From b6a4f28944de64bf6d94623ce717f6394d3a0c21 Mon Sep 17 00:00:00 2001 From: Emilia PecoradeBarros Date: Wed, 9 Nov 2022 16:47:49 +0100 Subject: [PATCH] corrected spelling pertubation to be compatible with PyGromosV1.2 --- .../jobScheduling_scripts/MD_simulation_scheduler.py | 8 ++++---- .../jobScheduling_scripts/RE_EDS_simulation_scheduler.py | 8 ++++---- .../pipeline/jobScheduling_scripts/scheduler_functions.py | 2 +- .../simulation_workers/MD_simulation_run_worker.py | 4 ++-- .../simulation_workers/RE_EDS_simulation_run_worker.py | 4 ++-- reeds/function_libs/utils/argument_parser.py | 2 +- reeds/modules/do_RE_EDS_eoffEstimation.py | 2 +- reeds/modules/do_RE_EDS_eoffRebalancing.py | 2 +- reeds/modules/do_RE_EDS_findLowerBound.py | 2 +- reeds/modules/do_RE_EDS_generateOptimizedStates.py | 2 +- reeds/modules/do_RE_EDS_production.py | 2 +- reeds/modules/do_RE_EDS_sOptimisation.py | 2 +- 12 files changed, 20 insertions(+), 20 deletions(-) diff --git a/reeds/function_libs/pipeline/jobScheduling_scripts/MD_simulation_scheduler.py b/reeds/function_libs/pipeline/jobScheduling_scripts/MD_simulation_scheduler.py index b3369d88..d8f5f904 100644 --- a/reeds/function_libs/pipeline/jobScheduling_scripts/MD_simulation_scheduler.py +++ b/reeds/function_libs/pipeline/jobScheduling_scripts/MD_simulation_scheduler.py @@ -107,9 +107,9 @@ def do(in_simSystem: fM.System, in_imd_path: str, check_path_dependencies_paths = [slave_script, in_simSystem.top.top_path, out_dir_path, programm_path, ] # Coord file is used by repex in_imd_path prepared_im ##variable paths - if (not isinstance(in_simSystem.top.pertubation_path, - type(None)) and not in_simSystem.top.pertubation_path == "None"): - check_path_dependencies_paths.append(in_simSystem.top.pertubation_path) + if (not isinstance(in_simSystem.top.perturbation_path, + type(None)) and not in_simSystem.top.perturbation_path == "None"): + check_path_dependencies_paths.append(in_simSystem.top.perturbation_path) if (not isinstance(in_simSystem.top.disres_path, type(None)) and not in_simSystem.top.disres_path == "None"): check_path_dependencies_paths.append(in_simSystem.top.disres_path) if (not isinstance(work_dir, type(None)) and work_dir != "None"): @@ -169,7 +169,7 @@ def do(in_simSystem: fM.System, in_imd_path: str, # formulate commands md_script_command = prefix_command + " && python " + slave_script + " -imd " + tmp_in_imd + " -top " + in_simSystem.top.top_path + " -disres " + str( in_simSystem.top.disres_path) + " -perttop " + str( - in_simSystem.top.pertubation_path) + " -coord " + in_simSystem.coordinates + " -nmpi " + str( + in_simSystem.top.perturbation_path) + " -coord " + in_simSystem.coordinates + " -nmpi " + str( nmpi) + " -nomp " + str(nomp) \ + " -bin " + programm_path + " -outdir " + tmp_outdir + " -workdir " + str( work_dir) + add_options diff --git a/reeds/function_libs/pipeline/jobScheduling_scripts/RE_EDS_simulation_scheduler.py b/reeds/function_libs/pipeline/jobScheduling_scripts/RE_EDS_simulation_scheduler.py index d08fd8f8..309f45ed 100644 --- a/reeds/function_libs/pipeline/jobScheduling_scripts/RE_EDS_simulation_scheduler.py +++ b/reeds/function_libs/pipeline/jobScheduling_scripts/RE_EDS_simulation_scheduler.py @@ -130,11 +130,11 @@ def do(in_simSystem: Simulation_System.System, in_imd_path: str, out_dir_path: s # accounting for the different types of restraint used: if(not simSystem.top.disres_path is None): check_path_dependencies_paths = [slave_script, simSystem.top.top_path, simSystem.top.disres_path, - simSystem.top.pertubation_path, + simSystem.top.perturbation_path, out_dir_path, ] # Coord file is used by repex in_imd_path prepared_imd else: check_path_dependencies_paths = [slave_script, simSystem.top.top_path, simSystem.top.posres_path, simSystem.top.refpos_path, - simSystem.top.pertubation_path, + simSystem.top.perturbation_path, out_dir_path, ] # Coord file is used by repex in_imd_path prepared_imd # optional paths @@ -321,7 +321,7 @@ def do(in_simSystem: Simulation_System.System, in_imd_path: str, out_dir_path: s additional_argparse_argument(name='in_coord_path', type=str, required=True, desc="input coordinate .cn file."), additional_argparse_argument(name='in_top_path', type=str, required=True, desc="input topology .top file."), additional_argparse_argument(name='in_perttop_path', type=str, required=True, - desc="input pertubation topology .ptp file."), + desc="input perturbation topology .ptp file."), additional_argparse_argument(name='in_disres_path', type=str, required=True, desc="input distance restraint .dat file.") ] @@ -340,7 +340,7 @@ def do(in_simSystem: Simulation_System.System, in_imd_path: str, out_dir_path: s in_disres_path = args.disres in_perttopo_path = args.perttop - top = fM.Topology(top_path=in_topo_path, disres_path=in_disres_path, pertubation_path=in_perttopo_path) + top = fM.Topology(top_path=in_topo_path, disres_path=in_disres_path, perturbation_path=in_perttopo_path) system = Simulation_System.System(top=top, coordinates=in_coord_path, name=in_system_name) # do everything in here :) diff --git a/reeds/function_libs/pipeline/jobScheduling_scripts/scheduler_functions.py b/reeds/function_libs/pipeline/jobScheduling_scripts/scheduler_functions.py index 84fdea2d..a4d62c6c 100644 --- a/reeds/function_libs/pipeline/jobScheduling_scripts/scheduler_functions.py +++ b/reeds/function_libs/pipeline/jobScheduling_scripts/scheduler_functions.py @@ -207,7 +207,7 @@ def chain_submission(gromosXX_bin_dir: str, in_imd_path: str, simSystem:Simulati else: raise ValueError("No restraint file, suuuure?") - md_script_command += "-in_perttop " + simSystem.top.pertubation_path + "\n" + md_script_command += "-in_perttop " + simSystem.top.perturbation_path + "\n" md_script_command += "-in_coord " + simSystem.coordinates + "\n" md_script_command += "-nmpi " + str(nmpi) + "\n" md_script_command += "-gromosXX_bin_dir " + gromosXX_bin_dir + "\n" diff --git a/reeds/function_libs/pipeline/worker_scripts/simulation_workers/MD_simulation_run_worker.py b/reeds/function_libs/pipeline/worker_scripts/simulation_workers/MD_simulation_run_worker.py index 73552cc0..a9ab2eed 100644 --- a/reeds/function_libs/pipeline/worker_scripts/simulation_workers/MD_simulation_run_worker.py +++ b/reeds/function_libs/pipeline/worker_scripts/simulation_workers/MD_simulation_run_worker.py @@ -26,7 +26,7 @@ def work(out_dir: str, in_coord: str, in_imd_path: str, in_topo_path: str, in_pe in_topo_path : str input topology in_perttopo_path : str - input pertubation + input perturbation in_disres_path : str input disres nmpi : int, optional @@ -103,7 +103,7 @@ def work(out_dir: str, in_coord: str, in_imd_path: str, in_topo_path: str, in_pe parser.add_argument('-imd', type=str, required=True, help="give .imd file which should be used.") parser.add_argument('-top', type=str, required=True, help="give input .top - file.") parser.add_argument('-coord', type=str, required=True, help="give input coordinates .cnf file.") - parser.add_argument('-perttop', type=str, required=True, help="give input pertubation topology.") + parser.add_argument('-perttop', type=str, required=True, help="give input perturbation topology.") parser.add_argument('-disres', type=str, required=False, default=False, help="give input distance restraints.") parser.add_argument('-nmpi', type=int, required=False, default=1, help="number of MPI threads for the sopt_job.") diff --git a/reeds/function_libs/pipeline/worker_scripts/simulation_workers/RE_EDS_simulation_run_worker.py b/reeds/function_libs/pipeline/worker_scripts/simulation_workers/RE_EDS_simulation_run_worker.py index 55255f47..6d8ed80c 100644 --- a/reeds/function_libs/pipeline/worker_scripts/simulation_workers/RE_EDS_simulation_run_worker.py +++ b/reeds/function_libs/pipeline/worker_scripts/simulation_workers/RE_EDS_simulation_run_worker.py @@ -29,7 +29,7 @@ def work(out_dir: str, in_coord: str, in_imd_path: str, in_topo_path: str, in_pe in_topo_path : str input topology in_perttopo_path : str - input pertubation topology + input perturbation topology in_disres_path : str, optional input distance restraints (default: None) in_posres_path : str, optional @@ -154,7 +154,7 @@ def work(out_dir: str, in_coord: str, in_imd_path: str, in_topo_path: str, in_pe parser.add_argument('-in_imd', type=str, required=True, help="give .imd file which should be used.") parser.add_argument('-in_top', type=str, required=True, help="give input .top - file.") parser.add_argument('-in_coord', type=str, required=True, help="give input coordinates .cnf file.") - parser.add_argument('-in_perttop', type=str, required=True, help="give input pertubation topology.") + parser.add_argument('-in_perttop', type=str, required=True, help="give input perturbation topology.") parser.add_argument('-in_disres', type=str, required=False, default=None, help="give input distance restraints.") parser.add_argument('-in_posres', type=str, required=False, default=None, help="give input for position restraints.") parser.add_argument('-in_refpos', type=str, required=False, default=None, help="give input for reference positoins.") diff --git a/reeds/function_libs/utils/argument_parser.py b/reeds/function_libs/utils/argument_parser.py index 81c2ef56..b0eb959f 100644 --- a/reeds/function_libs/utils/argument_parser.py +++ b/reeds/function_libs/utils/argument_parser.py @@ -151,7 +151,7 @@ def execute_module_via_bash(module_doc: str, execute_function: callable, print("ERROR - could not find Coordinate file: " + str(in_cnf_path)) exit(1) - top = fM.Topology(top_path=in_topo_path, disres_path=in_disres_path, pertubation_path=in_perttopo_path) + top = fM.Topology(top_path=in_topo_path, disres_path=in_disres_path, perturbation_path=in_perttopo_path) system = fM.System(top=top, coordinates=in_coord_path, name=in_system_name) args.update({"in_simSystem":system}) diff --git a/reeds/modules/do_RE_EDS_eoffEstimation.py b/reeds/modules/do_RE_EDS_eoffEstimation.py index 4ddd7c43..53b21c5f 100644 --- a/reeds/modules/do_RE_EDS_eoffEstimation.py +++ b/reeds/modules/do_RE_EDS_eoffEstimation.py @@ -321,7 +321,7 @@ def do(out_root_dir: str, in_simSystem: fM.System, in_ene_ana_lib: str, print(spacer + "\t\tRE-EDS ENERGY OFFSET ESTIMATION \n" + spacer + "\n") requiers_gromos_files = [("in_top_path", "input topology .top file."), ("in_coord_path", "input coordinate .cn file."), - ("in_perttop_path", "input pertubation topology .ptp file."), + ("in_perttop_path", "input perturbation topology .ptp file."), ("in_disres_path", "input distance restraint .dat file.")] execute_module_via_bash(__doc__, do, requiers_gromos_files) diff --git a/reeds/modules/do_RE_EDS_eoffRebalancing.py b/reeds/modules/do_RE_EDS_eoffRebalancing.py index 22c712e3..91734db1 100644 --- a/reeds/modules/do_RE_EDS_eoffRebalancing.py +++ b/reeds/modules/do_RE_EDS_eoffRebalancing.py @@ -157,6 +157,6 @@ def do(out_root_dir: str, in_simSystem: fM.System, in_template_imd: str = None, print(spacer + "\t\tRE-EDS S-OPTIMIZATION \n" + spacer + "\n") requiers_gromos_files = [("in_top_path", "input topology .top file."), ("in_coord_path", "input coordinate .cn file."), - ("in_perttop_path", "input pertubation topology .ptp file."), + ("in_perttop_path", "input perturbation topology .ptp file."), ("in_disres_path", "input distance restraint .dat file.")] execute_module_via_bash(__doc__, do, requiers_gromos_files) diff --git a/reeds/modules/do_RE_EDS_findLowerBound.py b/reeds/modules/do_RE_EDS_findLowerBound.py index 8cc66422..8e57bf48 100644 --- a/reeds/modules/do_RE_EDS_findLowerBound.py +++ b/reeds/modules/do_RE_EDS_findLowerBound.py @@ -201,6 +201,6 @@ def do(out_root_dir: str, in_simSystem: fM.System, undersampling_occurrence_frac print(spacer + "\t\tRE-EDS ENERGY OFFSET ESTIMATION \n" + spacer + "\n") requiers_gromos_files = [("in_top_path", "input topology .top file."), ("in_coord_path", "input coordinate .cn file."), - ("in_perttop_path", "input pertubation topology .ptp file."), + ("in_perttop_path", "input perturbation topology .ptp file."), ("in_disres_path", "input distance restraint .dat file.")] execute_module_via_bash(__doc__, do, requiers_gromos_files) diff --git a/reeds/modules/do_RE_EDS_generateOptimizedStates.py b/reeds/modules/do_RE_EDS_generateOptimizedStates.py index ed354107..a866fc22 100644 --- a/reeds/modules/do_RE_EDS_generateOptimizedStates.py +++ b/reeds/modules/do_RE_EDS_generateOptimizedStates.py @@ -223,6 +223,6 @@ def do(out_root_dir: str, in_simSystem: fM.System, print(spacer + "\t\tRE-EDS ENERGY OFFSET ESTIMATION \n" + spacer + "\n") requiers_gromos_files = [("in_top_path", "input topology .top file."), ("in_coord_path", "input coordinate .cn file."), - ("in_perttop_path", "input pertubation topology .ptp file."), + ("in_perttop_path", "input perturbation topology .ptp file."), ("in_disres_path", "input distance restraint .dat file.")] execute_module_via_bash(__doc__, do, requiers_gromos_files) diff --git a/reeds/modules/do_RE_EDS_production.py b/reeds/modules/do_RE_EDS_production.py index 5b9d6cbd..8c70c430 100644 --- a/reeds/modules/do_RE_EDS_production.py +++ b/reeds/modules/do_RE_EDS_production.py @@ -290,6 +290,6 @@ def do(out_root_dir: str, in_simSystem: fM.System, in_template_imd: str, print(spacer + "\n\t\tRE_EDS PRODUCTION\n" + spacer + "\n") requiers_gromos_files = [("in_top_path", "input topology .top file."), ("in_coord_path", "input coordinate .cn file."), - ("in_perttop_path", "input pertubation topology .ptp file."), + ("in_perttop_path", "input perturbation topology .ptp file."), ("in_disres_path", "input distance restraint .dat file.")] execute_module_via_bash(__doc__, do, requiers_gromos_files) diff --git a/reeds/modules/do_RE_EDS_sOptimisation.py b/reeds/modules/do_RE_EDS_sOptimisation.py index 7ee627cb..0c11c3e0 100644 --- a/reeds/modules/do_RE_EDS_sOptimisation.py +++ b/reeds/modules/do_RE_EDS_sOptimisation.py @@ -160,7 +160,7 @@ def do(out_root_dir: str, in_simSystem: fM.System, in_template_imd: str = None, print(spacer + "\t\tRE-EDS S-OPTIMIZATION \n" + spacer + "\n") requiers_gromos_files = [("in_top_path", "input topology .top file."), ("in_coord_path", "input coordinate .cn file."), - ("in_perttop_path", "input pertubation topology .ptp file."), + ("in_perttop_path", "input perturbation topology .ptp file."), ("in_disres_path", "input distance restraint .dat file.")] execute_module_via_bash(__doc__, do, requiers_gromos_files)