4.7.0 new minor upate: you can now stride (read every Xth frames) you…

…r trajectories with "-s" argument

README.md

@@ -161,6 +161,7 @@ the interactive prompt.
   -h, --help            show this help message and exit
   -f TRAJ, --traj TRAJ  trajectory file(s). You can give a list of trajectory (see usage example)
   -t TOP, --top TOP     topfile
+  -s INT, --stride INT  stride, read every Xth frames
   -o OUTPUT, --output OUTPUT (default: clustering.log)
                         logfile 
   -st SELECT_TRAJ, --select_traj SELECT_TRAJ (default: all)
@@ -196,6 +197,8 @@ Please note that the trajectory is reduced to the backbone in order to reduce th
 Caution: You have to put quote beside your selection string (for *sr*, *st*, and *sa* arguments) 
  - Simple usage (clustering on backbone, logfile is called clustering.log, output folder is "clustering")
  ```python ttclust.py -f examples/example.xtc -t examples/example.pdb```
+  - Simple usage with reading every 10 frames
+ ```python ttclust.py -f examples/example.xtc -t examples/example.pdb -s 10```
   - Simple usage with multiple trajectories  
  ```python ttclust.py -f traj1.xtc traj2.xtc  -t examples/example.pdb```  
  ```python ttclust.py -f *.xtc  -t examples/example.pdb```

setup.py

@@ -1,8 +1,8 @@
 from setuptools import setup, find_packages
 
 MAJOR = 4
-MINOR = 6
-PATCH = 10
+MINOR = 7
+PATCH = 0
 VERSION = "{}.{}.{}".format(MAJOR, MINOR, PATCH)
 
 with open("ttclust/version.py", "w") as f:

ttclust/ttclust.py

@@ -136,6 +136,7 @@ def init_log(args, mdtrajectory):
         select_align))
     LOGFILE.write("      Atoms selected for RMSD = {} \n".format(select_rmsd))
     LOGFILE.write("  trajectory file  : {} \n".format(','.join(traj)))
+    LOGFILE.write("   Stride          : {} \n".format(args["stride"]))
     LOGFILE.write("   Number of frames  : {} \n".format(mdtrajectory.n_frames))
     LOGFILE.write("   Number of atoms  : {} \n".format(mdtrajectory.n_atoms))
     LOGFILE.write("  topology file    : {} \n".format(topo))
@@ -320,6 +321,7 @@ def parseArg():
         pass
     arguments.add_argument('-f', "--traj", help="trajectory file(s). You can give a list of files.", required=True, nargs='+')
     arguments.add_argument('-t', '--top', help="topfile", default=None)
+    arguments.add_argument('-s', '--stride', help="stride (read every Xth frames", default=1)
     arguments.add_argument('-l', '--logfile', help="logfile (default : clustering.log). The "
                                                    "name of your output file will be the basename (name before the extention "
                                                    "of this logfile", default="clustering")
@@ -1162,7 +1164,7 @@ def Cluster_analysis_call(args):
         else:
 
             traj = md.load(trajfile,
-                           top=topfile)
+                           top=topfile, stride=args["stride"])
     elif len(trajfile) > 1:
         print(">Several trajectories given. Will concatenate them.")
         trajList = []
@@ -1171,7 +1173,7 @@ def Cluster_analysis_call(args):
                 trajList.append(md.load_pdb(t))
             else:
                 trajList.append(md.load(t,
-                               top=topfile))
+                               top=topfile,stride=args["stride"]))
         traj = md.join(trajList)
 
         #resting the timetable
@@ -1236,7 +1238,7 @@ def main():
     """
 
     print("********************************************************")
-    print("******************  TTCLUST {} **********************".format(
+    print("******************  TTCLUST {} *********************".format(
         __version__))
     print("********************************************************")
     print("")

ttclust/version.py

@@ -1 +1 @@
-__version__ = '4.6.10'
+__version__ = '4.7.0'