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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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A macro for running all the basic operations of analysis. More...
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.
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.pmi.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 |
| def IMP.pmi.macros.AnalysisReplicaExchange0.add_protocol_output | ( | self, | |
| p | |||
| ) |
Capture details of the modeling protocol.
| p | an instance of IMP.pmi.output.ProtocolOutput or a subclass. |
| def IMP.pmi.macros.AnalysisReplicaExchange0.clustering | ( | self, | |
score_key = 'Total_Score', |
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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. |
| 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 |
| def IMP.pmi.macros.AnalysisReplicaExchange0.get_modeling_trajectory | ( | self, | |
score_key = 'Total_Score', |
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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.