UniDec
Universal Deconvolution of Mass and Ion Mobility Spectra
Functions | Variables
UniDec.unidec_modules.IM_functions Namespace Reference

Functions

def smooth_2d (igrid, smooth, smoothdt)
 
def min_array (igrid, xwidth, ywidth)
 
def intensitythresh (igrid, thresh)
 
def subtract_complex_2d (igrid, config)
 
def compress_2d (xgrid, ygrid, zgrid, num)
 
def linearize_2d (xvals, yvals, igrid, binsize)
 
def detectoreff_2d (igrid, xgrid, va)
 
def process_data_2d (xgrid, ygrid, igrid, config)
 
def calc_twave_dt (mass, z, ccs, config)
 
def calc_linear_dt (mass, z, ccs, config)
 
def calc_native_ccs (mass, gasmass)
 

Variables

string __author__ = 'Michael.Marty'
 

Function Documentation

def UniDec.unidec_modules.IM_functions.calc_linear_dt (   mass,
  z,
  ccs,
  config 
)
Calculate drift time in a linear cell
:param mass: Mass in Da
:param z: Charge
:param ccs: CCS in Angstrom^2
:param config: UniDecConfig object (carries the key parameters of temp, pressure, etc)
:return: Drift time (ms)

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def UniDec.unidec_modules.IM_functions.calc_native_ccs (   mass,
  gasmass 
)
Predict native CCS value for a particular mass in a given mass
:param mass: Mass of protein in Da
:param gasmass: Mass of IM background gas in Da
:return: Predicted CCS in Angstroms^2
def UniDec.unidec_modules.IM_functions.calc_twave_dt (   mass,
  z,
  ccs,
  config 
)
Calculate drift time in a T-wave cell
:param mass: Mass in Da
:param z: Charge
:param ccs: CCS in Angstrom^2
:param config: UniDecConfig object (carries the key parameters of calibration)
:return: Drift time (ms)

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def UniDec.unidec_modules.IM_functions.compress_2d (   xgrid,
  ygrid,
  zgrid,
  num 
)
Compresses a 2D grid in to smaller grids by merging n data points in the x dimension together as their average.
:param xgrid: 2D numpy array
:param ygrid: 2D numpy array
:param zgrid: 2D numpy array
:param num: number of consecutive data points in the x-dimension to average together
:return: x, y, and z grids compressed along the x dimension to a new size
def UniDec.unidec_modules.IM_functions.detectoreff_2d (   igrid,
  xgrid,
  va 
)
Corrects for Q-TOF detector efficiency
:param igrid: Intensity 2D numpy array
:param xgrid: 2D numpy array of m/z values
:param va: TOF acceleration voltage
:return: igrid corrected for detector efficiency

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def UniDec.unidec_modules.IM_functions.intensitythresh (   igrid,
  thresh 
)
Intensity threshold for 2D grid
:param igrid: 2D numpy array
:param thresh: Threshold
:return: igrid with all elements below thresh set to 0

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def UniDec.unidec_modules.IM_functions.linearize_2d (   xvals,
  yvals,
  igrid,
  binsize 
)
Linearize the x-axis of a 2D grid
:param xvals: 2D numpy array (x values)
:param yvals: 2D numpy array (y values)
:param igrid: 2D numpy array (intensity values)
:param binsize: difference between consecutive linear x points
:return: x, y, and z grid linearized along the x-axis

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def UniDec.unidec_modules.IM_functions.min_array (   igrid,
  xwidth,
  ywidth 
)
Creates an array of local minimum values in a neighborhood of +/- width
:param igrid: 2D numpy array
:param xwidth: width in x direction
:param ywidth: width in y direction
:return: array of local minimum values in the same dimensions as igrid

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def UniDec.unidec_modules.IM_functions.process_data_2d (   xgrid,
  ygrid,
  igrid,
  config 
)
Process IM-MS raw data.

1. Chop data to defined limits
2. Linearize
3. Smooth
4. Subtract background
5. Detector efficiency correction
6. Normalize
:param xgrid: 2D numpy array (x values)
:param ygrid: 2D numpy array (y values)
:param igrid: 2D numpy array (intensity values values)
:param config: UniDecConfig object carrying parameters for processing
:return: x, y, and z grids of processed data

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def UniDec.unidec_modules.IM_functions.smooth_2d (   igrid,
  smooth,
  smoothdt 
)
Gaussian smooth of 2D grid
:param igrid: 2D numpy array
:param smooth: width in x dimension (in data points)
:param smoothdt: width in y dimension (in data points)
:return: smoothed 2D numpy array

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def UniDec.unidec_modules.IM_functions.subtract_complex_2d (   igrid,
  config 
)
Subtract a complex curved baseline.
Creates a baseline using min_array, smooths it using smooth_2d, and subtracts it.
:param igrid: 2D numpy array
:param config: UniDecConfig object specifying width parameters in x and y dimensions
:return: igrid with background subtraction applied

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Variable Documentation

string UniDec.unidec_modules.IM_functions.__author__ = 'Michael.Marty'