Numpy 2 Support (#7531)

* facilitate numpy 2.0 support

* so that all tests run smoothly

* not yet ready for this

* w/ casting to bool

* remove formatting changes from this PR

Code/GraphMol/Descriptors/test3D.py

@@ -27,7 +27,7 @@ def generateAll():
     r = get3D(m, True)
     print(r)
   end = time.time()
-  print end - start
+  print(end - start)
 
 
 def simple_case():
@@ -35,9 +35,9 @@ def simple_case():
   smi = 'CCC(C)COCCCC'
   m = Chem.MolFromSmiles(smi)
   T = get3D(m, False)
-  print T
+  print(T)
   end = time.time()
-  print end - start
+  print(end - start)
 
 
 if (__name__ == '__main__'):
@@ -49,6 +49,6 @@ if (__name__ == '__main__'):
   smi = 'CCC(C)COCCCC'
   m = Chem.MolFromSmiles(smi)
   T = get3D(m, False)
-  print T
+  print(T)
   end = time.time()
-  print end - start
+  print(end - start)

Code/GraphMol/Descriptors/test3D_old.py

@@ -5,8 +5,8 @@ from rdkit.Chem import AllChem
 from rdkit.Chem import rdMolDescriptors as rdMD
 from rdkit.Chem.EState import AtomTypes, EStateIndices
 
-print rdBase.rdkitVersion
-print rdBase.boostVersion
+print(rdBase.rdkitVersion)
+print(rdBase.boostVersion)
 
 
 def getEState(mol):
@@ -27,7 +27,7 @@ def make3D(mol, steps=50):
   if success == -1:  # Failed
     success = AllChem.EmbedMolecule(mol, useRandomCoords=True)
     if success == -1:
-      raise Error, "Embedding failed!"
+      raise (Error, "Embedding failed!")
   mol = localopt(mol, steps)
   return mol
 
@@ -56,7 +56,7 @@ def generateALL():
     thefile.write("\n")
 
   end = time.time()
-  print end - start
+  print(end - start)
 
 
 thefile = open('testSMWHIM.txt', 'w')
@@ -72,14 +72,14 @@ for smi in A:
   m = Chem.MolFromSmiles(smi)
   m = localopt(m, 100)
   #r=get3D(m,True)
-  print smi
-  print "---------"
+  print(smi)
+  print("---------")
   r = rdMD.CalcWHIM(m)
-  print "Ei:" + str(r[0]) + "," + str(r[1]) + "," + str(r[2]) + "\n"
-  print "Gi:" + str(r[5]) + "," + str(r[6]) + "," + str(r[7]) + "\n"
-  print "SI:" + str(rdMD.CalcSpherocityIndex(m))
-  print "AS:" + str(rdMD.CalcAsphericity(m))
-  print "EX:" + str(rdMD.CalcEccentricity(m))
+  print("Ei:" + str(r[0]) + "," + str(r[1]) + "," + str(r[2]) + "\n")
+  print("Gi:" + str(r[5]) + "," + str(r[6]) + "," + str(r[7]) + "\n")
+  print("SI:" + str(rdMD.CalcSpherocityIndex(m)))
+  print("AS:" + str(rdMD.CalcAsphericity(m)))
+  print("EX:" + str(rdMD.CalcEccentricity(m)))
   for item in r:
     thefile.write("%.3f," % item)
   thefile.write("\n")
@@ -110,4 +110,4 @@ for smi in B:
   #writer.write(m)
 
 A = "G1w,G2w,G3w,Gw"
-print dir(rdMD)
+print(dir(rdMD))

Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp

@@ -14,6 +14,7 @@
 #include <boost/python.hpp>
 #include <RDBoost/boost_numpy.h>
 #include <numpy/npy_common.h>
+#include <numpy/ndarrayobject.h>
 #include <RDBoost/import_array.h>
 #include <GraphMol/RDKitBase.h>
 #include <GraphMol/Fingerprints/FingerprintGenerator.h>

Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py

@@ -48,7 +48,9 @@ def assignFilters(data, nameSmilesColumn='smiles'):
   sma = Chem.MolFromSmarts(NO_filter, mergeHs=True)
 
   for smi in data[nameSmilesColumn]:
-    qc, NO_filter, fracNO, co, sc, sm = [np.NaN] * 6
+    qc, NO_filter, fracNO, co, sc, sm = [np.nan] * 6
+
+# The following files require numpy and were explicitely checked for their compatibility.
 
     try:
       mol = Chem.MolFromSmiles(smi)

rdkit/Chem/Pharm3D/EmbedLib.py

@@ -507,9 +507,9 @@ def OptimizeMol(mol, bm, atomMatches=None, excludedVolumes=None, forceConstant=1
     >>> p0 = conf.GetAtomPosition(0)
     >>> p3 = conf.GetAtomPosition(3)
     >>> d03 = p0.Distance(p3)
-    >>> d03 >= pcophore.getLowerBound(0,1) - 0.01
+    >>> bool(d03 >= pcophore.getLowerBound(0,1) - 0.01)
     True
-    >>> d03 <= pcophore.getUpperBound(0,1) + 0.01
+    >>> bool(d03 <= pcophore.getUpperBound(0,1) + 0.01)
     True
 
     If we optimize without the distance constraints (provided via the atomMatches
@@ -525,9 +525,9 @@ def OptimizeMol(mol, bm, atomMatches=None, excludedVolumes=None, forceConstant=1
     >>> p0 = conf.GetAtomPosition(0)
     >>> p3 = conf.GetAtomPosition(3)
     >>> d03 = p0.Distance(p3)
-    >>> d03 >= pcophore.getLowerBound(0, 1) - 0.01
+    >>> bool(d03 >= pcophore.getLowerBound(0, 1) - 0.01)
     True
-    >>> d03 <= pcophore.getUpperBound(0, 1) + 0.01
+    >>> bool(d03 <= pcophore.getUpperBound(0, 1) + 0.01)
     False
 
   """
@@ -862,7 +862,7 @@ def CombiEnum(sequence):
 
 
 def DownsampleBoundsMatrix(bm, indices, maxThresh=4.0):
-  """ Removes rows from a bounds matrix that are that are greater 
+  """ Removes rows from a bounds matrix that are that are greater
   than a threshold value away from a set of other points
 
   Returns the modfied bounds matrix
@@ -992,10 +992,10 @@ def CoarseScreenPharmacophore(atomMatch, bounds, pcophore, verbose=False):
   >>> pcophore.setUpperBound(1,3, 1.9)
   >>> pcophore.setLowerBound(2,3, 1.1)
   >>> pcophore.setUpperBound(2,3, 1.9)
-  >>> bounds = numpy.array([[0, 3, 3, 3], 
-  ...                       [2, 0, 2, 2], 
-  ...                       [2, 1, 0, 2], 
-  ...                       [2, 1, 1, 0]], 
+  >>> bounds = numpy.array([[0, 3, 3, 3],
+  ...                       [2, 0, 2, 2],
+  ...                       [2, 1, 0, 2],
+  ...                       [2, 1, 1, 0]],
   ...                      dtype=numpy.float64)
 
   >>> CoarseScreenPharmacophore(((0, ), (1, ), (2, ), (3, )), bounds, pcophore)