Merge pull request #237 from rinikerlab/GromosOBJWrapFixes

pleasing pep8

examples/example_hvap.ipynb

@@ -17,7 +17,7 @@
    "source": [
     "from pygromos.files.gromos_system.ff.forcefield_system import forcefield_system\n",
     "from pygromos.files.gromos_system.gromos_system import Gromos_System\n",
-    "from pygromos.simulations.hvap_calculation.hvap_calculation import Hvap_calculation\n",
+    "from pygromos.simulations.approaches.hvap_calculation.hvap_calculation import Hvap_calculation\n",
     "from pygromos.data.simulation_parameters_templates import template_sd"
    ]
   },
@@ -27,7 +27,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pygro_env={'SHELL': '/bin/bash', 'LIBGL_ALWAYS_INDIRECT': '1', 'CONDA_EXE': '/home/mlehner/anaconda3/bin/conda', '_CE_M': '', 'WSL_DISTRO_NAME': 'Ubuntu-20.04', 'NAME': 'MarcSurface', 'GSETTINGS_SCHEMA_DIR': '/home/mlehner/anaconda3/envs/pygro/share/glib-2.0/schemas', 'LOGNAME': 'mlehner', 'CONDA_PREFIX': '/home/mlehner/anaconda3/envs/pygro', 'GSETTINGS_SCHEMA_DIR_CONDA_BACKUP': '', 'HOME': '/home/mlehner', 'LANG': 'C.UTF-8', 'WSL_INTEROP': '/run/WSL/451_interop', 'CONDA_PROMPT_MODIFIER': '(pygro) ', 'PERL5LIB': '/home/mlehner/anaconda3/envs/pygro/lib/perl/mm_pbsa', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'TERM': 'xterm-256color', '_CE_CONDA': '', 'LESSOPEN': '| /usr/bin/lesspipe %s', 'USER': 'mlehner', 'CONDA_SHLVL': '2', 'AMBERHOME': '/home/mlehner/anaconda3/envs/pygro', 'DISPLAY': '172.21.240.1:0', 'SHLVL': '1', 'CONDA_PYTHON_EXE': '/home/mlehner/anaconda3/bin/python', 'CONDA_DEFAULT_ENV': 'pygro', 'WSLENV': '', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'PATH': '/home/mlehner/anaconda3/envs/pygro/bin:/home/mlehner/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu20.04onWindows_2004.2021.222.0_x64__79rhkp1fndgsc:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program Files/Wolfram Research/WolframScript:/mnt/c/Users/thier/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/thier/AppData/Local/Programs/Microsoft VS Code/bin:/mnt/c/Users/thier/AppData/Local/GitHubDesktop/bin:/snap/bin:/usr/local/gromacs/bin/GMXRC', 'HOSTTYPE': 'x86_64', 'CONDA_PREFIX_1': '/home/mlehner/anaconda3', '_': '/home/mlehner/anaconda3/envs/pygro/bin/python3'}"
+    "work_dir=os.getcwd()+\"/example_files/Hvap_files/\"\n",
+    "gromosXX_path=None \n",
+    "gromosPP_path=None"
    ]
   },
   {
@@ -36,9 +38,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "work_dir=os.getcwd()+\"/example_files/Hvap_files/\"\n",
-    "gromosXX_path=None #\"/home/mlehner/gromosXX/gromosXX/BUILD/program/\"\n",
-    "gromosPP_path=None# \"/home/mlehner/gromosPlsPls/gromos++/BUILD/programs/\""
+    "ff = forcefield_system(name=\"54A7\")\n",
+    "ff.mol_name = \"H2O\""
    ]
   },
   {
@@ -47,8 +48,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ff = forcefield_system(name=\"54A7\")\n",
-    "ff.mol_name = \"H2O\""
+    "groSys = Gromos_System(work_folder=work_dir+\"init/\", system_name=\"Hvap_test\", in_smiles=\"O\",\n",
+    "                       auto_convert=True, Forcefield=ff, in_imd_path=template_sd,\n",
+    "                       in_gromosPP_bin_dir=gromosPP_path, in_gromosXX_bin_dir=gromosXX_path)"
    ]
   },
   {
@@ -57,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "groSys = Gromos_System(work_folder=work_dir+\"init/\", system_name=\"Hvap_test\", in_smiles=\"O\", auto_convert=True, Forcefield=ff, in_imd_path=template_sd, in_gromosPP_bin_dir=gromosPP_path, in_gromosXX_bin_dir=gromosXX_path)"
+    "hvap_sys=Hvap_calculation(input_system=groSys, work_folder=work_dir+\"hvap\", forcefield=ff, system_name=\"test\", useGromosPlsPls=True)"
    ]
   },
   {
@@ -66,7 +68,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hvap_sys=Hvap_calculation(input_system=groSys, work_folder=work_dir+\"hvap\", forcefield=ff, system_name=\"test\")"
+    "hvap_sys.create_liq()"
    ]
   },
   {
@@ -75,7 +77,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hvap_sys.submissonSystem._enviroment = pygro_env"
+    "hvap_sys.run_gas()"
    ]
   },
   {
@@ -84,7 +86,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hvap_sys.create_liq()"
+    "hvap_sys.run_liq()"
    ]
   },
   {
@@ -93,16 +95,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hvap_sys.run_gas()"
+    "hvap_sys.calc_hvap()\n"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "hvap_sys.run_liq()"
+    "## How to deactivate binary checks:"
    ]
   },
   {
@@ -111,7 +111,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hvap_sys.calc_hvap()"
+    "#GromosLayer\n",
+    "from pygromos.gromos.gromosXX import GromosXX\n",
+    "\n",
+    "grom = GromosXX(_dont_check_binary=True)\n",
+    "\n",
+    "\n",
+    "#System Layer\n",
+    "from pygromos.files.gromos_system.gromos_system import Gromos_System\n",
+    "\n",
+    "Gromos_System._gromos_noBinary_checks = True\n",
+    "sys = Gromos_System()"
    ]
   },
   {
@@ -123,8 +133,25 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "b1b7b2ea43b8e767316eee98e01335d045804d2d47db68b6a5827e187ee91a7e"
+  },
+  "kernelspec": {
+   "display_name": "Python 3.9.7 ('pygro2')",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,

examples/tutorial_gromos_pipeline.ipynb

@@ -921,6 +921,7 @@
     "# Check simulation params\n",
     "in_eminBox_system.imd = template_emin   #Here we use template simulation parameters, The blocks are the same as above in the vacuum case with slight deviations.\n",
     "in_eminBox_system.imd.INITIALISE.NTISHI = 1\n",
+    "\n",
     "in_eminBox_system.prepare_for_simulation()\n",
     "\n",
     "in_eminBox_system"
@@ -1565,8 +1566,8 @@
    "source": [
     "from matplotlib import pyplot as plt\n",
     "\n",
-    "plt.plot(temperatures.TIMESTEP_time, temperatures.bath1, label=\"TBath1\")\n",
-    "plt.plot(temperatures.TIMESTEP_time, temperatures.bath2, label=\"TBath2\")\n",
+    "plt.plot(temperatures.index, temperatures.bath1, label=\"TBath1\")\n",
+    "plt.plot(temperatures.index, temperatures.bath2, label=\"TBath2\")\n",
     "\n",
     "plt.legend()\n",
     "plt.ylabel(\"$T~[K]$\")\n",
@@ -1774,7 +1775,7 @@
    "source": [
     "#Next we plot some data of the energies to se their development.\n",
     "\n",
-    "time_axis = energy_traj.database.TIMESTEP_time\n",
+    "time_axis = energy_traj.time\n",
     "total_energies.totene.plot(x=time_axis, xlabel=\"t [ps]\", ylabel=\"V [kJ/mol]\", title=\"Simulation Data\", legend=True)\n",
     "total_energies.totpot.plot(legend=True)\n",
     "total_energies.totkin.plot(legend=True)\n"
@@ -1815,7 +1816,7 @@
    "outputs": [],
    "source": [
     "#First lets get the Force Group Energy contributions:\n",
-    "forceGroupNonbondedContributions = energy_traj.get_nonbondedForceGroupContributions()\n",
+    "forceGroupNonbondedContributions = energy_traj.get_nonbondedContributions()\n",
     "\n",
     "#Here we give each Force Group contribution category nice names:\n",
     "peptide_peptide_nonbonded = forceGroupNonbondedContributions[1][1]\n",
@@ -1894,13 +1895,6 @@
     "coordinate_traj = out_md_system.trc\n"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "#### RMSD"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1982,8 +1976,25 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "e7d5b70120806d05daeaf98b799438b40f063b8cf99696cad03a40d92a237582"
+  },
+  "kernelspec": {
+   "display_name": "Python 3.9.10 ('pygromosDev')",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,

pygromos/files/_basics/_general_gromos_file.py

@@ -8,7 +8,7 @@
 import copy
 import inspect
 import warnings
-from typing import List, Dict, Callable
+from typing import List, Dict, Callable, Union
 
 from pygromos.files.blocks import all_blocks
 
@@ -30,7 +30,7 @@ class _general_gromos_file:
     _block_order: List[str] = []
     _future_file: bool
 
-    def __init__(self, in_value: (str or dict or None or __class__), _future_file: bool = False):
+    def __init__(self, in_value: Union[str, dict, None], _future_file: bool = False):
         self._future_file = _future_file
         if isinstance(in_value, str):
             self.path = self._orig_file_path = in_value
@@ -43,10 +43,12 @@ def __init__(self, in_value: (str or dict or None or __class__), _future_file: b
 
         elif isinstance(type(in_value), __class__):
             raise NotImplementedError("This variant is not implemented")
+
         elif in_value is None:
             self.path = None
             self._orig_file_path = None
             # print("Empty class")
+
         else:
             raise ValueError("The given type of input could not be translated in " + str(__class__) + ".__init__")
 
@@ -302,11 +304,9 @@ def write(self, out_path: str) -> str:
         str
             out_path
         """
-        os.makedirs(os.path.dirname(out_path), exist_ok=True)
-        file = open(out_path, "w")
-        file.write(str(self))
-        file.close()
-        self.path = out_path
+        self._write_to_file(out_path=out_path, content_str=str(self))
+        self.path = os.path.abspath(out_path)
+        self._future_file = False
 
         return out_path
 

pygromos/files/blocks/_general_blocks.py

@@ -88,14 +88,18 @@ def read_content_from_str(self, content: str):
 
     def block_to_string(self) -> str:
         result = self.name + self.line_seperator
-        if isinstance(self.content, list) and len(self.content) > 0 and all([isinstance(x, str) for x in self.content]):
-            result += self.field_seperator.join(self.content) + self.line_seperator
+        if (
+            isinstance(self.content, list)
+            and len(self.content) > 0
+            and all([isinstance(x, (str, Number)) for x in self.content])
+        ):
+            result += self.field_seperator.join(map(str, self.content)) + self.line_seperator
         elif (
             isinstance(self.content, list)
             and len(self.content) > 0
-            and all([isinstance(x, list) and all([isinstance(y, str) for y in x]) for x in self.content])
+            and all([isinstance(x, list) and all([isinstance(y, (str, Number)) for y in x]) for x in self.content])
         ):
-            result += self.line_seperator.join(map(lambda x: self.field_seperator.join(x), self.content))
+            result += self.line_seperator.join(map(lambda x: self.field_seperator.join(map(str, x)), self.content))
         elif isinstance(self.content, (str, Number)):
             result += self.field_seperator + str(self.content) + self.line_seperator
         else:

pygromos/files/blocks/topology_blocks.py

@@ -3027,34 +3027,68 @@ def block_to_string(self) -> str:
         return result
 
 
-class SOLUTEMOLECULES(_topology_block):
+class _generic_topology_groups(_topology_block):
+    NSM: int
+    NSP: List[int]
+
     def __init__(
         self,
-        content: (str or dict or None or __class__),
+        content: Union[str, dict] = None,
         FORCEFIELD: FORCEFIELD = None,
         MAKETOPVERSION: MAKETOPVERSION = None,
+        NSM: int = None,
+        NSP: List[int] = None,
     ):
-        super().__init__(FORCEFIELD=FORCEFIELD, MAKETOPVERSION=MAKETOPVERSION, content=content)
+        if NSP is not None:
+            if NSM is not None:
+                if len(NSP) == NSM:
+                    self.NSM = NSM
+                else:
+                    raise ValueError("FUn")
+            else:
+                self.NSM = len(NSP)
+            self.NSP = list(map(int, NSP))
+            super().__init__(
+                FORCEFIELD=FORCEFIELD, MAKETOPVERSION=MAKETOPVERSION, content=[str(NSM)] + list(map(str, NSP))
+            )
+        else:
+            super().__init__(FORCEFIELD=FORCEFIELD, MAKETOPVERSION=MAKETOPVERSION, content=content)
+
+            if len(self.content) == 1 and len(self.content[0]) - 1 == int(self.content[0][0]):
+                self.NSM = int(self.content[0][0])
+                self.NSP = [int(x) for x in self.content[0][1:]]
+            elif len(self.content) > 1:
+                self.NSM = int(self.content[0][0])
+                self.NSP = []
+                [
+                    self.NSP.extend(list(map(int, t))) if (isinstance(t, list)) else self.NSP.extend([int(t)])
+                    for t in self.content[1:]
+                ]
+            else:
+                raise ValueError("SOLUTEMOLECULES has not the correct number of fields.")
 
+        # Clean COntent
+        self.content = [[self.NSM]]
+        self.content.extend([[x] for x in self.NSP])
 
-class TEMPERATUREGROUPS(_topology_block):
-    def __init__(
-        self,
-        content: (str or dict or None or __class__),
-        FORCEFIELD: FORCEFIELD = None,
-        MAKETOPVERSION: MAKETOPVERSION = None,
-    ):
-        super().__init__(FORCEFIELD=FORCEFIELD, MAKETOPVERSION=MAKETOPVERSION, content=content)
+    def block_to_string(self) -> str:
+        # Clean COntent
+        self.content = [[self.NSM]]
+        self.content.extend([[x] for x in self.NSP])
 
+        return super().block_to_string()
 
-class PRESSUREGROUPS(_topology_block):
-    def __init__(
-        self,
-        content: (str or dict or None or __class__),
-        FORCEFIELD: FORCEFIELD = None,
-        MAKETOPVERSION: MAKETOPVERSION = None,
-    ):
-        super().__init__(FORCEFIELD=FORCEFIELD, MAKETOPVERSION=MAKETOPVERSION, content=content)
+
+class SOLUTEMOLECULES(_generic_topology_groups):
+    pass
+
+
+class TEMPERATUREGROUPS(_generic_topology_groups):
+    pass
+
+
+class PRESSUREGROUPS(_generic_topology_groups):
+    pass
 
 
 class LJEXCEPTIONS(_topology_table_block):