IMP logo
IMP Reference Guide  develop.cc86c9801d,2022/11/22
The Integrative Modeling Platform
IMP.pmi1.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.

Deprecated:
As of IMP release 2.8. See the IMP Deprecation Policy for more information about deprecation in IMP. Use AnalysisReplicaExchange instead
Note
This class is only available in Python.

Definition at line 1269 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.pmi1.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 1281 of file /macros.py.

Member Function Documentation

def IMP.pmi1.macros.AnalysisReplicaExchange0.add_protocol_output (   self,
  p 
)

Capture details of the modeling protocol.

Parameters
pan instance of IMP.pmi1.output.ProtocolOutput or a subclass.

Definition at line 1320 of file /macros.py.

def IMP.pmi1.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 1412 of file /macros.py.

def IMP.pmi1.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 1329 of file /macros.py.


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