merge

Code/GraphMol/Descriptors/test_data/pmi.py

@@ -13,16 +13,17 @@ from rdkit.Chem import AllChem
 import numpy as np
 from numpy import linalg
 
+
 def GetMoments(mol, includeWeights):
   conf = mol.GetConformer()
   if includeWeights:
     weights = [x.GetMass() for x in mol.GetAtoms()]
   else:
-    weights = [1.0]*mol.GetNumAtoms()
+    weights = [1.0] * mol.GetNumAtoms()
 
   pts = [conf.GetAtomPosition(i) for i in range(mol.GetNumAtoms())]
   wSum = sum(weights)
-  origin = np.sum([pts[i]*weights[i] for i in range(mol.GetNumAtoms())], 0)
+  origin = np.sum([pts[i] * weights[i] for i in range(mol.GetNumAtoms())], 0)
   origin /= wSum
   sumXX = 0
   sumXY = 0
@@ -31,8 +32,8 @@ def GetMoments(mol, includeWeights):
   sumYZ = 0
   sumZZ = 0
   sums = np.zeros((3, 3), np.double)
-  for j,pt in enumerate(pts):
-    dp = weights[j]*(pt - origin)
+  for j, pt in enumerate(pts):
+    dp = weights[j] * (pt - origin)
     for i in range(3):
       sums[i, i] += dp[i] * dp[i]
       for j in range(i + 1, 3):
@@ -43,10 +44,12 @@ def GetMoments(mol, includeWeights):
   vals = sorted(vals)
   return vals
 
+
 if __name__ == '__main__':
   suppl = Chem.SDMolSupplier('./PBF_egfr.sdf', removeHs=False)
   output = open('./PMI_egfr.out', 'w+')
   for m in suppl:
-    i1,i2,i3 = GetMoments(m,True)
-    mi1,mi2,mi3 = GetMoments(m,False)
-    print("%s %.4f %.4f %.4f %.4f %.4f %.4f"%(m.GetProp("_Name"),i1,i2,i3,mi1,mi2,mi3),file=output)
+    i1, i2, i3 = GetMoments(m, True)
+    mi1, mi2, mi3 = GetMoments(m, False)
+    print("%s %.4f %.4f %.4f %.4f %.4f %.4f" % (m.GetProp("_Name"), i1, i2, i3, mi1, mi2, mi3),
+          file=output)

Code/GraphMol/MolDraw2D/test_dir/test_rdkit_draw.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-
+from __future__ import print_function
 from rdkit import RDConfig
 import os, sys
 from rdkit import Chem
@@ -12,11 +12,11 @@ if sys.argv[1].endswith('.sdf'):
 elif sys.argv[1].endswith('.smi'):
   suppl = Chem.SmilesMolSupplier(sys.argv[1])
 else:
-  print 'Need a file ending in .sdf or .smi'
+  print('Need a file ending in .sdf or .smi')
   exit(1)
 
 for mol in suppl:
-  print mol.GetProp('_Name')
+  print(mol.GetProp('_Name'))
   fn = mol.GetProp('_Name') + '.png'
   AllChem.Compute2DCoords(mol)
   Draw.MolToFile(mol, fn)

Code/GraphMol/StructChecker/Wrap/rough_test.py

@@ -159,20 +159,21 @@ M  CHG  1  11   1
 M  END
 """
 
-class TestCase(unittest.TestCase):
-    def testStructOptions(self):
-        rdStructChecker.StructCheckerOptions()
 
-    def testStructChecker(self):
-        checker = rdStructChecker.StructChecker()
-        
-        
-        m = Chem.MolFromMolBlock(data)
-        self.assertTrue(m)
-        
-        res = checker.CheckMolStructure(m)
-        self.assertEquals(res, rdStructChecker.StructureFlags.ATOM_CHECK_FAILED)
+class TestCase(unittest.TestCase):
+
+  def testStructOptions(self):
+    rdStructChecker.StructCheckerOptions()
+
+  def testStructChecker(self):
+    checker = rdStructChecker.StructChecker()
+
+    m = Chem.MolFromMolBlock(data)
+    self.assertTrue(m)
+
+    res = checker.CheckMolStructure(m)
+    self.assertEquals(res, rdStructChecker.StructureFlags.ATOM_CHECK_FAILED)
+
 
 if __name__ == '__main__':
-    unittest.main()
-        
+  unittest.main()

Code/GraphMol/Wrap/rough_test.py

@@ -514,14 +514,11 @@ class TestCase(unittest.TestCase):
     m.SetProp("int", "1000")
     m.SetProp("double", "10000.123")
     print(m.GetPropsAsDict())
-    self.assertEquals(m.GetPropsAsDict(),
-                      {"int":1000,
-                       "double":10000.123})
+    self.assertEquals(m.GetPropsAsDict(), {"int": 1000, "double": 10000.123})
 
     self.assertEquals(type(m.GetPropsAsDict()['int']), int)
     self.assertEquals(type(m.GetPropsAsDict()['double']), float)
 
-
   def test17Kekulize(self):
     m = Chem.MolFromSmiles('c1ccccc1')
     smi = Chem.MolToSmiles(m)

Code/GraphMol/Wrap/testConformer.py

@@ -122,7 +122,6 @@ class TestCase(unittest.TestCase):
     confs = m.GetConformers()
     self.assertTrue(confs == ())
 
-
   def test5PositionsArray(self):
     smi = 'c1ccccc1'
     m = Chem.MolFromSmiles(smi)
@@ -133,7 +132,7 @@ class TestCase(unittest.TestCase):
 
     for conf in confs:
       pos = conf.GetPositions()
-      self.assertTrue(pos.shape, (6,3))
+      self.assertTrue(pos.shape, (6, 3))
 
     m.RemoveAllConformers()
     self.assertTrue(m.GetNumConformers() == 0)

Code/cmake/Modules/fixup_coverage.py

@@ -3,10 +3,10 @@ the coverage tool mistakenly finds in the build tree.
 It replaces the paths with the ones from the source tree
 n.b. if a file with the same name (i.e. sln.yy) is found twice
  in the source tree, this will break"""
-
+from __future__ import print_function
 import os, sys
 source_dir, info_file = sys.argv[1:3]
-print source_dir, info_file
+print(source_dir, info_file)
 
 paths = {}
 for root, dir, files in os.walk(source_dir):
@@ -20,13 +20,13 @@ for line in lines:
   if "SF:" in line:
     fn = line.split("SF:")[-1].strip()
     if not os.path.exists(fn):
-      print "Does not exist:", fn.strip()
+      print("Does not exist:", fn.strip())
       head, rest = os.path.split(fn)
       potential = paths[rest]
       if len(potential) == 1:
         line = "SF:" + potential[0]
       else:
-        asdf
+        raise NotImplementedError('asdf')
   newlines.append(line)
 
 open(info_file, 'w').write("\n".join(newlines))

Scripts/PythonFormat.py

@@ -0,0 +1,69 @@
+'''
+
+Script will test the RDkit python code for conformance with the agreed format using
+yapf.
+
+For each Python file that is found in $RDBASE (excluding the build and External
+directories), yapf is used with the style configuration in $RDBASE/setup.cfg.
+If a change is required, the difference is printed. At the end of the process,
+all non-conformant files are listed and the required yapf command(s) printed.
+
+If changes are found, the script will exit with error code 1, otherwise 0.
+
+'''
+from __future__ import print_function
+import os
+from yapf.yapflib.yapf_api import FormatCode
+import sys
+
+rdbase = os.environ.get('RDBASE', '')
+styleConfig = os.path.join(rdbase, 'setup.cfg')
+
+excludeDirs = [os.path.join(rdbase, 'build'),
+               os.path.join(rdbase, 'External'), ]
+
+
+def pythonFiles(dirname=rdbase):
+  """ Find all python files below directory dirname """
+  for root, _, files in os.walk(dirname):
+    if any(root.startswith(d) for d in excludeDirs):
+      continue
+    for file in files:
+      if file.endswith(".py"):
+        yield os.path.join(root, file)
+
+
+def yapfChanges(filename):
+  """ Use yapf with the default settings to format file filename """
+  try:
+    with open(filename) as f:
+      codeBefore = f.read()
+  except UnicodeError:
+    with open(filename, encoding='latin-1') as f:
+      codeBefore = f.read()
+  try:
+    changes, changed = FormatCode(codeBefore, style_config=styleConfig, print_diff=True,
+                                  filename=filename)
+  except Exception:
+    print(filename)
+    raise
+  if changed:
+    print(changes)
+  return changed
+
+
+if __name__ == "__main__":
+  changedFiles = []
+  for s in pythonFiles():
+    if yapfChanges(s):
+      changedFiles.append(s)
+  print()
+  if changedFiles:
+    print('yapf will make changes to the following files:')
+    print('\n'.join(sorted(changedFiles)))
+    print('To apply the required changes to your code use the following command(s)')
+    for s in sorted(set(s.replace(rdbase, '').split(os.sep)[1] for s in changedFiles)):
+      print('yapf --style $RDBASE/setup.cfg --in-place --recursive $RDBASE/{0}'.format(s))
+    sys.exit(1)
+  print('Code complies with the agreed formatting rules.')
+  sys.exit(0)

rdkit/Chem/Descriptors3D.py

@@ -13,10 +13,10 @@
 from __future__ import print_function
 from rdkit.Chem import rdMolDescriptors
 
-if hasattr(rdMolDescriptors,'CalcPMI1'):
-    PMI1 = lambda *x,**y:rdMolDescriptors.CalcPMI1(*x,**y)
-    PMI1.version = rdMolDescriptors._CalcPMI1_version
-    PMI1.__doc__= """ First (smallest) principal moment of inertia
+if hasattr(rdMolDescriptors, 'CalcPMI1'):
+  PMI1 = lambda *x, **y: rdMolDescriptors.CalcPMI1(*x, **y)
+  PMI1.version = rdMolDescriptors._CalcPMI1_version
+  PMI1.__doc__ = """ First (smallest) principal moment of inertia
 
     **Arguments**
 
@@ -27,9 +27,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    PMI2 = lambda *x,**y:rdMolDescriptors.CalcPMI2(*x,**y)
-    PMI2.version = rdMolDescriptors._CalcPMI2_version
-    PMI2.__doc__= """ Second principal moment of inertia
+  PMI2 = lambda *x, **y: rdMolDescriptors.CalcPMI2(*x, **y)
+  PMI2.version = rdMolDescriptors._CalcPMI2_version
+  PMI2.__doc__ = """ Second principal moment of inertia
 
     **Arguments**
 
@@ -40,9 +40,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    PMI3 = lambda *x,**y:rdMolDescriptors.CalcPMI3(*x,**y)
-    PMI3.version = rdMolDescriptors._CalcPMI3_version
-    PMI3.__doc__= """ Third (largest) principal moment of inertia
+  PMI3 = lambda *x, **y: rdMolDescriptors.CalcPMI3(*x, **y)
+  PMI3.version = rdMolDescriptors._CalcPMI3_version
+  PMI3.__doc__ = """ Third (largest) principal moment of inertia
 
     **Arguments**
 
@@ -53,9 +53,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    NPR1 = lambda *x,**y:rdMolDescriptors.CalcNPR1(*x,**y)
-    NPR1.version = rdMolDescriptors._CalcNPR1_version
-    NPR1.__doc__= """ Normalized principal moments ratio 1 (=I1/I3)
+  NPR1 = lambda *x, **y: rdMolDescriptors.CalcNPR1(*x, **y)
+  NPR1.version = rdMolDescriptors._CalcNPR1_version
+  NPR1.__doc__ = """ Normalized principal moments ratio 1 (=I1/I3)
 
         from Sauer and Schwarz JCIM 43:987-1003 (2003)
         https://dx.doi.org/10.1021/ci025599w
@@ -70,9 +70,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    NPR2 = lambda *x,**y:rdMolDescriptors.CalcNPR2(*x,**y)
-    NPR2.version = rdMolDescriptors._CalcNPR2_version
-    NPR2.__doc__= """ Normalized principal moments ratio 2 (=I2/I3)
+  NPR2 = lambda *x, **y: rdMolDescriptors.CalcNPR2(*x, **y)
+  NPR2.version = rdMolDescriptors._CalcNPR2_version
+  NPR2.__doc__ = """ Normalized principal moments ratio 2 (=I2/I3)
 
         from Sauer and Schwarz JCIM 43:987-1003 (2003)
         https://dx.doi.org/10.1021/ci025599w
@@ -87,9 +87,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    RadiusOfGyration = lambda *x,**y:rdMolDescriptors.CalcRadiusOfGyration(*x,**y)
-    RadiusOfGyration.version = rdMolDescriptors._CalcRadiusOfGyration_version
-    RadiusOfGyration.__doc__= """ Radius of gyration
+  RadiusOfGyration = lambda *x, **y: rdMolDescriptors.CalcRadiusOfGyration(*x, **y)
+  RadiusOfGyration.version = rdMolDescriptors._CalcRadiusOfGyration_version
+  RadiusOfGyration.__doc__ = """ Radius of gyration
 
        from Todeschini and Consoni "Descriptors from Molecular Geometry"
        Handbook of Chemoinformatics
@@ -108,9 +108,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    InertialShapeFactor = lambda *x,**y:rdMolDescriptors.CalcInertialShapeFactor(*x,**y)
-    InertialShapeFactor.version = rdMolDescriptors._CalcInertialShapeFactor_version
-    InertialShapeFactor.__doc__= """ Inertial shape factor
+  InertialShapeFactor = lambda *x, **y: rdMolDescriptors.CalcInertialShapeFactor(*x, **y)
+  InertialShapeFactor.version = rdMolDescriptors._CalcInertialShapeFactor_version
+  InertialShapeFactor.__doc__ = """ Inertial shape factor
 
        from Todeschini and Consoni "Descriptors from Molecular Geometry"
        Handbook of Chemoinformatics
@@ -128,9 +128,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    Eccentricity = lambda *x,**y:rdMolDescriptors.CalcEccentricity(*x,**y)
-    Eccentricity.version = rdMolDescriptors._CalcEccentricity_version
-    Eccentricity.__doc__= """ molecular eccentricity
+  Eccentricity = lambda *x, **y: rdMolDescriptors.CalcEccentricity(*x, **y)
+  Eccentricity.version = rdMolDescriptors._CalcEccentricity_version
+  Eccentricity.__doc__ = """ molecular eccentricity
 
        from Todeschini and Consoni "Descriptors from Molecular Geometry"
        Handbook of Chemoinformatics
@@ -148,9 +148,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    Asphericity = lambda *x,**y:rdMolDescriptors.CalcAsphericity(*x,**y)
-    Asphericity.version = rdMolDescriptors._CalcAsphericity_version
-    Asphericity.__doc__= """ molecular asphericity
+  Asphericity = lambda *x, **y: rdMolDescriptors.CalcAsphericity(*x, **y)
+  Asphericity.version = rdMolDescriptors._CalcAsphericity_version
+  Asphericity.__doc__ = """ molecular asphericity
 
        from Todeschini and Consoni "Descriptors from Molecular Geometry"
        Handbook of Chemoinformatics
@@ -168,9 +168,9 @@ if hasattr(rdMolDescriptors,'CalcPMI1'):
       - useAtomicMasses: (optional) toggles use of atomic masses in the
         calculation. Defaults to True
     """
-    SpherocityIndex = lambda *x,**y:rdMolDescriptors.CalcSpherocityIndex(*x,**y)
-    SpherocityIndex.version = rdMolDescriptors._CalcSpherocityIndex_version
-    SpherocityIndex.__doc__= """ Molecular spherocityIndex
+  SpherocityIndex = lambda *x, **y: rdMolDescriptors.CalcSpherocityIndex(*x, **y)
+  SpherocityIndex.version = rdMolDescriptors._CalcSpherocityIndex_version
+  SpherocityIndex.__doc__ = """ Molecular spherocityIndex
 
        from Todeschini and Consoni "Descriptors from Molecular Geometry"
        Handbook of Chemoinformatics

rdkit/Chem/Draw/IPythonConsole.py

@@ -60,6 +60,7 @@ shader_3d = "lambert"
 #  in the IPythonConsole not the server logs.
 Chem.WrapLogs()
 
+
 def _toJSON(mol):
   """For IPython notebook, renders 3D webGL objects."""
 
@@ -220,8 +221,7 @@ def InstallIPythonRenderer():
   _MolsToGridImageSaved = Draw.MolsToGridImage
   Draw.MolsToGridImage = ShowMols
   rdchem.Mol.__DebugMol = rdchem.Mol.Debug
-  rdchem.Mol.Debug = lambda self,useStdout=False:self.__DebugMol(useStdout=useStdout)
-
+  rdchem.Mol.Debug = lambda self, useStdout=False: self.__DebugMol(useStdout=useStdout)
 
 
 InstallIPythonRenderer()

rdkit/Chem/Draw/UnitTestIPython.py

@@ -13,31 +13,29 @@ import unittest
 from rdkit import Chem
 from rdkit.Chem import Draw
 try:
-    from rdkit.Chem.Draw import IPythonConsole
-    from IPython.core.display import SVG
+  from rdkit.Chem.Draw import IPythonConsole
+  from IPython.core.display import SVG
 except ImportError:
-    IPythonConsole = None
+  IPythonConsole = None
+
 
 class TestCase(unittest.TestCase):
+
   def testGithub1089(self):
     if IPythonConsole is None:
-        return
+      return
     m = Chem.MolFromSmiles('CCCC')
 
     IPythonConsole.ipython_useSVG = False
-    res = Draw.MolsToGridImage((m,m))
-    self.assertFalse(isinstance(res,SVG))
+    res = Draw.MolsToGridImage((m, m))
+    self.assertFalse(isinstance(res, SVG))
 
-    res = Draw.MolsToGridImage((m,m),useSVG=True)
-    self.assertTrue(isinstance(res,SVG))
+    res = Draw.MolsToGridImage((m, m), useSVG=True)
+    self.assertTrue(isinstance(res, SVG))
 
     IPythonConsole.ipython_useSVG = True
-    res = Draw.MolsToGridImage((m,m))
-    self.assertTrue(isinstance(res,SVG))
-
-
-
-
+    res = Draw.MolsToGridImage((m, m))
+    self.assertTrue(isinstance(res, SVG))
 
 
 if __name__ == '__main__':

rdkit/Chem/Draw/cairoCanvas.py

@@ -126,7 +126,7 @@ if not 'RDK_NOPANGO' in os.environ:
       except ImportError:
         exec(libType + ' = None')
     have_pango = (pango and pangocairo)
-    
+
 if not hasattr(cairo.ImageSurface,'get_data') and \
    not hasattr(cairo.ImageSurface,'get_data_as_rgba'):
   raise ImportError('cairo version too old')
@@ -296,7 +296,7 @@ class Canvas(CanvasBase):
     # for whatever reason, the font size using pango is larger
     # than that w/ default cairo (at least for me)
     pangoCoeff = 0.8
-    
+
     if (have_cairocffi):
       measureLout = pangocairo.pango_cairo_create_layout(self.ctx._pointer)
       pango.pango_layout_set_alignment(measureLout, pango.PANGO_ALIGN_LEFT)
@@ -307,25 +307,25 @@ class Canvas(CanvasBase):
       fnt = pango.pango_font_description_new()
       pango.pango_font_description_set_family(fnt, font.face.encode('latin1'))
       pango.pango_font_description_set_size(fnt,
-        int(round(font.size * pango.PANGO_SCALE * pangoCoeff)))
+                                            int(round(font.size * pango.PANGO_SCALE * pangoCoeff)))
       pango.pango_layout_set_font_description(lout, fnt)
       pango.pango_layout_set_font_description(measureLout, fnt)
       pango.pango_font_description_free(fnt)
     else:
-      cctx=pangocairo.CairoContext(self.ctx)
+      cctx = pangocairo.CairoContext(self.ctx)
       measureLout = cctx.create_layout()
       measureLout.set_alignment(pango.ALIGN_LEFT)
       measureLout.set_markup(plainText)
       lout = cctx.create_layout()
       lout.set_alignment(pango.ALIGN_LEFT)
       lout.set_markup(text)
-      fnt = pango.FontDescription('%s %d'%(font.face,font.size*pangoCoeff))
+      fnt = pango.FontDescription('%s %d' % (font.face, font.size * pangoCoeff))
       lout.set_font_description(fnt)
       measureLout.set_font_description(fnt)
 
     # this is a bit kludgy, but empirically we end up with too much
     # vertical padding if we use the text box with super and subscripts
-    # for the measurement. 
+    # for the measurement.
     if (have_cairocffi):
       iext = ffi.new('PangoRectangle *')
       lext = ffi.new('PangoRectangle *')

rdkit/TestRunner.py

@@ -107,8 +107,8 @@ def RunScript(script, doLongTests, verbose):
   nTests = len(tests) + len(longTests)
   del sys.modules[script]
   if verbose and failed:
-    for exeName,args,extras in failed:
-        print("!!! TEST FAILURE: ",exeName,args,extras,file=sys.stderr)
+    for exeName, args, extras in failed:
+      print("!!! TEST FAILURE: ", exeName, args, extras, file=sys.stderr)
   return failed, nTests