file. canonicalTermName(name) Return the registered term name given a string. Currently, this simply makes the term name search case insensitive. genHeaderHelp(term) Return reStructured text string for the specified term. getHeaderNames() getPotTerms(potList, names) return in a list all the potential terms in potList whose potType() matches names. names can be a string or a list of strings. loadRegisteringModules() Load all modules which call registerTerm- to populate the header help information. moduleName(termName) Return module name of associated term reduce(...) reduce(function, iterable[, initial]) -> value   Apply a function of two arguments cumulatively to the items of a sequence or iterable, from left to right, so as to reduce the iterable to a single value.  For example, reduce(lambda x, y: x+y, [1, 2, 3, 4, 5]) calculates ((((1+2)+3)+4)+5).  If initial is present, it is placed before the items of the iterable in the calculation, and serves as a default when the iterable is empty. registerExtraStats(potType, name, function, supportsList=False, precision=3) register extra terms, averages over selected structures will be reported by restraintStats.    The four arguments are the potential type as given by the potName accessor, the name of the property to be averaged (a string), a function to be called on the pot term, like this: function(term) and which returns a floating value, and whether this function supports a list of terms. The function argument can also return a list of float values, but in this case registerExtraStats should be called only a single time for each potType. The precision argument specifies number of digits after the decimal point printed in the .stats file. registerTerm(analyzeFunc, termTitle, termPrefix, termDoc) register an analysis function to be called by the analyze() function [see below].   One should specify an analysis function which takes a list of potential terms as an argument, and two strings to identify the potential term - long form, and short form, respectively.   The termDoc argument documents the output of the returned string - in reStructuredText. This string is produced by the headerHelp helper program.   analyzeFunc should return a string containing an analysis summary. A more detailed analysis can be printed to stdout. summarizePotentials(potList) get rms, violations summaries from potential terms xplorDocMarkupToRST(text) Convert Xplor-NIH-specific documentation markup to reStructuredText.   Converted tags include        <\m NAME> - creates a link for Xplor-NIH module named NAME        <\s NAME> - creates a link for Python module named NAME        <\l LINK NAME> - creates a link LINK with tag NAME

Data
		extraStats = {'DiffPot': [ExtraStatsInfo(name='Optimized Temperature, [K]'... 0x7f4947a4fe20>, supportsList=True, precision=3)], 'NOEPot': [ExtraStatsInfo(name='Corr.', function=<function ...0x7f4946776c00>, supportsList=False, precision=3)], 'PRE': [ExtraStatsInfo(name='Q-factor', function=<functi... 0x7f4947a61800>, supportsList=True, precision=3), ExtraStatsInfo(name='correlation', function=<fun... 0x7f4947a618a0>, supportsList=True, precision=3), ExtraStatsInfo(name='tau_c', function=<function ... 0x7f4947a62700>, supportsList=True, precision=3)], 'RDCPot1': [ExtraStatsInfo(name='R-fac', function=<function ...0x7f4947b15da0>, supportsList=False, precision=3), ExtraStatsInfo(name='R-infinite', function=<func...0x7f4947b15e40>, supportsList=False, precision=3), ExtraStatsInfo(name='Chi^2', function=<function ...0x7f4947b15f80>, supportsList=False, precision=3), ExtraStatsInfo(name='Correlation', function=<fun...0x7f4947b15d00>, supportsList=False, precision=3), ExtraStatsInfo(name='Da', function=<function Da at 0x7f4947b0f7e0>, supportsList=False, precision=3), ExtraStatsInfo(name='Rhombicity', function=<func...0x7f4947b0f880>, supportsList=False, precision=3)], 'SolnScatPot': [ExtraStatsInfo(name='Chi^2', function=<function ...0x7f49466a02c0>, supportsList=False, precision=3)], 'VarTensor': [ExtraStatsInfo(name='RDC R-fac', function=<funct...0x7f4947a4f2e0>, supportsList=False, precision=3), ExtraStatsInfo(name='RDC Chi^2', function=<funct...0x7f4947a4f380>, supportsList=False, precision=3)]} registeredTerms = [TermEntry(func=<function RDC_analyze at 0x7f4947...ficient between calculated and observed RDCs.\n"), TermEntry(func=<function analyze at 0x7f4947b29c...n different\n ensemble members.\n'), TermEntry(func=<function VarTensor_analyze at 0x...047 (1999).]\n\n\n '), TermEntry(func=<function analyze at 0x7f4947a4fd...xes," J. Am. Chem. Soc. 131, 9522-9531 (2009)\n'), TermEntry(func=<function analyze at 0x7f4947a61e...n J. Am. Chem. Soc. 126, 5879-5896 (2004).\n'), TermEntry(func=<function CSA_analyze at 0x7f4947...eholders not containing\nuseful information. \n'), TermEntry(func=<function analyze at 0x7f49467e1b... - the number of violated restraints.\n \n'), TermEntry(func=<function analyze at 0x7f49467754...between calculated and observed\nis reported.\n'), TermEntry(func=<function analyze at 0x7f4946776c...ion between calculated and observed distances\n'), TermEntry(func=<function analyze at 0x7f49466a01... of I_i.\n\n ')] registeringModules = ['anglePot', 'ccrPotTools', 'csaPotTools', 'cstMagTools', 'diffPotTools', 'distSymmTools', 'ensWeightsTools', 'globDiffPotTools', 'gyrPotTools', 'h3JNCPot', 'hbPotTools', 'hmxPotTools', 'jCoupPotTools', 'nbTargetPotTools', 'noePotTools', 'orderPotTools', 'posRMSDPotTools', 'planeDistTools', 'posDiffPotTools', 'prePotTools', ...]