--- a/extract_rmsd.py	Mon Aug 24 16:27:56 2020 -0400
+++ b/extract_rmsd.py	Wed Oct 28 21:38:43 2020 +0000
@@ -2,29 +2,23 @@
 import json
 
 import MDAnalysis as m
-from MDAnalysis.analysis import align, rms
-from MDAnalysis.analysis.base import AnalysisFromFunction
-from MDAnalysis.coordinates.memory import MemoryReader
+from MDAnalysis.analysis import rms
 
 import numpy as np
 
 
-def calc_rmsd(str_files, traj_files, ref_str, str_format, traj_format,
-              ref_str_format, filepath_out, group, start, end, step,
-              fitting_atoms):
+def calc_rmsd(str_files, traj_files, str_format, traj_format, filepath_out,
+              group, start, end, step):
     """
     the function will cycle through range 0 to no_t and load all files found.
 
     str_files: text file with filepaths for structures, one on each line
     traj_files: text file with filepaths for trajectories, one on each line
-    ref_str: reference structure for fitting
     filepath_in: directory where the files are located
     filepath_out: pickle file where results (3D matrix) should be saved to
 
     group: atoms for which RMSD should be calculated;
         use the MDAnalysis selection language
-    fitting_atoms: atoms used for str alignment prior to RMSD calculation;
-        use the MDAnalysis selection language
 
     start: first trajectory frame to calculate RMSD
     end: last trajectory frame to calculate RMSD
@@ -49,22 +43,10 @@
     universes = {}
 
     for traj in range(no_t):
-        mobile = m.Universe(str_file_list[traj], traj_file_list[traj],
-                            format=traj_format, topology_format=str_format)
-        ref = m.Universe(ref_str, topology_format=ref_str_format)
-
-        mobile.trajectory[-1]  # set mobile trajectory to last frame
-        ref.trajectory[0]  # set reference trajectory to first frame
-
-        # perform alignment
-        align.AlignTraj(mobile, ref, select=fitting_atoms,
-                        in_memory=True).run()
-
-        grp = mobile.select_atoms(group)
-        universes[traj] = m.core.universe.Merge(grp)  # create Universe w grp
-        coordinates = AnalysisFromFunction(lambda ag: ag.positions.copy(),
-                                           grp).run().results  # write to uv
-        universes[traj].load_new(coordinates, format=MemoryReader)
+        # We no longer align here, users should do this themselves.
+        universes[traj] = m.Universe(str_file_list[traj], traj_file_list[traj],
+                                     format=traj_format,
+                                     topology_format=str_format)
 
     print("All trajs loaded by MDAnalysis")
 
@@ -72,19 +54,14 @@
     for traj1 in range(no_t):
         print("Calculating differences for traj {}".format(traj1))
         for traj2 in range(traj1):
-
-            u1 = universes[traj1]
-            u2 = universes[traj2]
-
-            l1 = u1.select_atoms(group)
-            l2 = u2.select_atoms(group)
-
-            rmsd = rms.RMSD(l1, l2)
-
-            rmsd.run()
-
-            data[traj1, traj2] = rmsd.rmsd[:, 2]
-            data[traj2, traj1] = rmsd.rmsd[:, 2]
+            for frame in range(data.shape[2]):
+                universes[traj1].trajectory[frame]
+                universes[traj2].trajectory[frame]
+                A = universes[traj1].select_atoms(group).positions
+                B = universes[traj2].select_atoms(group).positions
+                r = rms.rmsd(A, B)
+                data[traj1, traj2, frame] = r
+                data[traj2, traj1, frame] = r
 
     with open(filepath_out, 'w') as f:
         json.dump(data.tolist(), f, indent=4, sort_keys=True)
@@ -99,19 +76,13 @@
                         help='File containing trajectory filepaths.')
     parser.add_argument("--strs",
                         help='File containing structure filepaths.')
-    parser.add_argument("--ref-str",
-                        help='File containing reference structure.')
     parser.add_argument('--traj-format', required=True,
                         help='Trajectory format.')
     parser.add_argument("--str-format", help='Structure format.')
-    parser.add_argument("--ref-str-format",
-                        help='Reference structure format.')
     parser.add_argument('-o', '--outfile',
                         help="Path to the output JSON file")
     parser.add_argument('--group', help="Atoms for which RMSD should be"
                         "calculated in MDAnalysis selection language")
-    parser.add_argument('--fitting', help="Fitting atoms for alignment"
-                        "prior to RMSD calculation")
     parser.add_argument('--start', type=int,
                         help="First trajectory frame to calculate RMSD")
     parser.add_argument('--end', type=int,
@@ -120,9 +91,9 @@
                         help="Frame sampling frequency for RMSD calculation")
     args = parser.parse_args()
 
-    calc_rmsd(args.strs, args.trajs, args.ref_str, args.str_format,
-              args.traj_format, args.ref_str_format, args.outfile,
-              args.group, args.start, args.end, args.step, args.fitting)
+    calc_rmsd(args.strs, args.trajs, args.str_format,
+              args.traj_format, args.outfile,
+              args.group, args.start, args.end, args.step)
 
 
 if __name__ == "__main__":