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- RestraintEntry
- RestraintStats
- TermEntry
class RestraintStats |
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Methods defined here:
- __init__(s)
reset all counters.
- accumulate(s, potList)
for each restraint in each potential term, determine whether it is violated
and update counters.
call this routine once for each structure
this processes energy terms with a restraints() method, and also
handled nonbonded interactions as a special case.
- summarizeExtraQuantities(s)
return a string with statistics for extra quantities for supported
potential terms.
- summarizeTerms(s)
return a string with statistics for each accumulated potential term
- summarizeViolations(s, cutoff=0)
summarize violation statistics for all accumulated potential terms.
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.
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class TermEntry |
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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)
return tuple of mean and std dev of energy of this term for all
accumulated structures.
- extraStatsAveDev(s, name)
return tuple of mean and std dev of the corresponding quatity
for all accumulated structures.
- recordViolation(s, index, v)
- rmsdAveDev(s)
return tuple of mean and std dev rmsd of this term for all
accumulated structures.
- violationsAveDev(s)
return tuple of mean and std dev number of violations for this
term for all accumulated structures.
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