IMP Reference Guide
develop.a3ebfe92e8,2023/01/27
The Integrative Modeling Platform

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 23 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 

) 
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 88 of file Statistics.py.
def IMP.isd.Statistics.Statistics.add_coordinates  (  self,  
key,  
name,  
format = 'raw' , 

append = True , 

extension = 'pdb' , 

hierarchies = None , 

restraints = None 

) 
adds a placeholder for coordinates
Definition at line 151 of file Statistics.py.
def IMP.isd.Statistics.Statistics.add_entry  (  self,  
key,  
name = None , 

entry = None 

) 
add an entry for the statistics file
Definition at line 109 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 188 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 136 of file Statistics.py.
def IMP.isd.Statistics.Statistics.update_coordinates  (  self,  
key,  
name,  
value = True 

) 
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 176 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 254 of file Statistics.py.