Extract a subset of frames from a DCD trajectory file with MDAnalysis

Usage:

./extract_frames_from_dcd.py file.pdb file.dcd outfile.dcd frame_list_file.txt

The frame_list_file.txt is an ASCII file containing one frame id per line, starting from 0. Repetitions of frames are allowed and will be kept in the output file. The order of the frames will be preserved in the output DCD file.

If the list of frames is not given as a file, the standard input is read instead. This feature is conveninant to pipe from awk, for example:

awk '{print $3}' some_text_file.txt | ./extract_frames_from_dcd.py file.pdb file.dcd outfile.dcd