Module Expr Str Import alias ClassDef bases NameLoad body Assign NameStore Num FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad If CompareIn Str SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index Str body Assign AttributeStore NameLoad attr Call NameLoad SubscriptLoad SubscriptLoad SubscriptLoad SubscriptLoad NameLoad Index Str Index Str Index Str Index Str orelse Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Return Dict Str NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Dict Str Str TupleLoad Num Num Num For NameStore Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr body For NameStore Call NameLoad BinOpAdd NameLoad Num AttributeLoad AttributeLoad NameLoad attr attr body If CompareGt SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad NameLoad NameLoad SubscriptLoad NameLoad Index Str body Assign SubscriptStore NameLoad Index Str TupleLoad NameLoad NameLoad Assign SubscriptStore NameLoad Index Str SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore Dict Str Str Str Num Num Num For NameStore Call NameLoad AttributeLoad AttributeLoad NameLoad attr attr body Assign NameStore Call AttributeLoad NameLoad attr ListLoad SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad NameLoad NameLoad SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad NameLoad NameLoad If CompareGt NameLoad SubscriptLoad NameLoad Index Str body Assign SubscriptStore NameLoad Index Str NameLoad Assign SubscriptStore NameLoad Index Str NameLoad Assign SubscriptStore NameLoad Index Str Call AttributeLoad NameLoad attr ListLoad SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad NameLoad NameLoad SubscriptLoad AttributeLoad NameLoad attr Index TupleLoad NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Str Index Num SubscriptLoad SubscriptLoad NameLoad Index Str Index Num Assign NameStore BinOpDiv SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr Assign NameStore ListLoad Assign NameStore NameLoad While CompareLt NameLoad SubscriptLoad NameLoad Index Str body Assign NameStore Call AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index Str NameLoad AugAssignAdd NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Return TupleLoad NameLoad ListLoad decorator_list decorator_list
N/A N/A 
Created on 27/05/2013

@author: victor
 N/A numpy ParametersGenerator N/A object N/A N/A GROMOS_DEFAULT_MAX 25 __init__ N/A N/A self parameters matrix_handler N/A N/A N/A 
        Class creator.

        @param parameters: Script parameters.

        @param distance_matrix: The distance matrix we are using.
         N/A N/A self distance_matrix N/A matrix_handler distance_matrix N/A N/A self parameters parameters N/A N/A max N/A N/A N/A parameters N/A clustering N/A algorithms N/A gromos N/A N/A N/A self max_gen_clusterings N/A float N/A N/A N/A N/A parameters N/A clustering N/A algorithms N/A gromos N/A max N/A N/A N/A self max_gen_clusterings N/A ParametersGenerator GROMOS_DEFAULT_MAX N/A get_base_parameters N/A N/A cls N/A N/A N/A 
        Defines the base parameters needed for each of the algorithms. Each parameter created will be based
        on one of those and must not have more keys than these.

        @return: A dictionary with the base parameters for this algorithm.
         N/A N/A cutoff None N/A classmethod get_most_separated_elements N/A N/A self N/A N/A N/A 
        Chooses the 2 most separated elements of the dataset based on the distance stored in distance matrix.
        @return: A dictionary with the elements and their distance value.
         N/A max_s N/A elements value N/A 0 0 0 N/A i N/A range N/A N/A self distance_matrix row_length N/A N/A j N/A range N/A i 1 N/A N/A self distance_matrix row_length N/A N/A N/A N/A N/A self distance_matrix N/A N/A i j N/A max_s N/A value N/A N/A N/A max_s N/A elements N/A i j N/A N/A max_s N/A value N/A N/A self distance_matrix N/A N/A i j N/A max_s N/A get_most_separated_from_two_elements N/A N/A self first second N/A N/A N/A 
        Gets the element which distance to two elements is maximum.

        @param first: First element to check against.
        @param second: Second element to check against.

        @return: A dictionary with the number of element and the
         N/A max_s N/A element mean_value value 0 0 0 N/A i N/A range N/A N/A self distance_matrix row_length N/A N/A my_mean N/A N/A numpy mean N/A N/A N/A self distance_matrix N/A N/A i first N/A N/A self distance_matrix N/A N/A i second N/A N/A my_mean N/A max_s N/A mean_value N/A N/A N/A max_s N/A element i N/A N/A max_s N/A mean_value my_mean N/A N/A max_s N/A value N/A N/A numpy max N/A N/A N/A self distance_matrix N/A N/A i first N/A N/A self distance_matrix N/A N/A i second N/A max_s N/A get_parameters N/A N/A self N/A N/A N/A 
        This function creates some parameters to be used with Gromos.
        @return: A tuple with the generated parameters and an empty list corresponding to the clusterings.
         N/A most_separated N/A N/A self get_most_separated_elements N/A central_element N/A N/A self get_most_separated_from_two_elements N/A N/A most_separated N/A elements N/A 0 N/A N/A most_separated N/A elements N/A 1 N/A step N/A N/A central_element N/A value N/A self max_gen_clusterings N/A run_parameters N/A N/A cutoff step N/A N/A cutoff N/A central_element N/A value N/A N/A run_parameter N/A N/A ParametersGenerator get_base_parameters N/A N/A run_parameter N/A cutoff cutoff N/A cutoff step N/A N/A N/A run_parameters append run_parameter N/A N/A run_parameters N/A N/A N/A