IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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Statistics gathering and printing class for ISD gibbs sampling. More...
Statistics gathering and printing class for ISD gibbs sampling.
Also manages the restart file (TODO).
TODO: check if everything was updated nicely
Definition at line 24 of file Statistics.py.
Public Member Functions | |
def | add_category |
creates a logging entry for a simulation substep of the gibbs sampler. More... | |
def | add_coordinates |
adds a placeholder for coordinates More... | |
def | add_entry |
add an entry for the statistics file More... | |
def | increment_counter |
increments the counter of category 'key' by 'value' steps. More... | |
def | update |
updates an entry and change its value to value More... | |
def | update_coordinates |
updates the coordinates of key:name entry. More... | |
def | write_stats |
Writes statistics to the stats file and writes/appends trajectories. More... | |
def IMP.isd.Statistics.Statistics.add_category | ( | self, | |
name = None |
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) |
creates a logging entry for a simulation substep of the gibbs sampler.
Each category has its own counter, initialized to zero. The global category does not need to be created, it's already created by the init method, and its key is 'global'.
Definition at line 89 of file Statistics.py.
def IMP.isd.Statistics.Statistics.add_coordinates | ( | self, | |
key, | |||
name, | |||
format = 'raw' , |
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append = True , |
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extension = 'pdb' , |
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hierarchies = None , |
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restraints = None |
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) |
adds a placeholder for coordinates
Definition at line 152 of file Statistics.py.
def IMP.isd.Statistics.Statistics.add_entry | ( | self, | |
key, | |||
name = None , |
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entry = None |
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) |
add an entry for the statistics file
Definition at line 110 of file Statistics.py.
def IMP.isd.Statistics.Statistics.increment_counter | ( | self, | |
key, | |||
value | |||
) |
increments the counter of category 'key' by 'value' steps.
Definition at line 189 of file Statistics.py.
def IMP.isd.Statistics.Statistics.update | ( | self, | |
key, | |||
name, | |||
value | |||
) |
updates an entry and change its value to value
Definition at line 137 of file Statistics.py.
def IMP.isd.Statistics.Statistics.update_coordinates | ( | self, | |
key, | |||
name, | |||
value = True |
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) |
updates the coordinates of key:name entry.
Format should match with the format specified at init time (raw or rmf3) note that setting value to None is equivalent to not calling this function
Definition at line 177 of file Statistics.py.
def IMP.isd.Statistics.Statistics.write_stats | ( | self | ) |
Writes statistics to the stats file and writes/appends trajectories.
Only does that if the global step matches the output rate. Trajectories are written more sparsely, see trajrate. Returns: True if data was written, False if not.
Definition at line 255 of file Statistics.py.