IMP Reference Guide
2.20.2
The Integrative Modeling Platform
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A macro for running all the basic operations of analysis. More...
Inherits object.
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.
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... | |
def IMP.pmi1.macros.AnalysisReplicaExchange0.__init__ | ( | self, | |
model, | |||
merge_directories = ['./'] , |
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stat_file_name_suffix = 'stat' , |
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best_pdb_name_suffix = 'model' , |
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do_clean_first = True , |
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do_create_directories = True , |
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global_output_directory = 'output/' , |
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replica_stat_file_suffix = 'stat_replica' , |
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global_analysis_result_directory = './analysis/' , |
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test_mode = False |
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) |
Constructor.
model | The IMP model |
stat_file_name_suffix | |
merge_directories | The directories containing output files |
best_pdb_name_suffix | |
do_clean_first | |
do_create_directories | |
global_output_directory | Where everything is |
replica_stat_file_suffix | |
global_analysis_result_directory | |
test_mode | If True, nothing is changed on disk |
Definition at line 1281 of file /macros.py.
def IMP.pmi1.macros.AnalysisReplicaExchange0.add_protocol_output | ( | self, | |
p | |||
) |
Capture details of the modeling protocol.
p | an 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' , |
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rmf_file_key = 'rmf_file' , |
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rmf_file_frame_key = 'rmf_frame_index' , |
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state_number = 0 , |
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prefiltervalue = None , |
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feature_keys = [] , |
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outputdir = './' , |
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alignment_components = None , |
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number_of_best_scoring_models = 10 , |
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rmsd_calculation_components = None , |
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distance_matrix_file = 'distances.mat' , |
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load_distance_matrix_file = False , |
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skip_clustering = False , |
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number_of_clusters = 1 , |
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display_plot = False , |
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exit_after_display = True , |
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get_every = 1 , |
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first_and_last_frames = None , |
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density_custom_ranges = None , |
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write_pdb_with_centered_coordinates = False , |
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voxel_size = 5.0 |
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) |
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
score_key | The score for ranking models. Use "Total_Score" instead of default for PMI2. |
rmf_file_key | Key pointing to RMF filename |
rmf_file_frame_key | Key pointing to RMF frame number |
state_number | State number to analyze |
prefiltervalue | Only include frames where the score key is below this value |
feature_keys | Keywords for which you want to calculate average, medians, etc. If you pass "Keyname" it'll include everything that matches "*Keyname*" |
outputdir | The local output directory used in the run |
alignment_components | Dictionary with keys=groupname, values are tuples for aligning the structures e.g. {"Rpb1": (20,100,"Rpb1"),"Rpb2":"Rpb2"} |
number_of_best_scoring_models | Num models to keep per run |
rmsd_calculation_components | For calculating RMSD (same format as alignment_components) |
distance_matrix_file | Where to store/read the distance matrix |
load_distance_matrix_file | Try to load the distance matrix file |
skip_clustering | Just extract the best scoring models and save the pdbs |
number_of_clusters | Number of k-means clusters |
display_plot | Display the distance matrix |
exit_after_display | Exit after displaying distance matrix |
get_every | Extract every nth frame |
first_and_last_frames | A tuple with the first and last frames to be analyzed. Values are percentages! Default: get all frames |
density_custom_ranges | For density calculation (same format as alignment_components) |
write_pdb_with_centered_coordinates | |
voxel_size | Used 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' , |
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rmf_file_key = 'rmf_file' , |
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rmf_file_frame_key = 'rmf_frame_index' , |
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outputdir = './' , |
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get_every = 1 , |
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nframes_trajectory = 10000 |
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) |
Get a trajectory of the modeling run, for generating demonstrative movies.
score_key | The score for ranking models |
rmf_file_key | Key pointing to RMF filename |
rmf_file_frame_key | Key pointing to RMF frame number |
outputdir | The local output directory used in the run |
get_every | Extract every nth frame |
nframes_trajectory | Total number of frames of the trajectory |
Definition at line 1329 of file /macros.py.