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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
IMP.pmi.macros.AnalysisReplicaExchange0 Class Reference

A macro for running all the basic operations of analysis. More...

Inherits object.

Detailed Description

A macro for running all the basic operations of analysis.

Includes clustering, precision analysis, and making ensemble density maps. A number of plots are also supported.

Note
This class is only available in Python.

Definition at line 1404 of file macros.py.

Public Member Functions

def __init__
 Constructor. More...
 
def add_protocol_output
 Capture details of the modeling protocol. More...
 
def clustering
 Get the best scoring models, compute a distance matrix, cluster them, and create density maps. More...
 
def get_modeling_trajectory
 Get a trajectory of the modeling run, for generating demonstrative movies. More...
 

Constructor & Destructor Documentation

def IMP.pmi.macros.AnalysisReplicaExchange0.__init__ (   self,
  model,
  merge_directories = ['./'],
  stat_file_name_suffix = 'stat',
  best_pdb_name_suffix = 'model',
  do_clean_first = True,
  do_create_directories = True,
  global_output_directory = 'output/',
  replica_stat_file_suffix = 'stat_replica',
  global_analysis_result_directory = './analysis/',
  test_mode = False 
)

Constructor.

Parameters
modelThe IMP model
stat_file_name_suffix
merge_directoriesThe directories containing output files
best_pdb_name_suffix
do_clean_first
do_create_directories
global_output_directoryWhere everything is
replica_stat_file_suffix
global_analysis_result_directory
test_modeIf True, nothing is changed on disk

Definition at line 1416 of file macros.py.

Member Function Documentation

def IMP.pmi.macros.AnalysisReplicaExchange0.add_protocol_output (   self,
  p 
)

Capture details of the modeling protocol.

Parameters
pan instance of IMP.pmi.output.ProtocolOutput or a subclass.

Definition at line 1454 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange0.clustering (   self,
  score_key = 'SimplifiedModel_Total_Score_None',
  rmf_file_key = 'rmf_file',
  rmf_file_frame_key = 'rmf_frame_index',
  state_number = 0,
  prefiltervalue = None,
  feature_keys = [],
  outputdir = './',
  alignment_components = None,
  number_of_best_scoring_models = 10,
  rmsd_calculation_components = None,
  distance_matrix_file = 'distances.mat',
  load_distance_matrix_file = False,
  skip_clustering = False,
  number_of_clusters = 1,
  display_plot = False,
  exit_after_display = True,
  get_every = 1,
  first_and_last_frames = None,
  density_custom_ranges = None,
  write_pdb_with_centered_coordinates = False,
  voxel_size = 5.0 
)

Get the best scoring models, compute a distance matrix, cluster them, and create density maps.

Tuple format: "molname" just the molecule, or (start,stop,molname,copy_num(optional),state_num(optional) Can pass None for copy or state to ignore that field. If you don't pass a specific copy number

Parameters
score_keyThe score for ranking models. Use "Total_Score" instead of default for PMI2.
rmf_file_keyKey pointing to RMF filename
rmf_file_frame_keyKey pointing to RMF frame number
state_numberState number to analyze
prefiltervalueOnly include frames where the score key is below this value
feature_keysKeywords for which you want to calculate average, medians, etc. If you pass "Keyname" it'll include everything that matches "*Keyname*"
outputdirThe local output directory used in the run
alignment_componentsDictionary with keys=groupname, values are tuples for aligning the structures e.g. {"Rpb1": (20,100,"Rpb1"),"Rpb2":"Rpb2"}
number_of_best_scoring_modelsNum models to keep per run
rmsd_calculation_componentsFor calculating RMSD (same format as alignment_components)
distance_matrix_fileWhere to store/read the distance matrix
load_distance_matrix_fileTry to load the distance matrix file
skip_clusteringJust extract the best scoring models and save the pdbs
number_of_clustersNumber of k-means clusters
display_plotDisplay the distance matrix
exit_after_displayExit after displaying distance matrix
get_everyExtract every nth frame
first_and_last_framesA tuple with the first and last frames to be analyzed. Values are percentages! Default: get all frames
density_custom_rangesFor density calculation (same format as alignment_components)
write_pdb_with_centered_coordinates
voxel_sizeUsed for the density output

Definition at line 1546 of file macros.py.

def IMP.pmi.macros.AnalysisReplicaExchange0.get_modeling_trajectory (   self,
  score_key = 'SimplifiedModel_Total_Score_None',
  rmf_file_key = 'rmf_file',
  rmf_file_frame_key = 'rmf_frame_index',
  outputdir = './',
  get_every = 1,
  nframes_trajectory = 10000 
)

Get a trajectory of the modeling run, for generating demonstrative movies.

Parameters
score_keyThe score for ranking models
rmf_file_keyKey pointing to RMF filename
rmf_file_frame_keyKey pointing to RMF frame number
outputdirThe local output directory used in the run
get_everyExtract every nth frame
nframes_trajectoryTotal number of frames of the trajectory

Definition at line 1463 of file macros.py.


The documentation for this class was generated from the following file: