Interactions (hpb improvements)

prody/proteins/hpbmodule/README

@@ -3,24 +3,30 @@ hpb is a python module written for calculating the hydrophobic interactions and
 accessible surface area using geometric method. The original program is in C++, so the
 module is an interface to call functions in C++.
 
-Follow the stpes to compile the C++ code into the *.so file of module (note that the directory to include python may need change):
+Follow the stpes to compile the C++ code into the *.so file of module (note that the 
+directory to include python may need change):
 
-cd libf2c
-make -f makefile.l hadd
-make -f makefile.l
+Step 1:
+gfortran -O3 -fPIC -c reg_tet.f
 
-cd ..
+Step 2:
+g++ -O3 -g -fPIC -c hpbmodule.cpp -o hpbmodule.o -I/usr/include/python2.7/
+or to compile the program for python 3.X use:
+g++ -O3 -g -fPIC -c hpbmodule.cpp -o hpbmodule.o -I/usr/include/python3.X/ 
+instead
 
-to compile the program for python 3.8 use:
-g++ -O3 -g -fPIC -c hpbmodule.cpp -o hpbmodule.o -I/usr/include/python3.8/
+If we ae using Anaconda we might have such pathway to python:
+g++ -O3 -g -fPIC -c hpbmodule.cpp -o hpbmodule.o -I/home/user_name/anaconda3/envs/name_of_environment/include/python3.9/
 
-and further:
-g++ -shared -Wl,-soname,hpb.so -o hpb.so hpbmodule.o reg_tet.o ./libf2c/libf2c.a -lm
+user_name, name_of_environment - need to be replaced
 
+Step 3:
+g++ -shared -Wl,-soname,hpb.so -o hpb.so hpbmodule.o reg_tet.o -lgfortran
+
+Note: You will need C++ compiler and Fortran compiler.
 
 ############################
-After compiling the code, the module 'hpbmodule.so' file is created and user can import the module in python.
-Try one example program 'testh.py' to use the functions in it.
-Two functions hpb.hpb and hpb.sasa are writtein in the same module. The inputs to call them are the same.
-The outputs are now in lists, with every element contains the information for one hydrophobic interaction or SASA value of one residue.
+After compiling the code, the module 'hpb.so' file is created and user can import 
+the module to ProDy or copy the file in the local directory to use it with calcSASA(), 
+calcVolume(), calcHydrophobicOverlapingAreas(), or calcHydrophobic().
 

prody/proteins/interactions.py

@@ -10,8 +10,6 @@
         (5) Pi-cation interactions
         (6) Hydrophobic interactions
         (7) Disulfide Bonds
-
-For protein-ligand interactions (3) is replaced by water bridges.
 """
 
 __author__ = 'Karolina Mikulska-Ruminska'
@@ -93,6 +91,7 @@ def calcAngleBetweenPlanes(a1, b1, c1, a2, b2, c2):
 
 
 def removeDuplicates(list_of_interactions):
+    """Remove duplicates from interactions."""
     ls=[]
     newList = []
     for no, i in enumerate(list_of_interactions):
@@ -154,7 +153,7 @@ def filterInteractions(list_of_interactions, atoms, **kwargs):
 
 def calcHydrophobicOverlapingAreas(atoms, **kwargs):
     """Provide information about hydrophobic contacts between pairs of residues based on 
-    the regsurf program.
+    the regsurf program. To use this function compiled hpb.so is needed.
 
     :arg atoms: an Atomic object from which residues are selected
     :type atoms: :class:`.Atomic`
@@ -182,7 +181,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs):
             import hpb
             imported_hpb = True
         except ImportError:
-            LOGGER.info('Please provide hpb.so file into the directory.')
+            raise ImportError('Please provide hpb.so file into the directory.')
 
     if imported_hpb:
         selection = kwargs.pop('selection', 'protein and noh')
@@ -227,7 +226,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs):
 
 def calcSASA(atoms, **kwargs):
     """Provide information about solvent accessible surface area (SASA) based on 
-    the sasa program.
+    the sasa program. To use this function compiled hpb.so is needed.
 
     :arg atoms: an Atomic object from which residues are selected
     :type atoms: :class:`.Atomic`
@@ -255,7 +254,7 @@ def calcSASA(atoms, **kwargs):
             import hpb
             imported_hpb = True
         except ImportError:
-            LOGGER.info('Please provide hpb.so file into the directory.')
+            raise ImportError('Please provide hpb.so file into the directory.')
 
     if imported_hpb:
         selection = kwargs.pop('selection', 'protein and noh')
@@ -284,7 +283,7 @@ def calcSASA(atoms, **kwargs):
 
 def calcVolume(atoms, **kwargs):
     """Provide information about volume for each residue/molecule/chain
-    or other selection".
+    or other selection". To use this function compiled hpb.so is needed.
 
     :arg atoms: an Atomic object from which residues are selected
     :type atoms: :class:`.Atomic`
@@ -318,7 +317,7 @@ def calcVolume(atoms, **kwargs):
             import hpb
             imported_hpb = True
         except ImportError:
-            LOGGER.info('Please provide hpb.so file into the directory.')
+            raise ImportError('Please provide hpb.so file into the directory.')
 
     if imported_hpb:
         selection = kwargs.pop('selection', 'protein and noh')