General code improvements

docs/releasehistory.rst

@@ -17,6 +17,7 @@ New features
 """"""""""""
 - `PR #28 <https://github.com/martimunicoy/offpele/pull/28>`_: Adds a new method to define a `Molecule` object through a SMILES tag. This molecule can be written as a PDB file later for PELE.
 - `PR #31 <https://github.com/martimunicoy/offpele/pull/31>`_: Adds the possibility to combine nonbonding and solvent parameters from OPLS2005 with bonding parameters from OFF.
+- `PR #36 <https://github.com/martimunicoy/offpele/pull/36>`_: Minor changes to improve the quality of the code.
 
 Bugfixes
 """"""""

offpele/topology/zmatrix.py

@@ -45,6 +45,7 @@ def __new__(cls, molecule):
 
         return obj
 
+    @staticmethod
     def _extract_coords(molecule):
         """
         It extracts the coordinates of the molecule's atoms.
@@ -65,6 +66,7 @@ def _extract_coords(molecule):
 
         return coords
 
+    @staticmethod
     def _get_absolute_parent(molecule):
         """
         It returns the absolute parent in the topology of the molecule.
@@ -88,6 +90,7 @@ def _get_absolute_parent(molecule):
 
         return absolute_parent[0]
 
+    @staticmethod
     def _calculate_bond(x1, y1, z1, x2, y2, z2):
         """
         It calculates the bond distance between two sets of coordinates.
@@ -118,6 +121,7 @@ def _calculate_bond(x1, y1, z1, x2, y2, z2):
 
         return np.sqrt(dx * dx + dy * dy + dz * dz)
 
+    @staticmethod
     def _calculate_angle(x1, y1, z1, x2, y2, z2, x3, y3, z3):
         """
         It calculates the angle between three sets of coordinates.
@@ -172,6 +176,7 @@ def _calculate_angle(x1, y1, z1, x2, y2, z2, x3, y3, z3):
 
         return np.arccos(xang) * 180.0 / np.pi
 
+    @staticmethod
     def _calculate_dihedral(x1, y1, z1, x2, y2, z2, x3, y3, z3, x4, y4, z4):
         """
         It calculates the dihedral between four sets of coordinates.
@@ -246,6 +251,7 @@ def _calculate_dihedral(x1, y1, z1, x2, y2, z2, x3, y3, z3, x4, y4, z4):
 
         return phi * 180.0 / np.pi
 
+    @staticmethod
     def _build_zmatrix(cls, obj, coords, molecule):
         """
         It buils the zmatrix.

offpele/utils/utils.py

@@ -2,6 +2,15 @@
 This module contains miscellaneous set of handy classes and functions.
 """
 
+
+__all__ = ["get_data_file_path",
+           "temporary_cd",
+           "warning_on_one_line",
+           "check_if_path_exists",
+           "create_path"
+           ]
+
+
 from pkg_resources import resource_filename
 import os
 import contextlib
@@ -83,5 +92,4 @@ def create_path(path):
     path : str
         The path that will be created
     """
-    import os
     os.makedirs(str(path), exist_ok=True)

setup.py

@@ -1,6 +1,6 @@
 import os
 from os.path import relpath, join
-from setuptools import setup, find_packages
+from setuptools import setup
 import versioneer
 
 
@@ -32,7 +32,7 @@ def find_package_data(data_root, package_root):
         'offpele/solvent',
         'offpele/topology',
         'offpele/utils',
-        ],
+    ],
     long_description=read('README.md'),
     classifiers=[
         "Development Status :: 1 - Planning",