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def low_pass_smoothing(all_raw_time_series, sigma, dt_fs):
    ''' uses Butterworth filter for low-pass smoothing                                                                                                                                                                                        
    '''
    traj_length = all_raw_time_series.shape[1]
    conversion = 33355.0/dt_fs
    order = 6
    # Frequency cutoff in units of inverse timestep                                                                                                                                                                                           
    low_cutoff = float(sigma)/conversion * (2.0 - 2.0/traj_length)

    # # sigma will be in units of cm-1, but function needs input of seconds                                                                                                                                                                   

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#!/usr/bin/env python

import mdtraj as md
import time
import numpy as np
from copy import deepcopy
import itertools
import sys

t0 = time.time()

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#!/usr/bin/env python                                                                                                                                       

"""
Currently the Monitor code has a bug where certain frames are not being written to disk.  
I'm currently doing something that requires comparing the Monitor trajectory to a "standard" trajectory, 
which means I need to either delete the "standard" frames or fill in the missing ones.
I thought it would be easier to fill in the missing ones, so that I may continue assuming that frames are spaced by the time step.
So this small script detects where frames are missing and fills them in by averaging the previous and current frame:
"""

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#!/bin/sh

show_help() 
{
    echo "Use: torque_submit_workers [options] <servername> <port> <num-workers>"
    echo "where options are:"
    echo "  -M <name>        Name of the preferred master for worker."
    echo "  -N <name>        Same as -M (backwards compatibility)."
    echo "  -c <num>         Set the number of cores each worker should use (0=auto). (default=1)"
    echo "  -C <catalog>     Set catalog server to <catalog>. <catalog> format: HOSTNAME:PORT."

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CRYST1   30.571   30.571   30.571  90.00  90.00  90.00 P 1           1
ATOM      1  S   dms     1       3.840  13.360   6.210                          
ATOM      2  C   dms     1       2.690  11.920   6.530                          
ATOM      3  H   dms     1       3.240  11.020   6.240                          
ATOM      4  H1  dms     1       2.310  11.790   7.540                          
ATOM      5  H2  dms     1       1.810  12.070   5.890                          
ATOM      6  C1  dms     1       5.350  12.830   7.030                          
ATOM      7  H3  dms     1       5.290  11.770   7.310                          
ATOM      8  H4  dms     1       6.200  13.040   6.390                          
ATOM      9  H5  dms     1       5.420  13.310   8.000