Fix import issues due to refactoring as package

enlighten2/__init__.py

@@ -1 +1 @@
-from enlighten2 import wrappers, sanderflow, utils, pdb_utils
+from enlighten2 import wrappers, sanderflow, utils, pdb_utils, tleap

enlighten2/dynam.py

@@ -15,83 +15,88 @@ def get_dynam_dir(system):
     return "dynam" + postfix
 
 
-parser = argparse.ArgumentParser(
-    description=""
-    "Performs a fast equilibration of a simulation system "
-    "prepared using prep.py. Does the following:"
-    " - initial  brief minimization of hydrogens (100 steps)"
-    " - simulated annealing (10000 steps)"
-    " - final brief minimization (100 steps)",
-    formatter_class=argparse.RawDescriptionHelpFormatter
-)
-
-parser.add_argument("system", help="name of the simulation system (as in prep.py)")
-parser.add_argument('-relax', action='store_true')
-parser.add_argument("params", help="additional parameters",
-                    type=argparse.FileType(), nargs='?')
-args = parser.parse_args()
-
-if not os.path.isdir(args.system):
-    print("Directory {} is not found. Please run prep first.".format(args.system),
-          file=sys.stderr)
-    print("If you HAVE run prep.sh, please run dynam.py "
-          "from the same directory as prep.sh.",
-          file=sys.stderr)
-    exit(1)
-
-params = {
-    "steps": 25000,
-    "belly_radius": 4.5,
-    "central_atom": None
-}
-
-if args.params is not None:
-    params = {**params, **json.load(args.params)}
-    args.params.close()
-
-prep_params_path = os.path.join(args.system, 'tleap', 'params')
-if os.path.isfile(prep_params_path):
-    with open(prep_params_path, 'r') as f:
-        params = {**params, **json.load(f)}
-
-bellymask = ":{} <@{}".format(params["central_atom"],
-                              params["belly_radius"])
-
-sander_params = {**params, "bellymask": bellymask}
-
-relax_params = [
-  {"name": "minimize_h_all", "template": "minh"},
-  {"name": "minimize_h_in_sphere", "template": "minh_ibelly", "params": sander_params},
-  {"name": "annealing_with_restraints", "template": "sa_ca", "params": sander_params},
-  {"name": "annealing_without_restraints", "template": "sa", "params": sander_params},
-  {"name": "minimize_all_in_sphere", "template": "min_ibelly", "params": sander_params}
-]
-
-params = {}
-dynam_params = [
-    {"name": "heat", "template": "heat", "params": sander_params},
-    {"name": "md", "template": "md", "params": sander_params, "monitor": True},
-    {"name": "minimize", "template": "min", "params": sander_params},
-]
-
-tleap_dir = os.path.abspath(os.path.join(args.system, 'tleap'))
-prmtop = "{}/{}.top".format(tleap_dir, args.system)
-mode = 'relax' if args.relax else 'dynam'
-
-if mode == 'relax':
-    crd = "{}/{}.rst".format(tleap_dir, args.system)
-    sanderflow_params = relax_params
-    working_dir = '{}/{}'.format(args.system, 'relax')
-else:
-    relax_dir = os.path.abspath(os.path.join(args.system, 'relax'))
-    crd = "{}/{}_relax.rst".format(relax_dir, args.system)
-    sanderflow_params = dynam_params
-    working_dir = '{}/{}'.format(args.system, get_dynam_dir(args.system))
-
-utils.set_working_directory(working_dir)
-status, result = sanderflow.run(prmtop, crd, sanderflow_params)
-if not status:
-    sys.exit(1)
-
-final_crd = "{system}_{mode}.rst".format(system=args.system, mode=mode)
-os.system("cp {crd} {final_crd}".format(crd=result.crd, final_crd=final_crd))
+def main():
+
+    parser = argparse.ArgumentParser(
+        description=""
+        "Performs a fast equilibration of a simulation system "
+        "prepared using prep.py. Does the following:"
+        " - initial  brief minimization of hydrogens (100 steps)"
+        " - simulated annealing (10000 steps)"
+        " - final brief minimization (100 steps)",
+        formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument("system", help="name of the simulation system (as in prep.py)")
+    parser.add_argument('-relax', action='store_true')
+    parser.add_argument("params", help="additional parameters",
+                        type=argparse.FileType(), nargs='?')
+    args = parser.parse_args()
+
+    if not os.path.isdir(args.system):
+        print("Directory {} is not found. Please run prep first.".format(args.system),
+              file=sys.stderr)
+        print("If you HAVE run prep.sh, please run dynam.py "
+              "from the same directory as prep.sh.",
+              file=sys.stderr)
+        exit(1)
+
+    params = {
+        "steps": 25000,
+        "belly_radius": 4.5,
+        "central_atom": None
+    }
+
+    if args.params is not None:
+        params = {**params, **json.load(args.params)}
+        args.params.close()
+
+    prep_params_path = os.path.join(args.system, 'tleap', 'params')
+    if os.path.isfile(prep_params_path):
+        with open(prep_params_path, 'r') as f:
+            params = {**params, **json.load(f)}
+
+    bellymask = ":{} <@{}".format(params["central_atom"],
+                                  params["belly_radius"])
+
+    sander_params = {**params, "bellymask": bellymask}
+
+    relax_params = [
+      {"name": "minimize_h_all", "template": "minh"},
+      {"name": "minimize_h_in_sphere", "template": "minh_ibelly", "params": sander_params},
+      {"name": "annealing_with_restraints", "template": "sa_ca", "params": sander_params},
+      {"name": "annealing_without_restraints", "template": "sa", "params": sander_params},
+      {"name": "minimize_all_in_sphere", "template": "min_ibelly", "params": sander_params}
+    ]
+
+    dynam_params = [
+        {"name": "heat", "template": "heat", "params": sander_params},
+        {"name": "md", "template": "md", "params": sander_params, "monitor": True},
+        {"name": "minimize", "template": "min", "params": sander_params},
+    ]
+
+    tleap_dir = os.path.abspath(os.path.join(args.system, 'tleap'))
+    prmtop = "{}/{}.top".format(tleap_dir, args.system)
+    mode = 'relax' if args.relax else 'dynam'
+
+    if mode == 'relax':
+        crd = "{}/{}.rst".format(tleap_dir, args.system)
+        sanderflow_params = relax_params
+        working_dir = '{}/{}'.format(args.system, 'relax')
+    else:
+        relax_dir = os.path.abspath(os.path.join(args.system, 'relax'))
+        crd = "{}/{}_relax.rst".format(relax_dir, args.system)
+        sanderflow_params = dynam_params
+        working_dir = '{}/{}'.format(args.system, get_dynam_dir(args.system))
+
+    utils.set_working_directory(working_dir)
+    status, result = sanderflow.run(prmtop, crd, sanderflow_params)
+    if not status:
+        sys.exit(1)
+
+    final_crd = "{system}_{mode}.rst".format(system=args.system, mode=mode)
+    os.system("cp {crd} {final_crd}".format(crd=result.crd, final_crd=final_crd))
+
+
+if __name__ == '__main__':
+    main()

enlighten2/prep.py

@@ -34,107 +34,113 @@ def run_propka(pdb, ph, ph_offset):
         return pdb
 
 
-parser = argparse.ArgumentParser(
-    description=""
-    "Prepares the simulation system by performing the following actions:\n"
-    " - ligand parameterisation (with antechamber/prmchk2)\n"
-    " - pdb protonation (apart from ligands, they need to "
-    "   be protonated already!)\n"
-    " - tleap to solvate and write starting parm7/rst7 (top/rst)\n\n",
-    formatter_class=argparse.RawDescriptionHelpFormatter
-)
-
-parser.add_argument("name", help="name of the job")
-parser.add_argument("pdb", help="protonated PDB file",
-                    type=argparse.FileType())
-parser.add_argument("ligand",
-                    help="name of the residue to be used as the ligand")
-parser.add_argument("charge", help="charge of the ligand", type=int)
-parser.add_argument("params", help="JSON file with advanced parameters",
-                    type=argparse.FileType(), nargs='?')
-
-args = parser.parse_args()
-
-job_name = args.name
-ligand_name = args.ligand
-ligand_charge = args.charge
-
-params = {
-    'antechamber': {
-        'ligand': args.ligand,
-        'charge': args.charge,
-        'ligand_chainID': "L",
-        'ligand_index': 1,
-    },
-    'propka': {
-        'with_propka': True,
-        'ph': 7.0,
-        'ph_offset': 0.7,
-    },
-    'tleap': {
-        'template': 'sphere',
-        'solvent_radius': 20.0,
-        'solvent_closeness': 0.75,
-        'include': []
+def main():
+
+    parser = argparse.ArgumentParser(
+        description=""
+                    "Prepares the simulation system by performing the following actions:\n"
+                    " - ligand parameterisation (with antechamber/prmchk2)\n"
+                    " - pdb protonation (apart from ligands, they need to "
+                    "   be protonated already!)\n"
+                    " - tleap to solvate and write starting parm7/rst7 (top/rst)\n\n",
+        formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+
+    parser.add_argument("name", help="name of the job")
+    parser.add_argument("pdb", help="protonated PDB file",
+                        type=argparse.FileType())
+    parser.add_argument("ligand",
+                        help="name of the residue to be used as the ligand")
+    parser.add_argument("charge", help="charge of the ligand", type=int)
+    parser.add_argument("params", help="JSON file with advanced parameters",
+                        type=argparse.FileType(), nargs='?')
+
+    args = parser.parse_args()
+
+    job_name = args.name
+    ligand_name = args.ligand
+    ligand_charge = args.charge
+
+    params = {
+        'antechamber': {
+            'ligand': args.ligand,
+            'charge': args.charge,
+            'ligand_chainID': "L",
+            'ligand_index': 1,
+        },
+        'propka': {
+            'with_propka': True,
+            'ph': 7.0,
+            'ph_offset': 0.7,
+        },
+        'tleap': {
+            'template': 'sphere',
+            'solvent_radius': 20.0,
+            'solvent_closeness': 0.75,
+            'include': []
+        }
     }
-}
-
-if args.params is not None:
-    params = utils.merge_dicts_of_dicts(params, json.load(args.params))
-    args.params.close()
-    params['tleap']['include'] = [os.path.abspath(path)
-                                  for path in params['tleap']['include']]
-
-if os.path.exists(job_name):
-    print("It appears you've already (attempted to) run prep.py with {0}. "
-          "Delete folder {0} or rename pdb if you want to run it again."
-          .format(job_name), file=sys.stderr)
-    sys.exit(1)
-
-print("Starting PREP protocol in {}/".format(job_name))
-sys.stdout.flush()
-utils.set_working_directory(job_name)
-
-pdb = pdb_utils.Pdb(args.pdb)
-ligand_index = params['antechamber']['ligand_index']
-ligand_atoms = get_ligand_atoms(pdb, ligand_name, ligand_index)
-
-# Only generate ligand frcmod if it is not found in include paths
-ligand_frcmod = utils.file_in_paths(ligand_name + '.frcmod',
-                                    params['tleap']['include'])
-antechamber = wrappers.AntechamberWrapper(
-    pdb_utils.Pdb(atoms=ligand_atoms), ligand_name, ligand_charge,
-    create_frcmod=ligand_frcmod is None
-)
-sys.stdout.flush()
-if ligand_frcmod is None:
-    params['tleap']['include'].append(antechamber.working_directory)
-
-# Change ligand chain ID to ligand_chainID
-ligand_chainID = params['antechamber']['ligand_chainID']
-pdb_utils.modify_atoms(ligand_atoms, 'chainID', ligand_chainID)
-
-# Run pdb4amber and reduce
-reduceResults = wrappers.Pdb4AmberReduceWrapper(pdb)
-sys.stdout.flush()
-pdb = reduceResults.pdb
-
-# Run propka31 if requested and found
-if params['propka']['with_propka']:
-    pdb = run_propka(pdb=pdb,
-                     ph=params['propka']['ph'],
-                     ph_offset=params['propka']['ph_offset'])
-sys.stdout.flush()
-
-ligand = pdb.get_residues_by_name(ligand_name)[ligand_index-1]
-params['tleap']['name'] = os.path.basename(job_name)
-params['tleap']['pdb'] = pdb
-params['tleap']['ligand'] = ligand
-tleap = wrappers.TleapWrapper(params['tleap']['template'],
-                              params['tleap']['include'],
-                              reduceResults.nonprot_residues,
-                              params['tleap'])
-sys.stdout.flush()
-os.system("cp {} .".format(tleap.top))
-os.system("cp {} .".format(tleap.rst))
-print("Finished PREP protocol.")
+
+    if args.params is not None:
+        params = utils.merge_dicts_of_dicts(params, json.load(args.params))
+        args.params.close()
+        params['tleap']['include'] = [os.path.abspath(path)
+                                      for path in params['tleap']['include']]
+
+    if os.path.exists(job_name):
+        print("It appears you've already (attempted to) run prep.py with {0}. "
+              "Delete folder {0} or rename pdb if you want to run it again."
+              .format(job_name), file=sys.stderr)
+        sys.exit(1)
+
+    print("Starting PREP protocol in {}/".format(job_name))
+    sys.stdout.flush()
+    utils.set_working_directory(job_name)
+
+    pdb = pdb_utils.Pdb(args.pdb)
+    ligand_index = params['antechamber']['ligand_index']
+    ligand_atoms = get_ligand_atoms(pdb, ligand_name, ligand_index)
+
+    # Only generate ligand frcmod if it is not found in include paths
+    ligand_frcmod = utils.file_in_paths(ligand_name + '.frcmod',
+                                        params['tleap']['include'])
+    antechamber = wrappers.AntechamberWrapper(
+        pdb_utils.Pdb(atoms=ligand_atoms), ligand_name, ligand_charge,
+        create_frcmod=ligand_frcmod is None
+    )
+    sys.stdout.flush()
+    if ligand_frcmod is None:
+        params['tleap']['include'].append(antechamber.working_directory)
+
+    # Change ligand chain ID to ligand_chainID
+    ligand_chainID = params['antechamber']['ligand_chainID']
+    pdb_utils.modify_atoms(ligand_atoms, 'chainID', ligand_chainID)
+
+    # Run pdb4amber and reduce
+    reduceResults = wrappers.Pdb4AmberReduceWrapper(pdb)
+    sys.stdout.flush()
+    pdb = reduceResults.pdb
+
+    # Run propka31 if requested and found
+    if params['propka']['with_propka']:
+        pdb = run_propka(pdb=pdb,
+                         ph=params['propka']['ph'],
+                         ph_offset=params['propka']['ph_offset'])
+    sys.stdout.flush()
+
+    ligand = pdb.get_residues_by_name(ligand_name)[ligand_index-1]
+    params['tleap']['name'] = os.path.basename(job_name)
+    params['tleap']['pdb'] = pdb
+    params['tleap']['ligand'] = ligand
+    tleap = wrappers.TleapWrapper(params['tleap']['template'],
+                                  params['tleap']['include'],
+                                  reduceResults.nonprot_residues,
+                                  params['tleap'])
+    sys.stdout.flush()
+    os.system("cp {} .".format(tleap.top))
+    os.system("cp {} .".format(tleap.rst))
+    print("Finished PREP protocol.")
+
+
+if __name__ == '__main__':
+    main()

enlighten2/tleap/sphere.py

@@ -1,6 +1,6 @@
 import os
 import sys
-import pdb_utils
+from enlighten2 import pdb_utils
 
 
 def run(params, template):