change subpackage structure

mordred/Atom/_descriptor.py

@@ -1,6 +1,12 @@
 from ._atom_count import AtomCount
 from ._carbon_types import CarbonTypes, HybridizationRatio
+from .._aromatic import AromaticAtomsCount
 
 
-_descriptors = [AtomCount, CarbonTypes, HybridizationRatio]
+_descriptors = [
+    AtomCount,
+    AromaticAtomsCount,
+    CarbonTypes,
+    HybridizationRatio
+]
 __all__ = [d.__name__ for d in _descriptors]

mordred/Matrix/_burden.py → mordred/BCUT/_descriptor.py

@@ -102,3 +102,7 @@ def calculate(self, mol, bev):
             return np.sort(bev)[nth]
         else:
             return np.nan
+
+
+_descriptors = [BCUT]
+__all__ = [d.__name__ for d in _descriptors]

mordred/Matrix/_barysz.py → mordred/BaryszMatrix/_descriptor.py

@@ -3,7 +3,7 @@
 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):
@@ -85,3 +85,7 @@ def __init__(self, prop='Z', method='SpMax'):
 
     def calculate(self, mol, result):
         return result
+
+
+_descriptors = [BaryszMatrix]
+__all__ = [d.__name__ for d in _descriptors]

mordred/Bond/_descriptor.py

@@ -1,9 +1,11 @@
 from ._bond_types import BondCount
+from .._aromatic import AromaticBondsCount
 from ._hbond import HBondAcceptor, HBondDonor
 from ._rotatable import RotatableBondsCount, RotatableBondsRatio
 
 _descriptors = [
     BondCount,
+    AromaticBondsCount,
     HBondAcceptor, HBondDonor,
     RotatableBondsCount, RotatableBondsRatio
 ]

mordred/DetourMatrix/_descriptor.py

@@ -0,0 +1,10 @@
+from ._matrix import DetourMatrix
+from ._index import DetourIndex
+
+
+_descriptors = [
+    DetourMatrix,
+    DetourIndex,
+]
+
+__all__ = [d.__name__ for d in _descriptors]

mordred/Indices/_detour.py → mordred/DetourMatrix/_index.py

@@ -1,5 +1,5 @@
 from .._base import Descriptor
-from ..Matrix._detour import detour_matrix
+from ._matrix import detour_matrix
 
 
 class DetourIndex(Descriptor):

mordred/Matrix/_detour.py → mordred/DetourMatrix/_matrix.py

@@ -1,7 +1,7 @@
 import networkx
 import numpy as np
 from .._base import Descriptor
-from . import _matrix_attributes as ma
+from .. import _matrix_attributes as ma
 
 
 class LongestSimplePath(object):

mordred/Matrix/_distance.py → mordred/DistanceMatrix/_descriptor.py

@@ -1,6 +1,6 @@
 from .._base import Descriptor
 from .._common import DistanceMatrix as D
-from ._matrix_attributes import methods, get_method
+from .._matrix_attributes import methods, get_method
 
 
 class DistanceMatrix(Descriptor):
@@ -48,3 +48,7 @@ def __init__(self, method='SpMax'):
 
     def calculate(self, mol, result):
         return result
+
+
+_descriptors = [DistanceMatrix]
+__all__ = [d.__name__ for d in _descriptors]

mordred/Indices/_eccentric_connectivity.py → mordred/EccentricConnectivityIndex/_descriptor.py

@@ -36,3 +36,7 @@ def dependencies(self):
 
     def calculate(self, mol, E, V):
         return (E.astype('int') * V).sum()
+
+
+_descriptors = [EccentricConnectivityIndex]
+__all__ = [d.__name__ for d in _descriptors]

mordred/Framework/_descriptor.py

@@ -1,5 +1,5 @@
 from .._base import Descriptor
-from ..Ring._descriptor import Rings
+from ..RingCount._descriptor import Rings
 import networkx as nx
 
 

mordred/Lipinski/_descriptor.py

@@ -1,6 +1,5 @@
 from .._base import Descriptor
-from ..Model import WildmanCrippen
-from ..Property import Weight
+from ..Property import Weight, WildmanCrippenLogP
 
 from rdkit.Chem import Lipinski as L
 
@@ -47,16 +46,16 @@ def __init__(self, variant='Lipinski'):
     @property
     def dependencies(self):
         return dict(
-            CLogP=WildmanCrippen.make_key('LogP'),
+            LogP=WildmanCrippenLogP.make_key('LogP'),
             Weight=Weight.make_key(),
         )
 
-    def Lipinski(self, mol, CLogP, Weight, **other):
+    def Lipinski(self, mol, LogP, Weight, **other):
         return\
             L.NumHDonors(mol) <= 5 and\
             L.NumHAcceptors(mol) <= 10 and\
             Weight <= 500 and\
-            CLogP <= 5
+            LogP <= 5
 
     def calculate(self, mol, **deps):
         return getattr(self, self.variant)(mol, **deps)

mordred/Property/_descriptor.py

@@ -1,6 +1,13 @@
 from ._weight import Weight
 from ._mc_gowan_volume import McGowanVolume
 from ._vdw_volume_abc import VdwVolumeABC
+from ._wildman_crippen_logp import WildmanCrippenLogP
+
+_descriptors = [
+    Weight,
+    McGowanVolume,
+    VdwVolumeABC,
+    WildmanCrippenLogP,
+]
 
-_descriptors = [Weight, McGowanVolume, VdwVolumeABC]
 __all__ = [d.__name__ for d in _descriptors]

mordred/Property/_vdw_volume_abc.py

@@ -1,6 +1,6 @@
 from .._base import Descriptor
 from ..Bond import BondCount
-from ..Ring import RingCount
+from ..RingCount import RingCount
 
 from rdkit import Chem
 from math import pi

mordred/Model/_descriptor.py → mordred/Property/_wildman_crippen_logp.py

@@ -2,7 +2,7 @@
 from rdkit.Chem import Crippen as _Crippen
 
 
-class WildmanCrippen(Descriptor):
+class WildmanCrippenLogP(Descriptor):
     r'''
     Wildman-Crippen LogP/MR descriptor
 
@@ -38,5 +38,5 @@ def calculate(self, mol):
         else:
             return _Crippen.MolMR(mol)
 
-_descriptors = [WildmanCrippen]
+_descriptors = [WildmanCrippenLogP]
 __all__ = [d.__name__ for d in _descriptors]

mordred/RingCount/__init__.py

@@ -0,0 +1 @@
+from ._descriptor import *

mordred/TopologicalIndex/__init__.py

@@ -0,0 +1 @@
+from ._descriptor import *

mordred/Indices/_topological.py → mordred/TopologicalIndex/_descriptor.py

@@ -110,3 +110,13 @@ def dependencies(self):
 
     def calculate(self, mol, R, D):
         return float(D - R) / float(D)
+
+
+_descriptors = [
+    Radius,
+    Diameter,
+    TopologicalShapeIndex,
+    PetitjeanIndex,
+]
+
+__all__ = [d.__name__ for d in _descriptors]

mordred/WalkCount/__init__.py

@@ -0,0 +1 @@
+from ._descriptor import *

mordred/WienerIndex/__init__.py

@@ -0,0 +1 @@
+from ._descriptor import *

mordred/Indices/_wiener.py → mordred/WienerIndex/_descriptor.py

@@ -46,3 +46,7 @@ def calculate(self, mol, D):
             return int(0.5 * (D == 3).sum())
         else:
             return int(0.5 * D.sum())
+
+
+_descriptors = [WienerIndex]
+__all__ = [d.__name__ for d in _descriptors]

mordred/ZagrebIndex/__init__.py

@@ -0,0 +1 @@
+from ._descriptor import *

mordred/Indices/_zagreb.py → mordred/ZagrebIndex/_descriptor.py

@@ -66,3 +66,7 @@ def calculate(self, mol, V):
                 (V[b.GetBeginAtomIdx()] * V[b.GetEndAtomIdx()]) ** self.variable
                 for b in mol.GetBonds()
             )
+
+
+_descriptors = [ZagrebIndex]
+__all__ = [d.__name__ for d in _descriptors]

mordred/Aromatic/_descriptor.py → mordred/_aromatic.py

@@ -1,4 +1,4 @@
-from .._base import Descriptor
+from ._base import Descriptor
 
 
 class AromaticAtomsCount(Descriptor):

mordred/Matrix/_matrix_attributes.py → mordred/_matrix_attributes.py

@@ -1,4 +1,4 @@
-from .._base import Descriptor
+from ._base import Descriptor
 import numpy as np
 from collections import namedtuple
 from six import string_types

tests/test_WildmanCrippen.py

@@ -1,13 +1,13 @@
-from mordred.Model import WildmanCrippen
+from mordred.Property import WildmanCrippenLogP as LogP
 from rdkit import Chem
 from numpy.testing import assert_almost_equal
 
 def test_WildmanCrippen1():
     mol = Chem.MolFromSmiles('Oc1ccccc1OC')
-    yield assert_almost_equal, WildmanCrippen('LogP')(mol), 1.4, 2
-    yield assert_almost_equal, WildmanCrippen('MR')(mol), 34.66, 2
+    yield assert_almost_equal, LogP('LogP')(mol), 1.4, 2
+    yield assert_almost_equal, LogP('MR')(mol), 34.66, 2
 
 
 def test_WildmanCrippen2():
     mol = Chem.MolFromSmiles('c1ccccc1c2ccccn2')
-    yield assert_almost_equal, WildmanCrippen('LogP')(mol), 2.75, 2
+    yield assert_almost_equal, LogP('LogP')(mol), 2.75, 2