atesa.tests package

Submodules

atesa.tests.test_information_error module

Unit and regression test for information_error.py.

class atesa.tests.test_information_error.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of class

test_main()

Tests information_error.main using sham shooting points in test_data

atesa.tests.test_jobtype module

Unit and regression test for jobtype.py.

class atesa.tests.test_jobtype.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of each method

test_algorithm_aimless_shooting_init()

Tests algorithm with job_type = ‘aimless_shooting’ and thread.current_type = [‘init’]

test_algorithm_aimless_shooting_prod_accepted()

Tests algorithm with job_type = ‘aimless_shooting’ and thread.current_type = [‘prod’, ‘prod’] for an accepted move

test_algorithm_aimless_shooting_prod_always_new_not_accepted()

Tests algorithm with job_type = ‘aimless_shooting’, always_new = True and thread.current_type = [‘prod’, ‘prod’] for a move that isn’t accepted

test_algorithm_aimless_shooting_prod_not_always_new_not_accepted()

Tests algorithm with job_type = ‘aimless_shooting’, always_new = False and thread.current_type = [‘prod’, ‘prod’] for a move that isn’t accepted

test_algorithm_equilibrium_path_sampling_init()

Tests algorithm with job_type = ‘equilibrium_path_sampling’ and thread.current_type = [‘init’]

test_algorithm_equilibrium_path_sampling_prod_accepted()

Tests algorithm with job_type = ‘equilibrium_path_sampling’ and thread.current_type = [‘prod’, ‘prod’] for an accepted move

test_algorithm_equilibrium_path_sampling_prod_not_accepted()

Tests algorithm with job_type = ‘equilibrium_path_sampling’ and thread.current_type = [‘prod’, ‘prod’] for a move that isn’t accepted

test_algorithm_equilibrium_path_sampling_prod_not_accepted_no_accepted_yet()

Tests algorithm with job_type = ‘equilibrium_path_sampling’ and thread.current_type = [‘prod’, ‘prod’] for a move that isn’t accepted and with no accepted moves in the thread’s history

test_check_for_successful_step_aimless_shooting_init()

Tests check_for_successful_step with job_type = ‘aimless_shooting’ and thread.current_type = [‘init’]

test_check_for_successful_step_aimless_shooting_prod()

Tests check_for_successful_step with job_type = ‘aimless_shooting’ and thread.current_type = [‘prod’, ‘prod’]

test_check_for_successful_step_committor_analysis()

Tests check_for_successful_step with job_type = ‘committor_analysis’

test_check_for_successful_step_equilibrium_path_sampling()

Tests check_for_successful_step with job_type = ‘equilibrium_path_sampling’

test_check_termination_aimless_shooting_init()

Tests check_termination with job_type = ‘aimless_shooting’ and thread.current_type = [‘init’]

test_check_termination_aimless_shooting_prod()

Tests check_termination with job_type = ‘aimless_shooting’ and thread.current_type = [‘prod’, ‘prod’]

test_check_termination_committor_analysis()

Tests check_termination with job_type = ‘committor_analysis’

test_check_termination_equilibrium_path_sampling_global()

Tests check_termination global criterion with job_type = ‘equilibrium_path_sampling’

test_check_termination_equilibrium_path_sampling_thread()

Tests check_termination thread criterion with job_type = ‘equilibrium_path_sampling’

test_gatekeep_aimless_shooting()

Tests gatekeep with job_type = ‘aimless_shooting’

test_gatekeep_committor_analysis()

Tests gatekeep with job_type = ‘committor_analysis’

test_gatekeep_equilibrium_path_sampling()

Tests gatekeep with job_type = ‘committor_analysis’

test_get_batch_file_aimless_shooting_amber()

Tests thread.get_batch_template with job_type = ‘aimless_shooting’ and md_engine = ‘amber’

test_get_batch_file_aimless_shooting_broken()

Tests thread.get_batch_template with job_type = ‘aimless_shooting’ and invalid type = ‘fwdd’

test_get_batch_file_equilibrium_path_sampling_amber()

Tests thread.get_batch_template with job_type = ‘equilibrium_path_sampling’ and md_engine = ‘amber’

test_get_batch_file_equilibrium_path_sampling_broken()

Tests thread.get_batch_template with job_type = ‘equilibrium_path_sampling’ and invalid type = ‘fwdd’

test_get_batch_template_committor_analysis()

Tests get_batch_template with job_type = ‘committor_analysis’

test_get_initial_coordinates_aimless_shooting()

Tests get_initial_coordinates with job_type = ‘aimless_shooting’

test_get_initial_coordinates_committor_analysis_rc_out()

Tests get_initial_coordinates with job_type = ‘committor_analysis’ using an RC out file

test_get_initial_coordinates_committor_analysis_rc_out_does_not_exist()

Tests get_initial_coordinates with job_type = ‘committor_analysis’ using an RC out file that does not exist

test_get_initial_coordinates_committor_analysis_rc_out_no_shooting_points()

Tests get_initial_coordinates with job_type = ‘committor_analysis’ using an RC out file containing no shooting points within the threshold

test_get_initial_coordinates_equilibrium_path_sampling()

Tests get_initial_coordinates with job_type = ‘equilibrium_path_sampling’

test_get_inpcrd_aimless_shooting_init()

Tests get_inpcrd with job_type = ‘aimless_shooting’ and thread.current_type = [‘init’]

test_get_inpcrd_aimless_shooting_prod()

Tests get_inpcrd with job_type = ‘aimless_shooting’ and thread.current_type = [‘prod’, ‘prod’]

test_get_inpcrd_committor_analysis()

Tests get_inpcrd with job_type = ‘committor_analysis’

test_get_inpcrd_equilibrium_path_sampling()

Tests get_inpcrd with job_type = ‘equilibrium_path_sampling’

test_get_input_file_aimless_shooting()

Tests get_input_file with job_type = ‘aimless_shooting’

test_get_input_file_committor_analysis()

Tests get_input_file with job_type = ‘committor_analysis’

test_get_input_file_equilibrium_path_sampling()

Tests get_input_file with job_type = ‘equilibrium_path_sampling’

test_get_input_file_rxncor_umbrella_sampling()

Tests get_input_file with job_type = ‘umbrella_sampling’

test_get_next_step_aimless_shooting_init()

Tests thread.get_next_step with job_type = ‘aimless_shooting’ and type = [‘init’]

test_get_next_step_aimless_shooting_prod()

Tests thread.get_next_step with job_type = ‘aimless_shooting’ and type = [‘fwd’,’bwd’]

test_get_next_step_committor_analysis()

Tests get_next_step with job_type = ‘committor_analysis’

test_get_next_step_equilibrium_path_sampling_first()

Tests get_next_step with job_type = ‘equilibrium_path_sampling’ and an empty current_type

test_get_next_step_equilibrium_path_sampling_init()

Tests get_next_step with job_type = ‘equilibrium_path_sampling’ and current_type = [‘init’]

test_get_next_step_equilibrium_path_sampling_prod()

Tests get_next_step with job_type = ‘equilibrium_path_sampling’ and current_type = [‘prod’, ‘prod’]

test_update_history_aimless_shooting_init()

Tests update_history with job_type = ‘aimless_shooting’ and thread.current_type = [‘init’]

test_update_history_aimless_shooting_prod()

Tests update_history with job_type = ‘aimless_shooting’ and thread.current_type = [‘prod’, ‘prod’]

test_update_history_committor_analysis()

Tests update_history with job_type = ‘committor_analysis’

test_update_history_equilibrium_path_sampling_init()

Tests update_history with job_type = ‘equilibrium_path_sampling’ with current_type = [‘init’]

test_update_history_equilibrium_path_sampling_out_of_bounds()

Tests update_history with job_type = ‘equilibrium_path_sampling’ with an initially out-of-bounds RC value

test_update_history_equilibrium_path_sampling_prod()

Tests update_history with job_type = ‘equilibrium_path_sampling’ with current_type = [‘prod’, ‘prod’]

test_update_results_aimless_shooting_init()

Tests update_results with job_type = ‘aimless_shooting’ and thread.current_type = [‘init’]

test_update_results_aimless_shooting_prod()

Tests update_results with job_type = ‘aimless_shooting’ and thread.current_type = [‘prod’, ‘prod’]

test_update_results_committor_analysis()

Tests update_results with job_type = ‘committor_analysis’

test_update_results_equilibrium_path_sampling()

Tests update_results with job_type = ‘equilibrium_path_sampling’

atesa.tests.test_jobtype.config_equilibrium_path_sampling()

Sets up configuration settings for equilibrium path sampling tests, to be overwritten as needed

atesa.tests.test_lmax module

Unit and regression test for lmax.py.

class atesa.tests.test_lmax.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of class

test_main_improper_input()

Tests main using an input file that does exist, but is improperly formatted

test_main_k_and_f()

Tests main using k and f

test_main_k_f_and_p()

Tests main using k and f

test_main_k_f_and_q()

Tests main using k, f, and q

test_main_non_existent_input()

Tests main using an input file name that does not exist

test_main_running()

Tests main using running

test_main_two_line_test()

Tests main using two_line_test

test_objective_function()

Tests objective_function using dummy data

test_two_line_test()

Tests two_line_test using dummy data

atesa.tests.test_lmax_temp module

atesa.tests.test_main module

Unit and regression test for the atesa_v2 package.

class atesa.tests.test_main.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of each method

test_atesa_v2_imported()

Sample test, will always pass so long as import statement worked

test_configure_broken()

Tests configure.py with a non-existent file

test_configure_directory()

Tests configure.py behavior in correcting an improperly formatted directory

test_import_cvs()

Tests importing CVs and commitment definitions from a given settings.pkl file

test_init_threads_new()

Tests successful initialization of new threads

test_init_threads_restart()

Tests successful initialization of restarted threads

test_main()

Tests main.main with DEBUG = True to skip actual job submission/monitoring

test_thread_get_frame_amber()

Tests thread.get_frame method with md_engine = ‘amber’ and frame = -1

atesa.tests.test_process module

Unit and regression test for process.py.

class atesa.tests.test_process.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of class

test_process_to_be_terminated()

Tests process.py for a thread with terminated = True

test_process_to_submit()

Tests process.py for a thread that should be submitted

atesa.tests.test_rc_eval module

Unit and regression test for utilities.py.

class atesa.tests.test_rc_eval.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of class

test_extrema_mdtraj()

Tests rc_eval.main with extrema=True using sham shooting points in test_data and pytraj cvs

test_extrema_pytraj()

Tests rc_eval.main with extrema=True using sham shooting points in test_data and pytraj cvs

test_main_mdtraj()

Tests rc_eval.main using sham shooting points in test_data and mdtraj cvs

test_main_pytraj()

Tests rc_eval.main using sham shooting points in test_data and pytraj cvs

atesa.tests.test_utilities module

Unit and regression test for utilities.py.

class atesa.tests.test_utilities.Tests

Bases: object

setup_method(test_method)

classmethod teardown_method(method)

Runs at end of class

test_check_commit_bwd()

Tests check_commit using a dummy coordinate file and commitments defined to get result ‘bwd’

test_check_commit_fwd()

Tests check_commit using a dummy coordinate file and commitments defined to get result ‘fwd’

test_check_commit_none()

Tests check_commit using a dummy coordinate file and commitments defined to get result ‘’

test_check_commit_traj()

Tests check_commit using a dummy trajectory file and commitments defined to get result ‘fwd’

test_check_commit_value_errors()

Tests check_commit using a dummy coordinate file and commitments defined to get ValueErrors

test_evaluate_rc()

Tests evaluate_rc

test_get_cvs_no_qdot()

Tests get_cvs with a dummy coordinate file and include_qdot = False

test_get_cvs_no_qdot_reduce()

Tests get_cvs with a dummy coordinate file, include_qdot = False, and reduce = True

test_get_cvs_with_qdot()

Tests get_cvs with a dummy coordinate file, include_qdot = True, and a coordinate file with velocities

test_get_cvs_with_qdot_broken()

Tests get_cvs with a dummy coordinate file, include_qdot = True, and a coordinate file without velocities

test_interpret_cv()

Test interpret_cv for a distance, angle, dihedral, and difference of distances for both pytraj and mdtraj

test_resample()

Tests resample

test_rev_vels()

Tests rev_vels by comparing to a known-correct file

Module contents

This is the docstring for an empty init file, to support testing packages besides PyTest such as Nose that may look for such a file