corrected spelling pertubation to be compatible with PyGromosV1.2

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

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 :)

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"

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.")

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.")

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})
 

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)

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)

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)

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)

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)

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)