joaomcteixeira / taurenmd

A command-line interface for analysis of Molecular Dynamics simulations.
https://taurenmd.readthedocs.io/en/latest/
GNU General Public License v2.0
9 stars 2 forks source link

[BUG] Progress bar for `fext` only prints upon completion #67

Open menoliu opened 2 years ago

menoliu commented 2 years ago

Describe the bug When extracting trajectories with fext the progress bar only prints upon completion. Seen when trying to extract frames from multiple .dcd trajectories. Also minor bug (typo) with "writen" should be "written" on the second last line in the Output section.

To Reproduce Steps to reproduce the behavior: taurenmd fext asyn_desres_a99sbdisp.pdb pnas2018b-asyn-a99SBdisp-protein*.dcd -p 29 --odir asynN1000ran/ Please see DropBox for required files: https://www.dropbox.com/s/oogxt8ezcaqwvqk/asyn_desres_pnas2018b.tar.xz?dl=0

Expected behavior As taurenmd processes and extracts each frame, it's expected for the progress bar to increment by 1 upon completion.

Output

Starting...
    loading trajectory(ies): (Path('pnas2018b-asyn-a99SBdisp-protein-0000.dcd'),
 Path('pnas2018b-asyn-a99SBdisp-protein-0001.dcd'),
 Path('pnas2018b-asyn-a99SBdisp-protein-0002.dcd'))
    with topology: asyn_desres_a99sbdisp.pdb

* Reporting On Universe ...
    number of frames: 29977
    duration: 0.49 ns
    timestep per frame: 0.00 ns
    number of atoms: 2017
    components:
    segid C1 with 140 residues from 1 to 140

* Creating Trajectory Frame Slicing From: ...
    start: None
    stop : None
    step : 29
29.0  0.04888821
    slicing: None:None:29
    created slice: slice(None, None, 29)
    extracting 1034 frames
 |-----------------------------------------------------------------| 0.0% 0/1034 frames    writen frame 29957, to frame_29957.pdb
 |-----------------------------------------------------------------| 0.1% 1/1034 frames

Additional context N/A

Version Current running version: 0.11.2