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- builtins.object
-
- ExtraStats
- RestraintEntry
- RestraintStats
- TermEntry
class ExtraStats(builtins.object) |
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ExtraStats(extraStatsInfo)
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Methods defined here:
- __init__(s, extraStatsInfo)
- fun: function to call on each term
fun: whether this function supports a list of terms.
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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class RestraintEntry(builtins.object) |
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RestraintEntry(index, restraint)
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Methods defined here:
- __init__(s, index, restraint)
- Initialize self. See help(type(self)) for accurate signature.
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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class RestraintStats(builtins.object) |
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Methods defined here:
- __init__(s)
- reset all counters.
- accumulate(s, potList, structNum)
- for each restraint in each potential term, determine whether it is
violated and save per-structure info.
call this routine once for each structure
this processes energy terms with a restraints() method, and also
handled nonbonded interactions as a special case.
- collect(s, comm, structNums=None, deleteUnusedData=True)
- Collect accumulated restraint stats from remote processes into
process 0. While summarizeTerms is called from process 0, collect
should be called directly from other processes. If deleteUnusedData
is True, data corresponding to structures not in the StructNums list
will be deleted, thus modifying the RestraintStats object.
- summarizeExtraQuantities(s, structNums=None)
- Return a string with statistics for extra quantities for supported
potential terms for the specified structures (all accumulated
structures if structNums is None).
- summarizeTerms(s, comm, structNums=None)
- Return a string with statistics for the accumulated potential term for
structures specified by structNums (all accumulated structures if
structNum=None).
When summarizeTerms is called by process 0, collect must be called by
all other processes.
- summarizeViolations(s, structNums=None, cutoff=0)
- Summarize violation statistics for all potential terms for
structures specified by structNums (all accumulated structures if
structNum=None).
A string is returned reporting violated restraints, sorted from most
violated to least. The cutoff argument can be used to specify the
fraction of violated structures below which to stop printing violated
restraints.
In the returned string is the percentage of structures violated,
the average restraint rmsd (for violated structures), the index of the
restraint, and an identifying name.
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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class TermEntry(builtins.object) |
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TermEntry(term, isSubTerm)
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Methods defined here:
- __init__(s, term, isSubTerm)
- term is a Pot.
isSubTerm denotes whether the term is a member of the toplevel PotList,
or a member of a lower-level PotList.
- energyAveDev(s, structNums=None)
- return tuple of mean and std dev of energy of this term for
structures in structNums.
- extraStatsAveDev(s, name, structNums=None)
- return tuple of mean and std dev of the corresponding quatity
for structures in structNums.
- rmsdAveDev(s, structNums=None)
- return tuple of mean and std dev rmsd of this term for
structures in structNums.
- violationsAveDev(s, structNums=None)
- return tuple of mean and std dev number of violations for
structures in structNums.
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
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