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IMP Reference Guide
2.10.1
The Integrative Modeling Platform
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A macro to help setup and run replica exchange. More...
Inherits object.
A macro to help setup and run replica exchange.
Supports Monte Carlo and molecular dynamics. Produces trajectory RMF files, best PDB structures, and output stat files.
Public Member Functions | |
| def | __init__ |
| Constructor. More... | |
| def IMP.pmi.macros.ReplicaExchange0.__init__ | ( | self, | |
| model, | |||
representation = None, |
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root_hier = None, |
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sample_objects = None, |
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monte_carlo_sample_objects = None, |
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molecular_dynamics_sample_objects = None, |
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output_objects = [], |
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rmf_output_objects = None, |
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crosslink_restraints = None, |
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monte_carlo_temperature = 1.0, |
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simulated_annealing = False, |
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simulated_annealing_minimum_temperature = 1.0, |
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simulated_annealing_maximum_temperature = 2.5, |
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simulated_annealing_minimum_temperature_nframes = 100, |
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simulated_annealing_maximum_temperature_nframes = 100, |
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replica_exchange_minimum_temperature = 1.0, |
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replica_exchange_maximum_temperature = 2.5, |
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replica_exchange_swap = True, |
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num_sample_rounds = 1, |
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number_of_best_scoring_models = 500, |
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monte_carlo_steps = 10, |
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self_adaptive = False, |
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molecular_dynamics_steps = 10, |
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molecular_dynamics_max_time_step = 1.0, |
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number_of_frames = 1000, |
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save_coordinates_mode = 'lowest_temperature', |
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nframes_write_coordinates = 1, |
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write_initial_rmf = True, |
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initial_rmf_name_suffix = 'initial', |
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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 = './', |
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rmf_dir = 'rmfs/', |
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best_pdb_dir = 'pdbs/', |
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replica_stat_file_suffix = 'stat_replica', |
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em_object_for_rmf = None, |
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atomistic = False, |
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replica_exchange_object = None, |
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test_mode = False |
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| ) |
Constructor.
| model | The IMP model |
| representation | PMI.representation.Representation object (or list of them, for multi-state modeling) |
| root_hier | Instead of passing Representation, pass the System hierarchy |
| monte_carlo_sample_objects | Objects for MC sampling; a list of structural components (generally the representation) that will be moved and restraints with parameters that need to be sampled. For PMI2: just pass flat list of movers |
| molecular_dynamics_sample_objects | Objects for MD sampling For PMI2: just pass flat list of particles |
| output_objects | A list of structural objects and restraints that will be included in output (ie, statistics "stat" files). Any object that provides a get_output() method can be used here. If None is passed the macro will not write stat files. |
| rmf_output_objects | A list of structural objects and restraints that will be included in rmf. Any object that provides a get_output() method can be used here. |
| crosslink_restraints | List of cross-link restraints that will be included in output RMF files (for visualization). |
| monte_carlo_temperature | MC temp (may need to be optimized based on post-sampling analysis) |
| simulated_annealing | If True, perform simulated annealing |
| simulated_annealing_minimum_temperature | Should generally be the same as monte_carlo_temperature. |
| simulated_annealing_minimum_temperature_nframes | Number of frames to compute at minimum temperature. |
| simulated_annealing_maximum_temperature_nframes | Number of frames to compute at temps > simulated_annealing_maximum_temperature. |
| replica_exchange_minimum_temperature | Low temp for REX; should generally be the same as monte_carlo_temperature. |
| replica_exchange_maximum_temperature | High temp for REX |
| replica_exchange_swap | Boolean, enable disable temperature swap (Default=True) |
| num_sample_rounds | Number of rounds of MC/MD per cycle |
| number_of_best_scoring_models | Number of top-scoring PDB models to keep around for analysis |
| monte_carlo_steps | Number of MC steps per round |
| self_adaptive | self adaptive scheme for monte carlo movers |
| molecular_dynamics_steps | Number of MD steps per round |
| molecular_dynamics_max_time_step | Max time step for MD |
| number_of_frames | Number of REX frames to run |
| save_coordinates_mode | string: how to save coordinates. "lowest_temperature" (default) only the lowest temperatures is saved "25th_score" all replicas whose score is below the 25th percentile "50th_score" all replicas whose score is below the 50th percentile "75th_score" all replicas whose score is below the 75th percentile |
| nframes_write_coordinates | How often to write the coordinates of a frame |
| write_initial_rmf | Write the initial configuration |
| global_output_directory | Folder that will be created to house output. |
| test_mode | Set to True to avoid writing any files, just test one frame. |
