Merge branch 'release/v0.5.0'

README.rst

@@ -184,7 +184,13 @@ Documentation
 -------------
 
 -  `master <http://mordred-descriptor.github.io/documentation/master>`__
+-  `develop <http://mordred-descriptor.github.io/documentation/develop>`__
 
+-  `v0.5.0 <http://mordred-descriptor.github.io/documentation/v0.5.0>`__
+-  `v0.4.1 <http://mordred-descriptor.github.io/documentation/v0.4.1>`__
+-  `v0.4.0 <http://mordred-descriptor.github.io/documentation/v0.4.0>`__
+-  `v0.3.2 <http://mordred-descriptor.github.io/documentation/v0.3.2>`__
+-  `v0.3.1 <http://mordred-descriptor.github.io/documentation/v0.3.1>`__
 -  `v0.3.0 <http://mordred-descriptor.github.io/documentation/v0.3.0>`__
 -  `v0.2.1 <http://mordred-descriptor.github.io/documentation/v0.2.1>`__
 -  `v0.2.0 <http://mordred-descriptor.github.io/documentation/v0.2.0>`__

docs/scripts/gen_default_descs.py

@@ -3,7 +3,7 @@
 
 load_path.nop()
 
-prelude = '''
+prelude = """
 Descriptor List
 ===============
 preset descriptors
@@ -13,42 +13,70 @@
     calc = Calculator(descriptors)
 
 .. csv-table:: Descriptor list
-    :header: "#", "module", "name", "constructor", "dim"
-    :widths: 10, 20, 20, 40, 10
+    :header: "#", "module", "name", "constructor", "dim", "description"
+    :widths: 1, 2, 2, 4, 1, 10
 
-'''[1:]
+"""[1:]
 
 
-def main(out):
-    out.write(prelude)
+class DescriptorInfo(object):
+    def __init__(self, d):
+        self.raw = d
 
-    i = 0
+    @property
+    def module(self):
+        return self.raw.__module__
 
-    for mdl in descriptors.all:
-        mdl_name = '.'.join(mdl.__name__.split('.'))
-        mdl_ppr = ':py:mod:`~{}`'.format(mdl_name)
-        first = True
+    @property
+    def constructor(self):
+        return self.raw.__class__.__name__
 
-        for Desc in get_descriptors_from_module(mdl):
+    @property
+    def parameters(self):
+        return [Descriptor._pretty(p) for p in self.raw.parameters()]
 
-            for desc in Desc.preset():
-                i += 1
+    @property
+    def dimention(self):
+        return "3D" if self.raw.require_3D else "2D"
+
+    @property
+    def description(self):
+        return self.raw.description()
+
+    def to_rst(self, hide_module=False):
+        mdl = "" if hide_module else ":py:mod:`~{}`".format(self.module)
+        desc = self.raw
+        cnst = ":py:class:`~{}.{}` ({})".format(
+            self.module, self.constructor, ", ".join(self.parameters))
+        info = self.description
+        dim = self.dimention
 
-                if not first:
-                    mdl_ppr = ''
+        return '{}, {}, "{}", {}, "{}"'.format(mdl, desc, cnst, dim, info)
 
-                cnst = desc.__class__.__name__
-                args = ', '.join(Descriptor._pretty(p) for p in desc.parameters())
 
-                cnst = ':py:class:`~{}.{}` ({})'.format(mdl_name, cnst, args)
+def get_all_descriptors():
+    for mdl in descriptors.all:
+        ds = []
+        for Desc in get_descriptors_from_module(mdl):
+            for desc in Desc.preset():
+                ds.append(desc)
 
-                dim = '3D' if desc.require_3D else '2D'
+        yield ds
 
-                out.write('    {}, {}, {}, "{}", {}\n'.format(i, mdl_ppr, desc, cnst, dim))
 
-                first = False
+def main(out):
+    out.write(prelude)
+
+    i = 0
+
+    for descs in get_all_descriptors():
+        first = True
+        for desc in descs:
+            i += 1
+            out.write("    {}, {}\n".format(i, DescriptorInfo(desc).to_rst(not first)))
+            first = False
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     import sys
     main(sys.stdout)

docs/scripts/gen_descriptor_list_xlsx.py

@@ -0,0 +1,41 @@
+from openpyxl import Workbook
+from openpyxl.styles import Font
+
+from gen_default_descs import DescriptorInfo, get_all_descriptors
+
+
+def main(out):
+    wb = Workbook()
+    ws = wb.active
+    ws.title = "descriptors"
+
+    ws.append(["index", "module", "name", "constructor", "dimention", "description"])
+    for cell in ws["1:1"]:
+        cell.font = Font(bold=True)
+
+    i = 0
+    for descs in get_all_descriptors():
+        first = True
+        for desc in descs:
+            i += 1
+            info = DescriptorInfo(desc)
+            ws.append([
+                i,
+                info.module.split(".")[-1] if first else None,
+                str(info.raw),
+                "{}({})".format(info.constructor, ", ".join(info.parameters)),
+                info.dimention,
+                info.description,
+            ])
+            first = False
+
+    for cells in ws.columns:
+        l = max(len(str(cell.value or "")) for cell in cells)
+        ws.column_dimensions[cells[0].column].width = l + 1
+
+    wb.save(out)
+
+
+if __name__ == "__main__":
+    import sys
+    main(sys.argv[1])

docs/subpackages/mordred.descriptors.rst

@@ -1,5 +1,5 @@
 mordred.descriptors
-=============
+===================
 
 .. automodule:: mordred.descriptors
     :members:

mordred/ABCIndex.py

@@ -41,6 +41,9 @@ class ABCIndex(ABCIndexBase):
 
     __slots__ = ()
 
+    def description(self):
+        return "atom-bond connectivity index"
+
     @staticmethod
     def _each_bond(bond):
         du = bond.GetBeginAtom().GetDegree()
@@ -67,6 +70,9 @@ class ABCGGIndex(ABCIndexBase):
 
     __slots__ = ()
 
+    def description(self):
+        return "Graovac-Ghorbani atom-bond connectivity index"
+
     def dependencies(self):
         return {"D": DistanceMatrix(self.explicit_hydrogens)}
 

mordred/AcidBase.py

@@ -51,6 +51,9 @@ class AcidicGroupCount(SmartsCountBase):
 
     __slots__ = ()
 
+    def description(self):
+        return "acidic group count"
+
     _name = "nAcid"
 
     SMARTS = (
@@ -66,6 +69,9 @@ class BasicGroupCount(SmartsCountBase):
 
     __slots__ = ()
 
+    def description(self):
+        return "basic group count"
+
     _name = "nBase"
 
     SMARTS = (

mordred/AdjacencyMatrix.py

@@ -15,6 +15,9 @@ class AdjacencyMatrix(Descriptor):
     __slots__ = ("_type",)
     explicit_hydrogens = False
 
+    def description(self):
+        return "{} of adjacency matrix".format(self._type.__name__)
+
     @classmethod
     def preset(cls):
         return map(cls, methods)

mordred/Aromatic.py

@@ -27,6 +27,9 @@ class AromaticAtomsCount(AromaticBase):
     __slots__ = ()
     _name = "nAromAtom"
 
+    def description(self):
+        return "aromatic atoms count"
+
     def calculate(self):
         return sum(
             1
@@ -41,6 +44,9 @@ class AromaticBondsCount(AromaticBase):
     __slots__ = ()
     _name = "nAromBond"
 
+    def description(self):
+        return "aromatic bonds count"
+
     def calculate(self):
         return sum(
             1

mordred/AtomCount.py

@@ -8,6 +8,15 @@
 )
 
 
+_desc_conv = {
+    "Atom": "all",
+    "Bridgehead": "bridgehead",
+    "HeavyAtom": "heavy",
+    "Spiro": "spiro",
+    "X": "halogen",
+}
+
+
 class AtomCount(Descriptor):
     r"""atom count descriptor.
 
@@ -24,6 +33,9 @@ class AtomCount(Descriptor):
 
     __slots__ = ("_type",)
 
+    def description(self):
+        return "number of {} atoms".format(_desc_conv.get(self._type, self._type))
+
     @classmethod
     def preset(cls):
         return map(cls, [

mordred/Autocorrelation.py

@@ -18,6 +18,10 @@ def __str__(self):
             self._avec.as_argument,
         )
 
+    def description(self):
+        return "{} of lag {} weighted by {}".format(
+            self._description_name, self._order, self._avec.get_long())
+
     def parameters(self):
         return self._order, self._prop
 
@@ -155,6 +159,8 @@ class ATS(AutocorrelationBase):
 
     __slots__ = ()
 
+    _description_name = "moreau-broto autocorrelation"
+
     @classmethod
     def preset(cls):
         return (
@@ -193,6 +199,8 @@ class AATS(ATS):
 
     __slots__ = ()
 
+    _description_name = "averaged moreau-broto autocorrelation"
+
     def dependencies(self):
         return {"ATS": self._ATS, "gsum": self._gsum}
 
@@ -216,6 +224,8 @@ class ATSC(AutocorrelationBase):
 
     __slots__ = ()
 
+    _description_name = "centered moreau-broto autocorrelation"
+
     @classmethod
     def preset(cls):
         return (
@@ -254,6 +264,8 @@ class AATSC(ATSC):
 
     __slots__ = ()
 
+    _description_name = "averaged and centered moreau-broto autocorrelation"
+
     def dependencies(self):
         return {"ATSC": self._ATSC, "gsum": self._gsum}
 
@@ -283,6 +295,8 @@ class MATS(AutocorrelationBase):
 
     __slots__ = ()
 
+    _description_name = "moran coefficient"
+
     @classmethod
     def preset(cls):
         return (
@@ -317,6 +331,8 @@ class GATS(MATS):
 
     __slots__ = ()
 
+    _description_name = "geary coefficient"
+
     def dependencies(self):
         return {
             "avec": self._avec,

mordred/BCUT.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from ._base import Descriptor
+from ._util import to_ordinal
 from ._atomic_property import AtomicProperty, get_properties
 
 __all__ = ("BCUT",)
@@ -87,6 +88,13 @@ class BCUT(BCUTBase):
 
     __slots__ = ("_prop", "_nth",)
 
+    def description(self):
+        return "{} {} eigenvalue of Burden matrix weighted by {}".format(
+            to_ordinal(np.abs(self._nth) if self._nth < 0 else 1 + self._nth),
+            "lowest" if self._nth < 0 else "heighest",
+            self._prop.get_long(),
+        )
+
     @classmethod
     def preset(cls):
         return (

mordred/BalabanJ.py

@@ -11,6 +11,9 @@ class BalabanJ(Descriptor):
 
     __slots__ = ()
 
+    def description(self):
+        return "Balaban's J index"
+
     explicit_hydrogens = False
 
     @classmethod

mordred/BaryszMatrix.py

@@ -64,6 +64,10 @@ class BaryszMatrix(BaryszMatrixBase):
 
     __slots__ = ("_prop", "_type",)
 
+    def description(self):
+        return "{} from Barysz matrix weighted by {}".format(
+            self._type.description(), self._prop.get_long())
+
     @classmethod
     def preset(cls):
         return (cls(p, m) for p in get_properties() for m in methods)

mordred/BertzCT.py

@@ -12,6 +12,9 @@ class BertzCT(Descriptor):
     __slots__ = ()
     explicit_hydrogens = False
 
+    def description(self):
+        return "Bertz CT"
+
     @classmethod
     def preset(cls):
         yield cls()