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Package gromacs :: Package analysis :: Package plugins :: Module cysaccessibility :: Class _CysAccessibility
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Class _CysAccessibility

source code

         object --+        
                  |        
utilities.FileUtils --+    
                      |    
            core.Worker --+
                          |
                         _CysAccessibility
Analysis of Cysteine accessibility.
Instance Methods [hide private]
 
__init__(self, **kwargs)
Set up customized Cysteine accessibility analysis.		 source code
 
_register_hook(self, **kwargs)
Run when registering; requires simulation.		 source code
 
run(self, cutoff=None, force=False, **gmxargs)
Run ``g_dist -dist cutoff`` for each cysteine and save output for further analysis.		 source code
 
analyze(self, **kwargs)
Mindist analysis for all cysteines.		 source code
 
plot(self, **kwargs)
Plot all results in one graph, labelled by the result keys.		 source code
 
make_index_cys(self)
Make index file for all cysteines and water oxygens.		 source code
 
_mindist(self, resid)
Analyze minimum distance for resid.		 source code

Inherited from core.Worker: figdir, plugindir, savefig, store_xvg, topdir

Inherited from utilities.FileUtils: __repr__, check_file_exists, filename, infix_filename

Inherited from utilities.FileUtils (private): _init_filename

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __str__

Class Variables [hide private]

Inherited from utilities.FileUtils: default_extension

Instance Variables [hide private]

Inherited from core.Worker: plugin, plugin_name

Inherited from utilities.FileUtils: real_filename

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, **kwargs)
(Constructor)

source code 

Set up customized Cysteine accessibility analysis.

Note that all Cys residues in the protein are analyzed. Therefore, the list of cysteine labels must contain as many entries as there are cysteines in the protein. There are no sanity checks.

Parameters:
  • cysteines (list) - list of all resids (eg from the sequence) that are used as labels or in the form 'Cys<resid>'. (required)
  • cys_cutoff (number) - cutoff in nm for the minimum S-OW distance [1.0]
Overrides: object.__init__

_register_hook(self, **kwargs)

source code 
Run when registering; requires simulation.
Overrides: core.Worker._register_hook

run(self, cutoff=None, force=False, **gmxargs)

source code  
Run ``g_dist -dist cutoff`` for each cysteine and save output for further analysis.

By default existing data files are *not* overwritten. If this
behaviour is desired then set the *force* = ``True`` keyword
argument.

All other parameters are passed on to :func:`gromacs.g_dist`.
Overrides: core.Worker.run

analyze(self, **kwargs)

source code 
Mindist analysis for all cysteines. Returns results for interactive analysis.
Overrides: core.Worker.analyze

plot(self, **kwargs)

source code 
Plot all results in one graph, labelled by the result keys.
Parameters:
  • figure -
    • True: save figures in the given formats
    • "name.ext": save figure under this filename (ext -> format)
    • False: only show on screen
  • formats (sequence) - sequence of all formats that should be saved [('png', 'pdf')]
  • plotargs - keyword arguments for pylab.plot()
Overrides: core.Worker.plot

make_index_cys(self)

source code 

Make index file for all cysteines and water oxygens.

NO SANITY CHECKS: The SH atoms are simply labelled consecutively with the resids from the cysteines parameter.


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