Moved gromacs module from mdevaluate to pygmx

pygmx/gromacs/xtcindex.py

@@ -0,0 +1,63 @@
+from .reader import XTCReader, index_filename_for_xtc, INDEX_MAGIC
+from xdrlib import Packer
+import os
+import sys
+import logging
+
+
+def index_xtcfile(filename):
+    """
+    Write an index-file for a xtc-file.
+
+    The resulting file will have the same name, except for the new extension .xtcindex.
+    This function has to be called only once for every xtcfile.
+
+    Args:
+        filename (str): Name of the xtc-file
+
+    """
+    # TODO: Would it be possible, to index files on the fly?
+    #       How long does indexing take?
+    index_filename = index_filename_for_xtc(filename)
+    print('Writing index file: {}'.format(index_filename))
+    packer = Packer()
+    xtc_stat = os.stat(filename)
+    c_time = int(xtc_stat.st_ctime)
+    m_time = int(xtc_stat.st_mtime)
+    size = xtc_stat.st_size
+
+    with XTCReader(filename, load_cache_file=False) as reader, open(index_filename, 'wb') as idx_fd:
+        packer.pack_hyper(INDEX_MAGIC)
+        # TODO Maybe store only the hashsum of the file for identification?
+        packer.pack_hyper(c_time)
+        packer.pack_hyper(m_time)
+        packer.pack_hyper(size)
+        count = 0
+        try:
+            while True:
+                if count % 300 == 0:
+                    print("Frame {}".format(count), end="\r")
+                position = reader.get_position()
+                frame = reader.decode_frame()
+                packer.pack_hyper(position)
+                packer.pack_float(frame.time)
+
+                count += 1
+
+        except EOFError:
+            pass
+        idx_fd.write(packer.get_buffer())
+        packer.reset()
+
+def main():
+    if len(sys.argv) < 2:
+        print("Usage {} xtc-file [xtc-file]".format(sys.argv[0]))
+        return -1
+
+    for filename in sys.argv[1:]:
+        index_xtcfile(filename)
+
+
+
+if __name__ == '__main__':
+    sys.exit(main())