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IMP Reference Guide
2.20.1
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.
Definition at line 54 of file /macros.py.
Public Member Functions | |
| def | __init__ |
| Constructor. More... | |
| def IMP.pmi1.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. |
Definition at line 110 of file /macros.py.