Initial test. [Fixes #10]

.github/workflows/CI.yaml

@@ -43,7 +43,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: devtools/conda-envs/test_env.yaml
-        mamba-version: "*"
+        # mamba-version: "*"
         channels: conda-forge, defaults
 
         activate-environment: test

mdakit_membcurv/core.py

@@ -5,11 +5,10 @@
 Handles the primary functions
 """
 
-from .lib.mods import *
+from .lib.mods import dict2pickle, core_fast, curvature
 import sys
 import os
 import time
-import argparse
 import mdtraj as md
 import MDAnalysis as mda
 import math

mdakit_membcurv/lib/mods.py

@@ -1,15 +1,7 @@
-#from collections import OrderedDict
-#from itertools import permutations
 import itertools as it
-import mdtraj as md
 import numpy as np
-import argparse
 import pickle
-import textwrap
-import time
 import math
-import os
-import re
 
 
 class Grid:
@@ -111,37 +103,6 @@ def list_head_beads(self):
         return def_po4_beads(self.lipid_types, self.leaflets, self.head_index, self.top)
 
 
-def input_options():
-    """
-    Command line arguments as input_options
-    """
-
-    #usage = (" [options] < input > output")
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-                                     description=textwrap.dedent('''\
-        Trial version KHURV.py | To calculate Gaussian (K) and mean (H) curvature from MD simulations
-        '''))
-
-    parser.add_argument(
-        "-f", metavar="<GRO INPUT FILE>", help="Input gro file.")
-    parser.add_argument(
-        "-x", metavar="<XTC INPUT>", help='Input trajectory.')
-    parser.add_argument(
-        "-io", type=str, metavar='<INDEX OUTER LEAFLET begin:end>', help='Index range outer leaflet.')
-    parser.add_argument(
-        "-ii", type=str, metavar='<INDEX INNER LEAFLET begin:end>', help='Index range inner leaflet.')
-    parser.add_argument(
-        "-uw", type=int, default=5, metavar='UNIT CELL WIDTH', help="Unit cell width in nm. Default: %(default)s .")
-    parser.add_argument("-name", type=str, metavar='<PREFIX NAME>', default='system',
-                        help="System name. Prefix used in OUTPUT K_G AND K_H files.")
-    parser.add_argument(
-        "-sk", type=int, default=10, metavar="<n>", help="Skip frames. Default: ")
-    parser.add_argument("-out", type=str, metavar="<OUTPUT DIR>", default='output/',
-                        help='Output file directory. Default: %(default)s')
-
-    return parser
-
-
 def parse_range(astr):
     """
     Split range provided by user
@@ -213,40 +174,6 @@ def def_all_beads(lipid_types, leaflets, head_list, topology):
     return dic_all_beads
 
 
-def xy2cell(coords, n_cells, max_width, bead, grid):
-    """
-    Maps coordinates to indexed unit grid of size `max_width`.
-
-    (x,y) |---> [i,j]
-
-
-    Parameters
-    ----------
-    coords : tuple.
-        (x,y) coordinates of `bead`.
-    n_cells : int.
-        number of cells in the grid of size `max_width`.
-    max_width : int.
-        Maximum width of simulation box. Determines size of grid.
-    bead : int.
-        Element in reference group.
-
-
-    Returns
-    -------
-    { grid[i,j] } : dict
-        Dictionary with [i,j] tuples.
-
-    """
-
-    grid[
-        math.floor((abs(coords[0]) / max_width * n_cells)),
-        math.floor((abs(coords[1]) / max_width * n_cells))
-    ].append(bead)
-
-    return grid
-
-
 def dict2pickle(name, dict_):
     """
     Exports values stored in a dictionary to a pickle file.
@@ -307,15 +234,15 @@ def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref,
 
     for leaflet in leaflets:
         core_fast_leaflet(z_ref[leaflet], leaflet, traj, jump, n_cells,
-                          lipid_types, lipid_ref, box_size, max_width)
+                          lipid_types, lipid_ref, max_width)
 
     dict2pickle(prefix, z_ref)
 
     return z_ref
 
 
 def core_fast_leaflet(z_Ref, leaflet, traj, jump, n_cells, lipid_types,
-                      lipid_ref, box_size, max_width):
+                      lipid_ref, max_width):
     """
     Runs core_fast_leaflet for each leaflet
 
@@ -444,8 +371,6 @@ def mean_curvature(Z):
 def curvature(dict_reference, leaflets, n_cells):
     """
     Calculates mean curvature from Z cloud points.
-
-
     Parameters
     ----------
     dict_reference : dict { [index]:[z_coords]}.
@@ -454,14 +379,11 @@ def curvature(dict_reference, leaflets, n_cells):
         Leaflets of bilayer.
     n_cells : int. default 20.
         Number of cells in grid.
-
-
     Returns
     -------
     K, H : 2d-array, 2d-array
         Returns 2-dimensional array objects for mean
         and gaussian curvature, respectively.
-
     """
 
     H, K = [{key2: [] for key2 in leaflets} for i in range(2)]
@@ -479,12 +401,3 @@ def curvature(dict_reference, leaflets, n_cells):
     else:
         print('No interpolation performed. Plot may display empty values.')
         return H, K
-
-
-def timer(current_time, start_time):
-
-    elapsed_time = current_time - start_time
-    m, s = divmod(elapsed_time, 60)
-    h, m = divmod(m, 60)
-    print('Elapsed time:', elapsed_time)
-    print("%d:%02d:%02d" % (h, m, s))

mdakit_membcurv/tests/datafiles.py

@@ -0,0 +1,23 @@
+
+
+"""
+Location of datafiles for Membrane Curvature unit tests
+=======================================================
+
+MD simulations files stored in `data` sub-directory.
+
+    from mdakit_membcurv.datafiles import *
+"""
+
+__all__ = [
+    "GRO_MEMBRANE_PROTEIN",  # Gromacs file of POPC POPE CHOL membrane
+    "XTC_MEMBRANE_PROTEIN"  # Gromacs trajectory of 10 frames.
+]
+
+from pkg_resources import resource_filename
+
+GRO_MEMBRANE_PROTEIN = resource_filename(__name__, '../data/test_curvature_abca1.gro')
+GRO_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.gro')
+XTC_MEMBRANE_PROTEIN = resource_filename(__name__, '../data/test_curvature_abca1.xtc')
+XTC_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.xtc')
+del resource_filename