Update wrapper and parsing functionality for mobility calculation, through Boltzmann averaging

isicle/conformers.py

@@ -398,13 +398,10 @@ def _check_attributes(self, attr):
             If all members do not have `attr`.
 
         '''
-
-        value = [x.get___dict__() for x in self]
-        for key in safelist(attr):
-            if not all(key in x for x in value):
-                raise AttributeError('"{}" not found for all conformational '
-                                     'ensemble members.'.format(attr))
-            value = [x.get(key) for x in value]
+
+        if not all(hasattr(x, attr) for x in self):
+            raise AttributeError('"{}" not found for all conformational '
+                                    'ensemble members.'.format(attr))
 
     def reduce(self, attr, func='boltzmann', **kwargs):
         '''
@@ -438,9 +435,7 @@ def reduce(self, attr, func='boltzmann', **kwargs):
             self._check_attributes('energy')
 
         # Extract (possibly nested) value attribute
-        value = [x.get___dict__() for x in self]
-        for key in safelist(attr):
-            value = [x.get(key) for x in value]
+        value = [getattr(x, attr) for x in self]
 
         # Check nested values
         if isinstance(value[0], dict):
@@ -463,7 +458,7 @@ def reduce(self, attr, func='boltzmann', **kwargs):
                 value = np.array([x['mean'] for x in value]).flatten()
 
             else:
-                value = np.array([x[attr] for x in value]).flatten()
+                value = np.array([getattr(x, attr) for x in value]).flatten()
 
         # Not nested
         else:
@@ -474,7 +469,7 @@ def reduce(self, attr, func='boltzmann', **kwargs):
         # Extract energy attribute
         if _energy_based(f):
             energy = np.array(
-                [np.repeat(x.get___dict__()['energy'], pad) for x in self])
+                [np.repeat(getattr(x, 'energy'), pad) for x in self])
             energy = energy.flatten()
 
             # Exectue energy-based method

isicle/geometry.py

@@ -24,7 +24,9 @@ class Geometry(GeometryInterface):
         "_frequency",
         "_molden",
         "_charge",
-        "_connectivity"
+        "_connectivity",
+        "_formal_charge",
+        "_ccs",
         ]
     _default_value = None
 
@@ -154,6 +156,20 @@ def formal_charge(self):
 
         return Chem.rdmolops.GetFormalCharge(self.to_mol())
 
+    @property
+    def ccs(self):
+        """
+        Get CCS of the molecule.
+
+        Returns
+        -------
+        float
+            Collision cross section.
+
+        """
+
+        return self._ccs
+
     def view(self):
         """
         View internal rdkit mol object representation.

isicle/interfaces.py

@@ -27,11 +27,6 @@ def parse(self):
         """Extract relevant information from data"""
         raise NotImplementedError
 
-    @abc.abstractmethod
-    def save(self, path: str):
-        """Write parsed object to file"""
-        raise NotImplementedError
-
 
 class XYZGeometryInterface(metaclass=abc.ABCMeta):
 

isicle/md.py

@@ -4,7 +4,7 @@
 from collections import defaultdict
 
 from rdkit import Chem
-from rdkit.Chem import rdDetermineBonds, rdDistGeom
+from rdkit.Chem import rdDistGeom
 
 import isicle
 from isicle.geometry import Geometry
@@ -16,43 +16,43 @@
 """
 
 
-def _program_selector(program):
+def _backend_selector(backend):
     """
-    Selects a supported molecular dynamics program for associated simulation.
+    Selects a supported molecular dynamics backend for associated simulation.
     Currently only NWChem has been implemented.
 
     Parameters
     ----------
-    program : str
-        Alias for program selection (xtb).
+    backend : str
+        Alias for backend selection (xtb).
 
     Returns
     -------
-    program
-        Wrapped functionality of the selected program. Must implement
+    backend
+        Wrapped functionality of the selected backend. Must implement
         :class:`~isicle.interfaces.WrapperInterface`.
 
     """
 
-    program_map = {"xtb": XTBWrapper, "rdkit": RDKitWrapper}
+    backend_map = {"xtb": XTBWrapper, "rdkit": RDKitWrapper}
 
-    if program.lower() in program_map.keys():
-        return program_map[program.lower()]()
+    if backend.lower() in backend_map.keys():
+        return backend_map[backend.lower()]()
     else:
         raise ValueError(
-            "{} not a supported molecular dynamics program.".format(program)
+            "{} not a supported molecular dynamics backend.".format(backend)
         )
 
 
-def md(geom, program="xtb", **kwargs):
+def md(geom, backend="xtb", **kwargs):
     """
     Optimize geometry via molecular dyanmics using supplied forcefield
     and basis set.
 
     Parameters
     ----------
-    program : str
-        Alias for program selection (xtb).
+    backend : str
+        Alias for backend selection (xtb).
 
     Returns
     -------
@@ -61,8 +61,8 @@ def md(geom, program="xtb", **kwargs):
 
     """
 
-    # Select program
-    return _program_selector(program).run(geom, **kwargs)
+    # Select backend
+    return _backend_selector(backend).run(geom, **kwargs)
 
 
 class XTBWrapper(WrapperInterface):
@@ -75,25 +75,19 @@ class XTBWrapper(WrapperInterface):
     ----------
     temp_dir : str
         Path to temporary directory used for simulation.
-    task_map : dict
-        Alias mapper for supported molecular dynamic presets. Includes
-        "optimize", "crest", "nmr", "protonate", "deprotonate", and "tautomer".
     geom : :obj:`isicle.geometry.Geometry`
         Internal molecule representation.
-    fmt : str
-        File extension indicator.
-    job_list : str
-        List of commands for simulation.
+    result : dict
+        Dictionary containing simulation results.
 
     """
 
-    _defaults = ["geom", "result"]
+    _defaults = ["geom", "result", "temp_dir"]
     _default_value = None
 
-    def __init__(self, **kwargs):
-        self.temp_dir = isicle.utils.mkdtemp()
+    def __init__(self):
         self.__dict__.update(dict.fromkeys(self._defaults, self._default_value))
-        self.__dict__.update(**kwargs)
+        self.temp_dir = isicle.utils.mkdtemp()
 
     def set_geometry(self, geom):
         """
@@ -124,13 +118,13 @@ def save_geometry(self, fmt="xyz"):
 
         """
         # Path operations
-        self.fmt = fmt.lower()
+        self._fmt = fmt.lower()
         geomfile = os.path.join(
-            self.temp_dir, "{}.{}".format(self.geom.basename, self.fmt.lower())
+            self.temp_dir, "{}.{}".format(self.geom.basename, self._fmt.lower())
         )
 
         # All other formats
-        isicle.io.save(geomfile, self.geom)
+        isicle.save(geomfile, self.geom)
         self.geom.path = geomfile
 
     def _configure_xtb(self, forcefield="gfn2", optlevel="normal", solvation=None):
@@ -154,7 +148,7 @@ def _configure_xtb(self, forcefield="gfn2", optlevel="normal", solvation=None):
         s = "xtb "
 
         # Add geometry
-        s += "{}.{}".format(self.geom.basename, self.fmt.lower())
+        s += "{}.{}".format(self.geom.basename, self._fmt.lower())
 
         # Add optimize tag
         s += " --opt " + optlevel + " "
@@ -226,7 +220,7 @@ def _configure_crest(
         # Add geometry
         s += str(
             os.path.join(
-                self.temp_dir, "{}.{}".format(self.geom.basename, self.fmt.lower())
+                self.temp_dir, "{}.{}".format(self.geom.basename, self._fmt.lower())
             )
         )
 
@@ -354,17 +348,17 @@ def configure(
                     "Task not assigned properly, please choose optimize, conformer, protonate, deprotonate, or tautomerize"
                 )
 
-        self.task = task
+        self._task = task
 
-        self.config = config
+        self._config = config
 
     def submit(self):
         """
         Run xtb or crest simulation according to configured inputs.
         """
         cwd = os.getcwd()
         os.chdir(self.temp_dir)
-        subprocess.call(self.config, shell=True)
+        subprocess.call(self._config, shell=True)
         os.chdir(cwd)
 
     def finish(self):
@@ -560,18 +554,19 @@ class RDKitWrapper(Geometry, WrapperInterface):
     ----------
     geom : :obj:`isicle.geometry.Geometry`
         Internal molecule representation.
-    method: str
+    method : str
         Method of RDKit conformer generation specified.
-    numConfs: int
+    numConfs : int
         The number of conformers to generate.
+    result : dict
+        Dictionary containing simulation results.
     """
 
     _defaults = ["geom", "method", "numConfs", "result"]
     _default_value = None
 
-    def __init__(self, **kwargs):
+    def __init__(self):
         self.__dict__.update(dict.fromkeys(self._defaults, self._default_value))
-        self.__dict__.update(**kwargs)
 
     def set_geometry(self, geom):
         """
@@ -704,6 +699,9 @@ def submit(self):
             raise ValueError(
                 "Failure to run RDKit MD, method and/or variant not recognized"
             )
+
+    def parse(self):
+        print("No need to parse RDKit result. Simply access `result` attribute.")
 
     def finish(self):
         """