IMP Reference Guide
develop.7cb8855c60,2024/10/08
The Integrative Modeling Platform
|
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 , |
|||
molecular_dynamics_sample_objects = None , |
|||
output_objects = [] , |
|||
rmf_output_objects = None , |
|||
monte_carlo_temperature = 1.0 , |
|||
simulated_annealing = False , |
|||
simulated_annealing_minimum_temperature = 1.0 , |
|||
simulated_annealing_maximum_temperature = 2.5 , |
|||
simulated_annealing_minimum_temperature_nframes = 100 , |
|||
simulated_annealing_maximum_temperature_nframes = 100 , |
|||
replica_exchange_minimum_temperature = 1.0 , |
|||
replica_exchange_maximum_temperature = 2.5 , |
|||
replica_exchange_swap = True , |
|||
num_sample_rounds = 1 , |
|||
number_of_best_scoring_models = 500 , |
|||
monte_carlo_steps = 10 , |
|||
self_adaptive = False , |
|||
molecular_dynamics_steps = 10 , |
|||
molecular_dynamics_max_time_step = 1.0 , |
|||
number_of_frames = 1000 , |
|||
save_coordinates_mode = 'lowest_temperature' , |
|||
nframes_write_coordinates = 1 , |
|||
write_initial_rmf = True , |
|||
initial_rmf_name_suffix = 'initial' , |
|||
stat_file_name_suffix = 'stat' , |
|||
best_pdb_name_suffix = 'model' , |
|||
mmcif = False , |
|||
do_clean_first = True , |
|||
do_create_directories = True , |
|||
global_output_directory = './' , |
|||
rmf_dir = 'rmfs/' , |
|||
best_pdb_dir = 'pdbs/' , |
|||
replica_stat_file_suffix = 'stat_replica' , |
|||
em_object_for_rmf = None , |
|||
atomistic = False , |
|||
replica_exchange_object = None , |
|||
test_mode = False , |
|||
score_moved = False , |
|||
use_nestor = False , |
|||
nestor_restraints = None , |
|||
nestor_rmf_fname_prefix = 'nested' |
|||
) |
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 . |