Clean code. [Issue #26] (#29)

* Removed all unused/unnecessary lines.

membrane_curvature/core.py

@@ -18,66 +18,10 @@
 
 sys.path.append('lib/')
 
-
-class Grid():
-    # instance variables
-    def __init__(self, box_width, max_width, unit_cell_width, skip):
-        self.box_width = box_width
-        self.max_width = max_width
-        self.unit_cell_width = unit_cell_width
-        self.skip = skip
-        self.n_cells = math.ceil(max_width / unit_cell_width * 10)
-
-
-class head_indexes:
-    # class variables
-    leaflets = ['lower', 'upper']
-
-    # instance variables
-    def __init__(self, lipid_types, head_index, top):
-        self.lipid_types = lipid_types
-        self.head_index = head_index
-        self.top = top
-
-    # @classmethod
-    def list_head_beads(self):
-        lfs = self.leaflets
-        return def_all_beads(self.lipid_types, lfs, self.head_index, self.top)
-
-
 def main():
 
     start_time = time.time()
 
-    # 1. Parse input files
-    parser = input_options()
-
-    args = parser.parse_args()
-    grofile, trjfile = args.f, args.x
-    unit_width, jump = args.uw, args.sk
-    output = args.out
-
-    try:
-        name_user = str(args.name)
-        print("Prefix assigned by user. Set as {}".format(name_user))
-
-    except NameError:
-        name_user = 'system'
-        print("Prefix not assigned by user. Set as {}".format(name_user))
-
-    # Define index leaflets
-    ii, jj = parse_range(args.io), parse_range(args.ii)
-    iil, iiu = def_range_leaflets(args.io, 1)
-    jjl, jju = def_range_leaflets(args.ii, 2)
-
-    # 2 --- Set OUTPUT files
-    # 2.1 Create output folder
-    os.makedirs(os.path.dirname('output/'), exist_ok=True)
-
-    # 2.2 -- Pickle files (head group height)
-    prefix = name_user
-    name_ = output + prefix
-
     # 3. Define leaflets and lipid type
     leaflets = ['lower', 'upper']
 

membrane_curvature/lib/mods.py

@@ -4,126 +4,6 @@
 import math
 
 
-class Grid:
-
-    """
-    A class to set a grid with n x n elements.
-
-    ...
-
-    Attributes
-    ----------
-    [Names are self explanatory]
-
-    box_width : <float>
-        Box dimensions in x.
-    max_width : <int>
-        Max width of the grid.
-    unit_cell_width(): <int>
-        Width of unit cell in grid.
-
-
-    Methods
-    -------
-    list_by_index(additional=""):
-        Returns list with [inner_leaflet_first_index, upper_leaflet_first_index, upper_leaflet_last_index].
-    """
-
-    # instance variables
-    def __init__(self, box_width, max_width, unit_cell_width):
-        self.box_width = box_width
-        self.max_width = max_width
-        self.unit_cell_width = unit_cell_width
-        self.n_cells = math.ceil(max_width / unit_cell_width * 10)
-
-
-class define_leaflets:
-
-    """
-    A class to define leaflets by index when provided by the user.
-
-    ...
-
-    Attributes
-    ----------
-    int_inner : str:str
-        Index interval of the inner leaflet.
-    surname : str:str
-        Index interval of the outer leaflet.
-
-    Methods
-    -------
-    list_by_index():
-        Returns list [i for i in range(<index interval>)]].
-    """
-
-    def __init__(self, int_inner, int_upper):
-        self.int_inner = int_inner
-        self.int_upper = int_upper
-
-    def list_by_index(self):
-        ii, jj = parse_range(self.int_upper), parse_range(self.int_inner)
-        iil, iiu = def_range_leaflets(self.int_upper, 1)
-        jjl, jju = def_range_leaflets(self.int_inner, 2)
-
-        return [iil, jjl, jju]
-
-
-class membrane_index:
-
-    """
-    A class to select PO4 beads from defined leaflets.
-
-    ...
-
-    Attributes
-    ----------
-    lipid_types : <list>
-        Index interval of the inner leaflet.
-    head_index : <>
-        Index interval of the outer leaflet.
-
-    Methods
-    -------
-    list_head_beads():
-        Returns list with [inner_leaflet_first_index, upper_leaflet_first_index, upper_leaflet_last_index].
-    """
-
-    # class variables
-    leaflets = ['upper', 'lower']
-
-    # instance variables
-    def __init__(self, lipid_types, head_index, top):
-        self.lipid_types = lipid_types
-        self.head_index = head_index
-        self.top = top
-
-    # #@classmethod
-    def list_head_beads(self):
-        return def_po4_beads(self.lipid_types, self.leaflets, self.head_index, self.top)
-
-
-def parse_range(astr):
-    """
-    Split range provided by user
-    """
-
-    rangeG = set()
-    x = [int(i) for i in astr.split(':')]
-    rangeG.update(range(x[0], x[1] + 1))
-
-    return list(rangeG)
-
-
-def def_range_leaflets(nn, ind):
-    """
-    Define range of index residues
-    """
-    mm = parse_range(nn)
-
-    return min(mm), max(mm)
-
-
 def def_all_beads(lipid_types, leaflets, head_list, topology):
     """
     Select reference elements to derive membrane surface.