Package coan

Package coan

This is the top module of the pyCoAn package that acts as a general
framework for the base distribution and the add-ons

Submodules
  • coan.clem: Clem add-on to pyCoAn.
    • coan.clem.holes: This module defines algorithms necessary to run the clem add-on
  • coan.coma: Coordinate Manipulation toolbox (CoMa)
    • coan.coma.contacts: This module defines a Contacts class for evaluating contacts between two molecular structure objects of the coordinate manipulation toolbox (CoMa)
    • coan.coma.coordinates: This module defines general functions that operate on molecular structure objects for the coordinate manipulation toolbox (CoMa)
    • coan.coma.io: This module populates and defines the high-level and molecular structure objects for the coordinate manipulation toolbox (CoMa)
  • coan.ctf: CTF add-on for ctf modeling (including phase shift) and pythonic interface...
    • coan.ctf.ctf: This module defines functions related to CTF operating on density...
  • coan.deman: Density Manipulation toolbox (DeMan)
    • coan.deman.curves: This module defines a class for 1D data, Curve.
    • coan.deman.edge: CoAn wrappers for scikit-image (version 0.9.3) and scipy ndimage...
    • coan.deman.filters: This module defines simple filter functions that operate on density ...
    • coan.deman.general: This module defines general functions that operate on density objects for the density manipulation toolbox (DeMan)
    • coan.deman.io: This module defines the volume and image classes and their methods ...
    • coan.deman.masking: This module contains routines for masking
    • coan.deman.morpho: CoAn wrappers for scikit-image morphology (version 0.9.3) and...
    • coan.deman.phantoms: Module to make various types of phantoms
    • coan.deman.proc: CoAn wrappers for scikit-image (version 0.9.3) and scipy ndimage...
    • coan.deman.stacks: This defines stack-like list classes and their methods for the Density Manipulation toolbox (DeMan)
    • coan.deman.stats: This module defines an object and functions for handling statistically connected densities such as an average and the corresponding variance or a difference and the corresponding confidence map.
    • coan.deman.trans: CoAn wrappers for scikit-image library (version 0.9.3)
  • coan.miller: Toolbox for conversion to Structure factors with Miller indicies (Miller)
    • coan.miller.io: This module populates and defines the high-level objects for the Structure factor Manipulation toolbox (StruMa)
  • coan.utils: This is the utility module of the CoAn packages.
  • coan.viewers: This is the viewers module of the CoAn packages.

Functions
 
test(pattern=None, verbose=False, stop=False)
if verbose is True: print long form...
Variables
  add_ons = True
Function Details

test(pattern=None, verbose=False, stop=False)

 
if verbose is True: print long form
if stop is True: stop after first error/failure