add Result type

docs/mordred.rst

@@ -3,6 +3,9 @@ mordred package
 
 .. automodule:: mordred
 
+.. autoclass:: mordred.Result
+    :members:
+
 .. autoclass:: mordred.Descriptor
     :members:
 

mordred/__init__.py

@@ -6,6 +6,7 @@
     Descriptor,
     get_descriptors_from_module,
     is_missing,
+    Result,
 )
 
 from ._version import __version__
@@ -17,4 +18,5 @@
     "all_descriptors",
     "get_descriptors_from_module",
     "is_missing",
+    "Result",
 )

mordred/_base/__init__.py

@@ -1,9 +1,5 @@
 """Mordred base package."""
 
-import os
-import warnings
-
-from importlib import import_module
 from ..error import MissingValueBase
 
 from .descriptor import (
@@ -12,6 +8,8 @@
 )
 from .calculator import Calculator, get_descriptors_from_module
 from .parallel import parallel
+from .util import is_missing, all_descriptors
+from .result import Result
 
 
 __all__ = (
@@ -20,32 +18,10 @@
     "Calculator",
     "get_descriptors_from_module",
     "is_missing",
+    "Result",
 )
 
 
-def all_descriptors():
-    r"""**[deprecated]** use mordred.descriptors module instead.
-
-    yield all descriptor modules.
-
-    :returns: all modules
-    :rtype: :py:class:`Iterator` (:py:class:`Descriptor`)
-    """
-    warnings.warn(
-        "all_descriptors() is deprecated, use mordred.descriptors module instead",
-        DeprecationWarning,
-        stacklevel=2,
-    )
-    base_dir = os.path.dirname(os.path.dirname(__file__))
-
-    for name in os.listdir(base_dir):
-        name, ext = os.path.splitext(name)
-        if name[:1] == "_" or ext != ".py" or name == "descriptors":
-            continue
-
-        yield import_module(".." + name, __package__)
-
-
 def _Descriptor__call__(self, mol, id=-1):
     r"""Calculate single descriptor value.
 
@@ -116,19 +92,6 @@ def _Descriptor_from_json(self, obj):
     return _from_json(obj, descs)
 
 
-def is_missing(v):
-    """Check argument is either MissingValue or not.
-
-    Parameters:
-        v(any): value
-
-    Returns:
-        bool
-
-    """
-    return isinstance(v, MissingValueBase)
-
-
 Descriptor.__call__ = _Descriptor__call__
 Descriptor.from_json = _Descriptor_from_json
 Calculator._parallel = parallel

mordred/_base/calculator.py

@@ -9,6 +9,7 @@
 
 from .._util import Capture, DummyBar, NotebookWrapper
 from ..error import Error, Missing, MultipleFragments, DuplicatedDescriptorName
+from .result import Result
 from .context import Context
 from .descriptor import Descriptor, MissingValueException, is_descriptor_class
 
@@ -235,16 +236,21 @@ def __call__(self, mol, id=-1):
         :type id: int
         :param id: conformer id
 
-        :rtype: [scalar or Error]
+        :rtype: Result[scalar or Error]
         :returns: iterator of descriptor and value
         """
-        return list(self._calculate(Context.from_calculator(self, mol, id)))
+        return self._wrap_result(
+            self._calculate(Context.from_calculator(self, mol, id)),
+        )
+
+    def _wrap_result(self, r):
+        return Result(r, self._descriptors)
 
     def _serial(self, mols, nmols, quiet, ipynb, id):
         with self._progress(quiet, nmols, ipynb) as bar:
             for m in mols:
                 with Capture() as capture:
-                    r = list(self._calculate(Context.from_calculator(self, m, id)))
+                    r = self._wrap_result(self._calculate(Context.from_calculator(self, m, id)))
 
                 for e in capture.result:
                     e = e.rstrip()
@@ -314,7 +320,7 @@ def map(self, mols, nproc=None, nmols=None, quiet=False, ipynb=False, id=-1):
             id(int): conformer id to use. default: -1.
 
         Returns:
-            Iterator[scalar]
+            Iterator[Result[scalar]]
 
         """
         if hasattr(mols, "__len__"):

mordred/_base/parallel.py

@@ -50,7 +50,7 @@ def do_task(mol):
 
                     bar.write(e)
 
-                yield r
+                yield self._wrap_result(r)
                 bar.update()
 
     finally:

mordred/_base/result.py

@@ -0,0 +1,63 @@
+from .util import is_missing
+
+
+class Result(list):
+    r"""Result type."""
+
+    def __init__(self, r, d):
+        super(Result, self).__init__(r)
+        self._descriptors = d
+
+    def fillna(self, value=float('nan')):
+        r"""Replace missing value to 'value'.
+
+        Parameters:
+            value: value that missing value is replaced
+
+        Returns:
+            Result
+
+        """
+        return self.__class__(
+            [(value if is_missing(v) else v) for v in self],
+            self._descriptors,
+        )
+
+    def dropna(self):
+        r"""Delete missing value.
+
+        Returns:
+            Result
+
+        """
+        newvalues = []
+        newdescs = []
+        for v, d in zip(self, self._descriptors):
+            if not is_missing(v):
+                newvalues.append(v)
+                newdescs.append(d)
+
+        return self.__class__(newvalues, newdescs)
+
+    def asdict(self, rawkey=False):
+        r"""Convert Result to dict.
+
+        Parameters:
+            rawkey(bool):
+                * True: dict key is Descriptor instance
+                * False: dict key is str
+
+        Returns:
+            dict
+
+        """
+        if rawkey:
+            def keyconv(k):
+                return k
+        else:
+            keyconv = str
+
+        return {
+            keyconv(k): v
+            for k, v in zip(self._descriptors, self)
+        }

mordred/_base/util.py

@@ -0,0 +1,41 @@
+import os
+import warnings
+from importlib import import_module
+
+from ..error import MissingValueBase
+
+
+def all_descriptors():
+    r"""**[deprecated]** use mordred.descriptors module instead.
+
+    yield all descriptor modules.
+
+    :returns: all modules
+    :rtype: :py:class:`Iterator` (:py:class:`Descriptor`)
+    """
+    warnings.warn(
+        "all_descriptors() is deprecated, use mordred.descriptors module instead",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    base_dir = os.path.dirname(os.path.dirname(__file__))
+
+    for name in os.listdir(base_dir):
+        name, ext = os.path.splitext(name)
+        if name[:1] == "_" or ext != ".py" or name == "descriptors":
+            continue
+
+        yield import_module(".." + name, __package__)
+
+
+def is_missing(v):
+    """Check argument is either MissingValue or not.
+
+    Parameters:
+        v(any): value
+
+    Returns:
+        bool
+
+    """
+    return isinstance(v, MissingValueBase)

scripts/requirements-flake8.txt

@@ -1,5 +1,5 @@
+pep8
 flake8
-flake8-isort
 flake8-double-quotes
 flake8-print
 flake8-commas