Package schrodinger :: Package application :: Package matsci :: Module order_parameter_mod :: Class SmartsDirector

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Class SmartsDirector

                                object --+            
                                         |            
desmond.packages.analysis.GeomAnalyzerBase --+        
                                             |        
  desmond.packages.analysis._CompositeAnalyzer --+    
                                                 |    
          desmond.packages.analysis.SmartsDirector --+
                                                     |
                                                    SmartsDirector

Manage a SMARTS director.

Instance Methods

__init__(self, msys_obj, cms_obj, asl, smarts)
Create an instance.

float

reduce_vec(self, n, m)
Specify how to reduce the reference director vector, n, and all of the description vectors, m, into an order parameter.

Inherited from desmond.packages.analysis.SmartsDirector: __call__

Inherited from desmond.packages.analysis._CompositeAnalyzer (private): _postcalc, _precalc

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Static Methods

Inherited from desmond.packages.analysis.GeomAnalyzerBase (private): _get_sites, _sites2gids

Properties

Inherited from object: __class__

Method Details

init(self, msys_obj, cms_obj, asl, smarts)
(Constructor)

Create an instance.

Parameters:

msys_obj (Desmond msys .System) - the msys object (from msys.LoadMAE)
cms_obj (schrodinger.application.desmond.cms.Cms) - the cms object
asl (str) - the ASL for the descriptor
smarts (str) - the SMARTS for the descriptor

Raises:

AslException - if there is an issue with the ASL
SmartsException - if there is an issue with the SMARTS

Overrides: object.__init__

reduce_vec(self, n, m)

Specify how to reduce the reference director vector, n, and all of the description vectors, m, into an order parameter.

Parameters:

n (numpy.array) - the reference director vector
m (numpy.array) - the description vectors

Returns: float

the order parameter

Overrides: desmond.packages.analysis.SmartsDirector.reduce_vec