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IMP Reference Guide
develop.63b38c487d,2024/12/30
The Integrative Modeling Platform
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A macro to help setup and run replica exchange. More...
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.ReplicaExchange.__init__ | ( | self, | |
| model, | |||
| root_hier, | |||
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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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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mmcif = False, |
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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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score_moved = False, |
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use_nestor = False, |
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nestor_restraints = None, |
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nestor_rmf_fname_prefix = 'nested' |
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| ) |
Constructor.
| model | The IMP model |
| root_hier | Top-level (System)hierarchy |
| monte_carlo_sample_objects | Objects for MC sampling, which should generally be a simple list of Mover objects, e.g. from DegreesOfFreedom.get_movers(). |
| molecular_dynamics_sample_objects | Objects for MD sampling, which should generally be a simple 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. |
| 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/mmCIF models to keep around for analysis. |
| mmcif | If True, write best scoring models in mmCIF format; if False (the default), write in legacy PDB format. |
| best_pdb_dir | The directory under global_output_directory where best-scoring PDB/mmCIF files are written. |
| best_pdb_name_suffix | Part of the file name for best-scoring PDB/mmCIF files. |
| 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. |
| score_moved | If True, attempt to speed up Monte Carlo sampling by caching scoring function terms on particles that didn't move. |
| use_nestor | If True, follows the Nested Sampling workflow of the NestOR module and skips writing stat files and replica stat files. |
| nestor_restraints | A list of restraints for which likelihoods are to be computed for use by NestOR module. |
| nestor_rmf_fname_prefix | Prefix to be used for storing .rmf3 files generated by NestOR . |