Merge pull request prody#1869 from jamesmkrieger/hpb

fix setup.py to copy hpb

MANIFEST.in

@@ -9,6 +9,7 @@ include prody/*/*.cpp
 include prody/*/*/*.cpp
 include prody/*/*.h
 include prody/*/*/*.h
+include prody/*/*/*/*.so
 include prody/tests/*/*.py
 include prody/tests/datafiles/*.coo
 include prody/tests/datafiles/*.dcd

prody/proteins/interactions.py

@@ -163,7 +163,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs):
     :arg selection: selection string of hydrophobic residues
     :type selection: str
     
-    :arg hpb_cutoff: cutoff for hydrophobic overlaping area values
+    :arg hpb_cutoff: cutoff for hydrophobic overlapping area values
         default is 0.0
     :type hpb_cutoff: float, int
     
@@ -200,7 +200,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs):
         lA = [ [x[i] + str(y[i]), z[i] +'_'+ str(w[i]), ch[i]] for i in range(len(x))]
 
         output = hpb.hpb((lB,lA))
-        LOGGER.info("Hydrophobic Overlaping Areas are computed.")
+        LOGGER.info("Hydrophobic Overlapping Areas are computed.")
         output_final = [i for i in output if i[-1] >= hpb_cutoff]
 
         if cumulative_values == None:            
@@ -1000,11 +1000,11 @@ def calcHydrophobic(atoms, **kwargs):
                         non_standard works too
     :type non_standard_Hph: dict
 
-    :arg zerosHPh: zero values of hydrophobic overlaping areas included
+    :arg zerosHPh: zero values of hydrophobic overlapping areas included
         default is False
     :type zerosHPh: bool
 
-    Last value in the output corresponds to the total hydrophobic overlaping area for two residues
+    Last value in the output corresponds to the total hydrophobic overlapping area for two residues
     not only for the atoms that are included in the list. Atoms that which are listed are the closest
     between two residues and they will be inluded to draw the line in VMD_.
     
@@ -1065,7 +1065,7 @@ def calcHydrophobic(atoms, **kwargs):
     aromatic_nr = list(set(zip(atoms.aromatic.getResnums(),atoms.aromatic.getChids())))   
     aromatic = list(set(atoms.aromatic.getResnames()))
 
-    # Computing hydrophobic overlaping areas for pairs of residues:
+    # Computing hydrophobic overlapping areas for pairs of residues:
     try:
         hpb_overlaping_results = calcHydrophobicOverlapingAreas(atoms_hydrophobic, cumulative_values='pairs')
     except: 

prody/tests/proteins/test_insty.py

@@ -12,6 +12,8 @@
 from prody.proteins.interactions import calcPiCationTrajectory, calcHydrophobicTrajectory
 from prody.proteins.interactions import calcDisulfideBondsTrajectory, calcProteinInteractions
 
+import sys
+
 class TestInteractions(unittest.TestCase):
 
     def setUp(self):
@@ -55,7 +57,7 @@ def setUp(self):
             self.data_disu = calcDisulfideBondsTrajectory(self.ATOMS)
             np.save('test_2k39_disu.npy', np.array(self.data_disu, dtype=object), allow_pickle=True)
 
-    def testAllInsteractions(self):
+    def testAllInteractions(self):
         """Test for all types of interactions."""
 
         if prody.PY3K:        
@@ -132,4 +134,28 @@ def testDisulfideBonds(self):
              assert_equal(sorted([i[-1][-1] for i in data_test if i]), sorted([i[-1][-1] for i in self.DISU_INTERACTIONS if i]),
                           'failed to get correct disulfide bonds')
 
-
+    def testImportHpb(self):
+
+        try:
+            import prody.proteins.hpb as hpb
+            imported_hpb = True
+        except ImportError:
+            try:
+                import hpb
+                imported_hpb = True
+            except ImportError:
+                imported_hpb = False
+
+        if sys.version_info[1] < 11:
+            self.assertTrue(imported_hpb)
+        else:
+            self.assertFalse(imported_hpb)
+
+    @classmethod
+    def tearDownClass(cls):
+        if prody.PY3K:
+            import os
+            for filename in ['test_2k39_all.npy', 'test_2k39_hbs.npy', 'test_2k39_sbs.npy', 
+                            'test_2k39_rib.npy', 'test_2k39_PiStack.npy', 'test_2k39_PiCat.npy',
+                            'test_2k39_hph.npy', 'test_2k39_disu.npy']:
+                os.remove(filename)

setup.py

@@ -7,6 +7,8 @@
 from setuptools import setup
 from setuptools import Extension
 
+import shutil
+
 if sys.version_info[:2] < (2, 7):
     sys.stderr.write('Python 2.6 and older is not supported\n')
     sys.exit()
@@ -94,7 +96,15 @@
 
 from glob import glob
 tntDir = join('prody', 'utilities', 'tnt')
-hpbDir = join('prody', 'proteins', 'hpbmodule')
+hpbSoDir = join('prody', 'proteins', 'hpbmodule',
+                'hpb_Python{0}.{1}'.format(sys.version_info[0],
+                                           sys.version_info[1]))
+proteinsDir = join('prody', 'proteins')
+
+try:
+    shutil.copy(hpbSoDir + "/hpb.so", proteinsDir)
+except FileNotFoundError:
+    pass
 
 EXTENSIONS = [
     Extension('prody.dynamics.rtbtools',
@@ -164,8 +174,8 @@
 setup(
     name='ProDy',
     version=__version__,
-    author='James Krieger, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others',
-    author_email='[email protected]',
+    author='James Krieger, Karolina Mikulska-Ruminska, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others',
+    author_email='[email protected]',
     description='A Python Package for Protein Dynamics Analysis',
     long_description=long_description,
     url='http://www.csb.pitt.edu/ProDy',