test core_def_all_beads added. [Issue #27] (#31)

* test core_def_all_bedas added.  Small system tests added in core_fast, core_fast_leaflet and test_all_beads.

membrane_curvature/core.py

@@ -5,9 +5,7 @@
 Handles the primary functions
 """
 
-from .lib.mods import dict2pickle, core_fast, curvature
-import sys
-import os
+from .lib.mods import dict2pickle, core_fast, curvature, def_all_beads
 import time
 import mdtraj as md
 import MDAnalysis as mda
@@ -16,7 +14,6 @@
 __author__ = "Estefania Barreto-Ojeda"
 version = 0.1
 
-sys.path.append('lib/')
 
 def main():
 

membrane_curvature/data/test_po4_inverted_indexes.gro

@@ -0,0 +1,13 @@
+Test file 10 lipids in grid with indexes inverted. Correct form is: Index 1 belongs to lower leaflet and index 10 belong to upper leaflet.
+10
+ 3000POPE   PO4    1   0.639   1.402  12.078
+ 2054POPC   PO4    2   0.704   2.229  15.981
+ 2298POPE   PO4    3   0.956   1.559  16.059
+ 2337POPE   PO4    4   0.707   0.736  15.711
+ 2622POPC   PO4    5   1.451   0.382  11.752
+ 2702POPC   PO4    6   0.081   0.610  11.835
+ 2708POPC   PO4    7   0.678   2.233  11.825
+ 2713POPC   PO4    8   0.988   0.554  11.838
+ 2999POPE   PO4    9   1.371   1.989  12.027
+ 1923POPC   PO4   10   1.361   0.630  16.101
+  2.60167  2.60167  32.07157   

membrane_curvature/data/test_po4_small.gro

@@ -0,0 +1,12 @@
+Test file 9 lipids in grid
+9
+ 1923POPC   PO4    1   0.000   0.000  15.000
+ 2054POPC   PO4    2   1.000   0.000  15.000
+ 2298POPC   PO4    3   2.000   0.000  15.000
+ 2337POPC   PO4    4   0.000   1.000  15.000
+ 2622POPC   PO4    5   1.000   1.000  12.000
+ 2702POPC   PO4    6   2.000   1.000  12.000
+ 2708POPC   PO4    7   0.000   2.000  12.000
+ 2713POPC   PO4    8   1.000   2.000  12.000
+ 2999POPC   PO4    9   2.000   2.000  12.000
+  3.00000  3.00000  3.00000   

membrane_curvature/lib/mods.py

@@ -30,24 +30,12 @@ def def_all_beads(lipid_types, leaflets, head_list, topology):
     print('==== Lipid types in membrane ==== ')
     for lt in lipid_types:
         print('====>', lt)
-        dic_all_beads['upper'][lt] = np.concatenate((topology.select('resname ' +
-                                                                     lt +
-                                                                     ' and index ' +
-                                                                     str(head_list[0]) +
-                                                                     ' to ' +
-                                                                     str(head_list[1]) +
-                                                                     ' and name PO4'), topology.select('resname ' +
-                                                                                                       lt +
-                                                                                                       ' and index ' +
-                                                                                                       str(head_list[0]) +
-                                                                                                       ' to ' +
-                                                                                                       str(head_list[1]) +
-                                                                                                       ' and name GM1'))).astype(int).tolist()
-        dic_all_beads['lower'][lt] = np.concatenate((topology.select(
-            'resname ' + lt + ' and index ' + str(head_list[1] + 1) + ' to ' + str(head_list[2]) + ' and name PO4'),
-            topology.select(
-            'resname ' + lt + ' and index ' + str(head_list[1] + 1) + ' to ' + str(head_list[2]) + ' and name GM1'))).astype(int).tolist()
-
+        dic_all_beads['upper'][lt] = topology.select(
+            'resname ' + lt + ' and index ' + str(head_list[0])
+            + ' to ' + str(head_list[1]) + ' and name PO4').astype(int).tolist()
+        dic_all_beads['lower'][lt] = topology.select(
+            'resname ' + lt + ' and index ' + str(head_list[1] + 1)
+            + ' to ' + str(head_list[2]) + ' and name PO4').astype(int).tolist()
         print("upper", len(dic_all_beads['upper'][lt]))
         print("lower", len(dic_all_beads['lower'][lt]))
 
@@ -75,8 +63,7 @@ def dict2pickle(name, dict_):
         pickle.dump(dict_, pk, protocol=pickle.HIGHEST_PROTOCOL)
 
 
-def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref,
-              box_size, max_width, prefix):
+def core_fast(traj, jump, n_cells, leaflets, lipid_types, lipid_ref, max_width, prefix):
     """
     Runs core_fast_leaflet for each leaflet
 

membrane_curvature/tests/datafiles.py

@@ -10,14 +10,31 @@
 """
 
 __all__ = [
+    # From lower to higher complexity
+    "GRO_PO4_SMALL",  # Gromacs file of PO4 beads in POPC POPE membrane with 10 lipids
+    "XTC_PO4_SMALL",  # Gromacs traj file of PO4 beacs in POPC POPE membrane with 10 lipids with indexes inverted.
+    "GRO_PO4_INVERTED_ID",
+    "GRO_PO4_MED",  # Gromacs file of PO4 beads in POPC POPE membrane with 25 lipids
+    "GRO_PO4_BIG",  # Gromacs file of PO4 beads in POPC POPE membrane with 50 lipids
+    "GRO_PO4",  # Gromacs file of PO4 beads in POPC POPE membrane with 914 lipids
+    "XTC_PO4",  # Gromacs trajectory of GRO_PO4
     "GRO_MEMBRANE_PROTEIN",  # Gromacs file of POPC POPE CHOL membrane
-    "XTC_MEMBRANE_PROTEIN"  # Gromacs trajectory of 10 frames.
+    "XTC_MEMBRANE_PROTEIN",  # Gromacs trajectory of 10 frames.
 ]
 
 from pkg_resources import resource_filename
 
+# Membrane protein systems
 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')
+# PO4 beads only
+GRO_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.gro')
 XTC_PO4 = resource_filename(__name__, '../data/test_curvature_po4_only.xtc')
+# Smaler systems derived from
+GRO_PO4_SMALL = resource_filename(__name__, '../data/test_po4_small.gro')
+XTC_PO4_SMALL = resource_filename(__name__, '../data/test_po4_small.xtc')
+GRO_PO4_MED = resource_filename(__name__, '../data/test_po4_med.gro')
+GRO_PO4_BIG = resource_filename(__name__, '../data/test_po4_big.gro')
+# Inverted indexes
+GRO_PO4_INVERTED_ID = resource_filename(__name__, '../data/test_po4_inverted_indexes.gro')
 del resource_filename