change subpackage to submodule

mordred-descriptor · Jan 15, 2016 · 9206f65 · 9206f65
1 parent 33e6325
commit 9206f65
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diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,4 @@ __pycache__
 /.id_rsa
 /.id_rsa.pub
 /docs/_build
+/docs/api
diff --git a/docs/Makefile b/docs/Makefile
@@ -55,7 +55,7 @@ clean:
 
 .PHONY: apidoc
 apidoc:
-	$(SPHINXAPIDOC) -o api ../mordred
+	$(SPHINXAPIDOC) -o api --separate ../mordred
 	sed -i.bak -e 's/:undoc-members:/:imported-members:/g' api/*
 	rm api/*.bak
 

diff --git a/mordred/AcidBase.py b/mordred/AcidBase.py
@@ -0,0 +1 @@
+from ._acid_base import AcidicGroupCount, BasicGroupCount
diff --git a/mordred/AcidBase/__init__.py b/mordred/AcidBase/__init__.py
diff --git a/mordred/Atom.py b/mordred/Atom.py
@@ -0,0 +1,3 @@
+from ._atom_count import AtomCount
+from ._aromatic import AromaticAtomsCount
+from ._carbon_types import CarbonTypes, HybridizationRatio
diff --git a/mordred/Atom/__init__.py b/mordred/Atom/__init__.py
diff --git a/mordred/Atom/_descriptor.py b/mordred/Atom/_descriptor.py
diff --git a/mordred/Autocorrelation.py b/mordred/Autocorrelation.py
@@ -0,0 +1 @@
+from ._autocorrelation import ATS, AATS, ATSC, AATSC, MATS, GATS
diff --git a/mordred/Autocorrelation/__init__.py b/mordred/Autocorrelation/__init__.py
diff --git a/mordred/BCUT.py b/mordred/BCUT.py
@@ -0,0 +1 @@
+from ._bcut import BCUT
diff --git a/mordred/BCUT/__init__.py b/mordred/BCUT/__init__.py
diff --git a/mordred/BaryszMatrix.py b/mordred/BaryszMatrix.py
@@ -0,0 +1 @@
+from ._barysz_matrix import BaryszMatrix
diff --git a/mordred/BaryszMatrix/__init__.py b/mordred/BaryszMatrix/__init__.py
diff --git a/mordred/Bond.py b/mordred/Bond.py
@@ -0,0 +1,4 @@
+from ._bond_types import BondCount
+from ._aromatic import AromaticBondsCount
+from ._hbond import HBondAcceptor, HBondDonor
+from ._rotatable_bond import RotatableBondsCount, RotatableBondsRatio
diff --git a/mordred/Bond/__init__.py b/mordred/Bond/__init__.py
diff --git a/mordred/Bond/_descriptor.py b/mordred/Bond/_descriptor.py
diff --git a/mordred/Chi.py b/mordred/Chi.py
@@ -0,0 +1 @@
+from ._chi import Chi
diff --git a/mordred/Chi/__init__.py b/mordred/Chi/__init__.py
diff --git a/mordred/Constitutional.py b/mordred/Constitutional.py
@@ -0,0 +1 @@
+from ._constitutional import Sum, Mean
diff --git a/mordred/Constitutional/__init__.py b/mordred/Constitutional/__init__.py
diff --git a/mordred/DetourMatrix.py b/mordred/DetourMatrix.py
@@ -0,0 +1,2 @@
+from ._detour_matrix import DetourMatrix
+from ._detour_index import DetourIndex
diff --git a/mordred/DetourMatrix/__init__.py b/mordred/DetourMatrix/__init__.py
diff --git a/mordred/DetourMatrix/_descriptor.py b/mordred/DetourMatrix/_descriptor.py
diff --git a/mordred/DistanceMatrix.py b/mordred/DistanceMatrix.py
@@ -0,0 +1 @@
+from ._distance_matrix import DistanceMatrix
diff --git a/mordred/DistanceMatrix/__init__.py b/mordred/DistanceMatrix/__init__.py
diff --git a/mordred/EState.py b/mordred/EState.py
@@ -0,0 +1 @@
+from ._e_state import AtomTypeEState
diff --git a/mordred/EState/__init__.py b/mordred/EState/__init__.py
diff --git a/mordred/EccentricConnectivityIndex.py b/mordred/EccentricConnectivityIndex.py
@@ -0,0 +1 @@
+from ._eccentric_connectivity_index import EccentricConnectivityIndex
diff --git a/mordred/EccentricConnectivityIndex/__init__.py b/mordred/EccentricConnectivityIndex/__init__.py
diff --git a/mordred/FragmentComplexity.py b/mordred/FragmentComplexity.py
@@ -0,0 +1 @@
+from ._fragment_complexity import FragmentComplexity
diff --git a/mordred/FragmentComplexity/__init__.py b/mordred/FragmentComplexity/__init__.py
diff --git a/mordred/Framework.py b/mordred/Framework.py
@@ -0,0 +1 @@
+from ._framework import Framework
diff --git a/mordred/Framework/__init__.py b/mordred/Framework/__init__.py
diff --git a/mordred/InformationContent.py b/mordred/InformationContent.py
@@ -0,0 +1 @@
+from ._information_content import InformationContent
diff --git a/mordred/InformationContent/__init__.py b/mordred/InformationContent/__init__.py
diff --git a/mordred/KappaShapeIndex.py b/mordred/KappaShapeIndex.py
@@ -0,0 +1 @@
+from ._kappa_shape_index import KappaShapeIndex
diff --git a/mordred/KappaShapeIndex/__init__.py b/mordred/KappaShapeIndex/__init__.py
diff --git a/mordred/Lipinski.py b/mordred/Lipinski.py
@@ -0,0 +1 @@
+from ._lipinski import LipinskiLike
diff --git a/mordred/Lipinski/__init__.py b/mordred/Lipinski/__init__.py
diff --git a/mordred/MolecularDistanceEdge.py b/mordred/MolecularDistanceEdge.py
@@ -0,0 +1 @@
+from ._molecular_distance_edge import MolecularDistanceEdge
diff --git a/mordred/MolecularDistanceEdge/__init__.py b/mordred/MolecularDistanceEdge/__init__.py
diff --git a/mordred/Polarizability.py b/mordred/Polarizability.py
@@ -0,0 +1 @@
+from ._polarizability import APol, BPol
diff --git a/mordred/Polarizability/__init__.py b/mordred/Polarizability/__init__.py
diff --git a/mordred/Property/_descriptor.py → mordred/Property.py b/mordred/Property/_descriptor.py → mordred/Property.py
@@ -2,12 +2,3 @@
 from ._mc_gowan_volume import McGowanVolume
 from ._vdw_volume_abc import VdwVolumeABC
 from ._wildman_crippen_logp import WildmanCrippenLogP
-
-_descriptors = [
-    Weight,
-    McGowanVolume,
-    VdwVolumeABC,
-    WildmanCrippenLogP,
-]
-
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/Property/__init__.py b/mordred/Property/__init__.py
diff --git a/mordred/RingCount.py b/mordred/RingCount.py
@@ -0,0 +1 @@
+from ._ring_count import RingCount
diff --git a/mordred/RingCount/__init__.py b/mordred/RingCount/__init__.py
diff --git a/mordred/TPSA.py b/mordred/TPSA.py
@@ -0,0 +1 @@
+from ._tpsa import TPSA
diff --git a/mordred/TPSA/__init__.py b/mordred/TPSA/__init__.py
diff --git a/mordred/TopologicalCharge.py b/mordred/TopologicalCharge.py
@@ -0,0 +1 @@
+from ._topological_charge import TopologicalCharge
diff --git a/mordred/TopologicalCharge/__init__.py b/mordred/TopologicalCharge/__init__.py
diff --git a/mordred/TopologicalIndex.py b/mordred/TopologicalIndex.py
@@ -0,0 +1 @@
+from ._topological_index import Diameter, Radius, TopologicalShapeIndex, PetitjeanIndex
diff --git a/mordred/TopologicalIndex/__init__.py b/mordred/TopologicalIndex/__init__.py
diff --git a/mordred/WalkCount.py b/mordred/WalkCount.py
@@ -0,0 +1 @@
+from ._walk_count import WalkCount
diff --git a/mordred/WalkCount/__init__.py b/mordred/WalkCount/__init__.py
diff --git a/mordred/WienerIndex.py b/mordred/WienerIndex.py
@@ -0,0 +1 @@
+from ._wiener_index import WienerIndex
diff --git a/mordred/WienerIndex/__init__.py b/mordred/WienerIndex/__init__.py
diff --git a/mordred/ZagrebIndex.py b/mordred/ZagrebIndex.py
@@ -0,0 +1 @@
+from ._zagreb_index import ZagrebIndex
diff --git a/mordred/ZagrebIndex/__init__.py b/mordred/ZagrebIndex/__init__.py
diff --git a/mordred/__init__.py b/mordred/__init__.py
@@ -1 +1 @@
-from ._base import Descriptor, Calculator
+from ._base import Descriptor, Calculator, all_descriptors
diff --git a/mordred/AcidBase/_descriptor.py → mordred/_acid_base.py b/mordred/AcidBase/_descriptor.py → mordred/_acid_base.py
@@ -1,4 +1,4 @@
-from .._base import Descriptor
+from ._base import Descriptor
 from rdkit import Chem
 
 
@@ -49,7 +49,3 @@ class BasicGroupCount(SmartsCount):
         "[$(N=C-N)]",
         "[$(N-C=N)]",
     ]
-
-
-_descriptors = [AcidicGroupCount, BasicGroupCount]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/all/_all.py → mordred/_all.py b/mordred/all/_all.py → mordred/_all.py
diff --git a/mordred/Atom/_atom_count.py → mordred/_atom_count.py b/mordred/Atom/_atom_count.py → mordred/_atom_count.py
@@ -1,4 +1,4 @@
-from .._base import Descriptor
+from ._base import Descriptor
 
 
 class AtomCount(Descriptor):

diff --git a/mordred/Autocorrelation/_descriptor.py → mordred/_autocorrelation.py b/mordred/Autocorrelation/_descriptor.py → mordred/_autocorrelation.py
@@ -1,7 +1,7 @@
-from .._base import Descriptor
-from .. import _atomic_property
+from ._base import Descriptor
+from . import _atomic_property
 import numpy as np
-from .._common import DistanceMatrix
+from ._common import DistanceMatrix
 
 
 class AutocorrelationBase(Descriptor):
@@ -318,6 +318,3 @@ def calculate(self, mol, avec, gmat, gsum, cavec):
         n = (gmat * (W - W.T) ** 2).sum() / (4 * (gsum or np.nan))
         d = (cavec ** 2).sum() / (len(avec) - 1)
         return n / d
-
-_descriptors = [ATS, AATS, ATSC, AATSC, MATS, GATS]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/BaryszMatrix/_descriptor.py → mordred/_barysz_matrix.py b/mordred/BaryszMatrix/_descriptor.py → mordred/_barysz_matrix.py
@@ -1,9 +1,9 @@
-from .._base import Descriptor
-from .. import _atomic_property
+from ._base import Descriptor
+from . import _atomic_property
 from rdkit import Chem
 from scipy.sparse.csgraph import shortest_path
 import numpy as np
-from .._matrix_attributes import methods, get_method
+from ._matrix_attributes import methods, get_method
 
 
 class BaryszMatrixDescriptor(Descriptor):
@@ -85,7 +85,3 @@ def __init__(self, prop='Z', method='SpMax'):
 
     def calculate(self, mol, result):
         return result
-
-
-_descriptors = [BaryszMatrix]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/_base.py b/mordred/_base.py
@@ -3,8 +3,11 @@
 from six import with_metaclass
 from abc import ABCMeta, abstractmethod
 from types import ModuleType
+import os
+from importlib import import_module
 
 from inspect import getsourcelines
+
 try:
     from inspect import getfullargspec as getargspec
 except ImportError:
@@ -274,3 +277,21 @@ def __call__(self, mol):
             (desc.descriptor_name, self._calculate(desc, cache))
             for desc in self.descriptors
         )
+
+
+def all_descriptors():
+    r'''
+    yield all descriptors
+
+    Returns:
+        iterator<module>: all modules
+    '''
+
+    base_dir = os.path.dirname(__file__)
+
+    for name in os.listdir(base_dir):
+        name, ext = os.path.splitext(name)
+        if name[:1] == '_' or ext != '.py':
+            continue
+
+        yield import_module('..' + name, __name__)
diff --git a/mordred/BCUT/_descriptor.py → mordred/_bcut.py b/mordred/BCUT/_descriptor.py → mordred/_bcut.py
@@ -1,5 +1,5 @@
-from .._base import Descriptor
-from .. import _atomic_property
+from ._base import Descriptor
+from . import _atomic_property
 import numpy as np
 
 
@@ -102,7 +102,3 @@ def calculate(self, mol, bev):
             return np.sort(bev)[nth]
         else:
             return np.nan
-
-
-_descriptors = [BCUT]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/Bond/_bond_types.py → mordred/_bond_types.py b/mordred/Bond/_bond_types.py → mordred/_bond_types.py
@@ -1,4 +1,4 @@
-from .._base import Descriptor
+from ._base import Descriptor
 from rdkit.Chem import BondType
 
 

diff --git a/mordred/Atom/_carbon_types.py → mordred/_carbon_types.py b/mordred/Atom/_carbon_types.py → mordred/_carbon_types.py
@@ -1,5 +1,5 @@
 from collections import defaultdict
-from .._base import Descriptor
+from ._base import Descriptor
 
 
 class CarbonTypesBase(Descriptor):

diff --git a/mordred/Chi/_descriptor.py → mordred/_chi.py b/mordred/Chi/_descriptor.py → mordred/_chi.py
@@ -1,5 +1,5 @@
-from .._base import Descriptor
-from .. import _atomic_property
+from ._base import Descriptor
+from . import _atomic_property
 from rdkit import Chem
 from networkx import Graph
 from collections import namedtuple
@@ -186,7 +186,3 @@ def calculate(self, mol, chi=None):
             x /= len(node_sets) or np.nan
 
         return x
-
-
-_descriptors = [Chi]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/Constitutional/_descriptor.py → mordred/_constitutional.py b/mordred/Constitutional/_descriptor.py → mordred/_constitutional.py
@@ -1,5 +1,5 @@
-from .._base import Descriptor
-from .. import _atomic_property
+from ._base import Descriptor
+from . import _atomic_property
 from rdkit import Chem
 
 
@@ -72,7 +72,3 @@ def dependencies(self):
 
     def calculate(self, mol, S):
         return S / mol.GetNumAtoms()
-
-
-_descriptors = [Sum, Mean]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/DetourMatrix/_index.py → mordred/_detour_index.py b/mordred/DetourMatrix/_index.py → mordred/_detour_index.py
@@ -1,5 +1,5 @@
-from .._base import Descriptor
-from ._matrix import detour_matrix
+from ._base import Descriptor
+from ._detour_matrix import detour_matrix
 
 
 class DetourIndex(Descriptor):

diff --git a/mordred/DetourMatrix/_matrix.py → mordred/_detour_matrix.py b/mordred/DetourMatrix/_matrix.py → mordred/_detour_matrix.py
@@ -1,7 +1,7 @@
 import networkx
 import numpy as np
-from .._base import Descriptor
-from .. import _matrix_attributes as ma
+from ._base import Descriptor
+from . import _matrix_attributes as ma
 
 
 class LongestSimplePath(object):

diff --git a/mordred/DistanceMatrix/_descriptor.py → mordred/_distance_matrix.py b/mordred/DistanceMatrix/_descriptor.py → mordred/_distance_matrix.py
@@ -1,6 +1,6 @@
-from .._base import Descriptor
-from .._common import DistanceMatrix as D
-from .._matrix_attributes import methods, get_method
+from ._base import Descriptor
+from ._common import DistanceMatrix as D
+from ._matrix_attributes import methods, get_method
 
 
 class DistanceMatrix(Descriptor):
@@ -48,7 +48,3 @@ def __init__(self, method='SpMax'):
 
     def calculate(self, mol, result):
         return result
-
-
-_descriptors = [DistanceMatrix]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/mordred/EState/_descriptor.py → mordred/_e_state.py b/mordred/EState/_descriptor.py → mordred/_e_state.py
@@ -1,4 +1,4 @@
-from .._base import Descriptor
+from ._base import Descriptor
 from rdkit.Chem import EState as ES
 from numpy import nan
 from functools import reduce
@@ -100,6 +100,3 @@ def calculate(self, mol, E):
             return float(getattr(builtins, self.aggregate)(indices))
         except ValueError:  # min, max to empty list
             return nan
-
-_descriptors = [AtomTypeEState]
-__all__ = [d.__name__ for d in _descriptors]
diff --git a/...EccentricConnectivityIndex/_descriptor.py → mordred/_eccentric_connectivity_index.py b/...EccentricConnectivityIndex/_descriptor.py → mordred/_eccentric_connectivity_index.py
@@ -1,5 +1,5 @@
-from .._base import Descriptor
-from .._common import Eccentricity, Valence
+from ._base import Descriptor
+from ._common import Eccentricity, Valence
 
 
 class EccentricConnectivityIndex(Descriptor):
@@ -36,7 +36,3 @@ def dependencies(self):
 
     def calculate(self, mol, E, V):
         return (E.astype('int') * V).sum()
-
-
-_descriptors = [EccentricConnectivityIndex]
-__all__ = [d.__name__ for d in _descriptors]