Updated Mol_analysis.py + README with new -nomkndx option

Mol_Analysis.py

@@ -964,6 +964,8 @@ def process_data(threadName, q):
     parser.add_argument("-end", type=int, default=None, help="End at time X (fs)")
     parser.add_argument("-large", action="store_true", help="Can plot 9 plots")
     parser.add_argument("-splitlen", metavar="slen", default=10, help="Length of timewindow for RMSF calculation (ns). If multiple than separated with comma")
+    parser.add_argument("-nomkndx", action="store_false",
+                    help="Do not recreate index file; reuse existing ndxfile")
     args = parser.parse_args()
     timescales = []
     try:
@@ -987,7 +989,7 @@ def process_data(threadName, q):
     config.listread(args.f)
     groupfolderlist = config.getlist()
     # Storing defaults here:
-    settings = {"odir": "Mol_An", "f": None, "tpr": None,
+    settings = {"odir": "Mol_An", "f": None, "tpr": None, 
                 "outf": "center_traj.xtc", "outs": "updated.gro",
                 "outp": "updated.tpr", "ndxfile": "index.ndx",
                 "ndxparams": None, "chains": ["Protein"], "center": "Protein",
@@ -998,7 +1000,7 @@ def process_data(threadName, q):
         try:
             option = config.get("Settings", key)
             if "," in option:
-                option = map(lambda s: s.strip(), option.split(","))
+                option = list(map(lambda s: s.strip(), option.split(",")))
             elif "none" in option.lower():
                 option = None
                 continue
@@ -1049,7 +1051,7 @@ def process_data(threadName, q):
     def runandplot(folder, group=0):
         runner = gTools_runner(wdir=folder, splitlen=timescales, dryrun=args.n, verbose=args.v,
                                group=group, **settings)
-        runner.runall(mindist=args.nomindist, pdbout=args.nopdb, num_cores=args.nt)
+        runner.runall(mkndx=args.nomkndx, mindist=args.nomindist, pdbout=args.nopdb, num_cores=args.nt)
         files_to_plot.append(runner.getfilenames())
 
     # Adding it all to the multithreader
@@ -1080,8 +1082,10 @@ def runandplot(folder, group=0):
                     groupedfnames = []
                     shift = 0
                     # Align chains here:
-                    #if ("p62" in label_g) and (chain == "chB"):
-                    #    shift = 709
+                    #if chain == "chA":
+                    #    shift = 124
+                    #elif chain == "chB":
+                    #    shift = 7
                     for model in model_g:
                         try:
                             groupedfnames.extend(model["rmsf"+str(i)+"_"+chain+"_n_C-alpha"])

README

@@ -27,6 +27,7 @@ optional arguments:
   -begin BEGIN   Begin from time X (fs)
   -end END       End at time X (fs)
   -large         Can plot 9 plots
+  -nomkndx	 Use custom index for multiple chains
   -splitlen      slen Lenght of timewindow for RMSF calculation (in ns, default=10 ns)
 		 if multiple times need to be calculated then separate with a comma
 

example/Mol_An/r_gyrate.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:45 2025
+# This file was created Tue May  5 11:22:02 2026
 # Created by:
 #                       :-) GROMACS - gmx gyrate, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi gyrate -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/r_gyrate.xvg
 # gmx gyrate is part of G R O M A C S:
 #
-# Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+# Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
 #
 @    title "Radius of gyration (total and around axes)"
 @    xaxis  label "Time (ps)"

example/Mol_An/rmsd.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:52 2025
+# This file was created Tue May  5 11:22:08 2026
 # Created by:
 #                        :-) GROMACS - gmx rms, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rms -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsd.xvg -m /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsd_matrix.xpm -dt 200
 # gmx rms is part of G R O M A C S:
 #
-# GROup of MAchos and Cynical Suckers
+# GROwing Monsters And Cloning Shrimps
 #
 @    title "RMSD"
 @    xaxis  label "Time (ps)"

example/Mol_An/rmsd_Protein.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:44 2025
+# This file was created Tue May  5 11:22:02 2026
 # Created by:
 #                        :-) GROMACS - gmx rms, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rms -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsd_Protein.xvg -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx
 # gmx rms is part of G R O M A C S:
 #
-# GROwing Monsters And Cloning Shrimps
+# Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
 #
 @    title "RMSD"
 @    xaxis  label "Time (ps)"

example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_10000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:47 2025
+# This file was created Tue May  5 11:22:03 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rmsf -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_10000.xvg -od /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_10000.xvg -b 0 -e 10000 -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx -res
 # gmx rmsf is part of G R O M A C S:
 #
-# Gnomes, ROck Monsters And Chili Sauce
+# Good gRace! Old Maple Actually Chews Slate
 #
 @    title "RMS fluctuation"
 @    xaxis  label "Residue"

example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_20000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:47 2025
+# This file was created Tue May  5 11:22:04 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rmsf -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_20000.xvg -od /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_20000.xvg -b 10020 -e 20000 -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx -res
 # gmx rmsf is part of G R O M A C S:
 #
-# Gnomes, ROck Monsters And Chili Sauce
+# S  C  A  M  O  R  G
 #
 @    title "RMS fluctuation"
 @    xaxis  label "Residue"

example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_30000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:48 2025
+# This file was created Tue May  5 11:22:05 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rmsf -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_30000.xvg -od /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_30000.xvg -b 20020 -e 30000 -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx -res
 # gmx rmsf is part of G R O M A C S:
 #
-# Glycine aRginine prOline Methionine Alanine Cystine Serine
+# Gromacs Runs On Most of All Computer Systems
 #
 @    title "RMS fluctuation"
 @    xaxis  label "Residue"

example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_40000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:49 2025
+# This file was created Tue May  5 11:22:06 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 

example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_50000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:50 2025
+# This file was created Tue May  5 11:22:06 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 

example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_10000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:47 2025
+# This file was created Tue May  5 11:22:03 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rmsf -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_10000.xvg -od /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_10000.xvg -b 0 -e 10000 -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx -res
 # gmx rmsf is part of G R O M A C S:
 #
-# Gnomes, ROck Monsters And Chili Sauce
+# Good gRace! Old Maple Actually Chews Slate
 #
 @    title "RMS Deviation"
 @    xaxis  label "Residue"

example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_20000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:47 2025
+# This file was created Tue May  5 11:22:04 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rmsf -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_20000.xvg -od /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_20000.xvg -b 10020 -e 20000 -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx -res
 # gmx rmsf is part of G R O M A C S:
 #
-# Gnomes, ROck Monsters And Chili Sauce
+# S  C  A  M  O  R  G
 #
 @    title "RMS Deviation"
 @    xaxis  label "Residue"

example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_30000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:48 2025
+# This file was created Tue May  5 11:22:05 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 
@@ -9,7 +9,7 @@
 #   gmx_mpi rmsf -f /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/center_traj.xtc -s /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/updated.tpr -o /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_Protein_n_C-alpha_30000.xvg -od /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_30000.xvg -b 20020 -e 30000 -n /data/user/pablosanchezb/devel/Mol-Analysis/example/Mol_An/index.ndx -res
 # gmx rmsf is part of G R O M A C S:
 #
-# Glycine aRginine prOline Methionine Alanine Cystine Serine
+# Gromacs Runs On Most of All Computer Systems
 #
 @    title "RMS Deviation"
 @    xaxis  label "Residue"

example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_40000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:49 2025
+# This file was created Tue May  5 11:22:06 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 # 

example/Mol_An/rmsf10/rmsf_od_Protein_n_C-alpha_50000.xvg

@@ -1,4 +1,4 @@
-# This file was created Mon May 26 12:01:50 2025
+# This file was created Tue May  5 11:22:06 2026
 # Created by:
 #                        :-) GROMACS - gmx rmsf, 2024 (-:
 #