IMP.em2d.solutions_io.ResultsDB Class Reference

Class for managing the results of the experiments. More...

Inheritance diagram for IMP.em2d.solutions_io.ResultsDB:

Public Member Functions
def	add_ccc_table
	Add a table to the database for store the values of the cross correlation coefficient between a model and the native configuration.
def	add_cluster_record
	Add a record to the cluster database. More...
def	add_clusters_table
	Add a table to store information about the clusters of structures. More...
def	add_native_record
	Add a record for the native structure to the database see add_record() for the meaning of the parameters.
def	add_placement_scores_table
	Creates a table to store the values of the placement scores for the models. More...
def	add_record
	Add a recorde to the database. More...
def	add_results_table
	Build the table of results. More...
def	format_ccc_record
	Format for the record to store in the ccc table.
def	format_placement_record
	both distances and angles are expected to be a list of floats
def	get_ccc
	Recover the cross-correlation coefficient for a solution. More...
def	get_individual_placement_statistics
	Recovers from the database the placement scores for a set of solutions, and returns the mean and standard deviation of the placement score for each of the components of the complex being scored. More...
def	get_left_join_command
	Format a left join SQL command that recovers all fileds from the tables given. More...
def	get_native_rank
	Get the position of the native configuration. More...
def	get_native_solution
	Recover data for the native solution. More...
def	get_nth_largest_cluster
	Recover the the information about the n-th largest cluster. More...
def	get_placement_fields
	Return the names of the placement score fields in the database.
def	get_placement_statistics
	Calculate the placement score and its standard deviation for the complexes in a set of solutions. More...
def	get_solutions
	Get solutions from the database. More...
def	get_solutions_from_list
	Recover solutions for a specific list of results. More...
def	get_solutions_results_table
	Recovers solutions. More...
def	store_cluster_data
	Store the data for the clusters.
Public Member Functions inherited from IMP.em2d.Database.Database2
def	add_column
	Add a column to a table column - the name of the column. More...
def	add_columns
	Add columns to the database. More...
def	check_if_is_connected
	Checks if the class is connected to the database filename.
def	close
	Closes the database.
def	connect
	Connects to the database in filename.
def	create
	Creates a database by simply connecting to the file.
def	create_table
	Creates a table. More...
def	create_view
	creates a view of the given table where the values are selected using the condition values. More...
def	drop_table
	Delete a table if it exists.
def	drop_view
	Removes a view from the database.
def	get_condition_string
	creates a condition applying each value to each field
def	get_table
	Returns th fields requested from the table.
def	get_table_column_names
	Get the names of the columns for a given table.
def	get_table_types
	Gets info about a table and retuns all the types in it.
def	retrieve_data
	Retrieves data from the database using the sql_command returns the records as a list of tuples.
def	select_table
	Prompt for tables so the user can choose one.
def	store_data
	Inserts information in a given table of the database. More...
def	store_dataV1
	Inserts information in a given table of the database. More...
def	update_data
	updates the register in the table identified by the condition values for the condition fields

Detailed Description

Note

This class is only available in Python.

Definition at line 266 of file solutions_io.py.

Member Function Documentation

def IMP.em2d.solutions_io.ResultsDB.add_cluster_record	(		self,
			cluster_id,
			n_elements,
			representative,
			elements,
			solutions_ids
	)

Actually, only stores it in a list (that will be added later)

Parameters

cluster_id	Number with the id of the cluster
n_elements	Number of elements in the cluster
representative	Number with the id of the representative element
elements	List with the number of the elements of the cluster
solutions_ids	The numbers above are provided by the clustering algorithm. The solutions_ids are the ids of the models in "elements".

Definition at line 559 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.add_clusters_table	(		self,
			name
	)

Parameters

name	Name of the table

Definition at line 546 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.add_placement_scores_table	(		self,
			names
	)

Parameters

names

Names of the components of the assembly

Definition at line 435 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.add_record	(		self,
			solution_id,
			assignment,
			RFs,
			total_score,
			restraints_scores,
			measures
	)

Parameters

solution_id	The key for the solution
assignment	The assigment for the solution provided by domino
RFs	Reference frames of the rigid bodies of the components of the assembly in the solution
total_score	Total value of the scoring function
restraints_scores	A list with all the values for the restraints
measures	A list with the values of all the measures for benchmark

Definition at line 391 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.add_results_table	(		self,
			restraints_names,
			add_measures = False
	)

Parameters

restraints_names	The names given to the columns of the table
add_measures	If True, add fields for comparing models and native conformation

Definition at line 288 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_ccc	(		self,
			solution_id
	)

Parameters

solution_id

Definition at line 488 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_individual_placement_statistics	(		self,
			solutions_ids
	)

This function will be typical used to compute the variation of the placement of each component within a cluster of solutions

Parameters

solutions_ids

The ids of the solutions used to compute the statistics

Returns

The output are 4 numpy vectors: placement_distances_mean - The mean placement distance for each component placement_distances_stddev - The standardd deviation of the placement distance for each component placement_angles_mean - The mean placement angle for each component placement_angles_stddev - The standard deviation of the placement angle for each component,

Definition at line 634 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_left_join_command	(		self,
			pairs_table_field,
			tables_names
	)

Parameters

pairs_table_field	Pairs of (table,field)
tables_names	Names of the tables

E.g. If pairs_table_filed = ((table1,a), (table2,b), (table3,c), (table2,d)) and tables_names = (table1, table2, table3)

The SQL command is: SELECT table1.a, table2.b, table3.c, table2.d FROM table1 LEFT JOIN table2 ON table1.solution_id = table2.solution_id LEFT JOIN table3 ON table1.solution_id = table3.solution_id WHERE table1.solution_id IS NOT NULL AND table2.solution_id IS NOT NULL AND table3.solution_id IS NOT NULL

Definition at line 506 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_native_rank	(		self,
			orderby
	)

Parameters

orderby

Criterium used to sort the solutions

Definition at line 601 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_native_solution	(		self,
			fields = False
	)

Parameters

fields

Fields to recover

Definition at line 378 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_nth_largest_cluster	(		self,
			position,
			table_name = 'clusters'
	)

Parameters

position	Cluster position (by size) requested (1 is the largest cluster)
table_name	Table where the information about the clusters is stored

Definition at line 616 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_placement_statistics	(		self,
			solutions_ids
	)

The values returned are averages, as the placement score for a complex is the average of the placement scores of the components. This function is used to obtain global placement for a cluster of solutions.

Parameters

solutions_ids

The ids of the solutions used to compute the statistics

Returns

The output are 4 values: plcd_mean - Average of the placement distance for the entire complex over all the solutions. plcd_std - Standard deviation of the placement distance for the entire complex over all the solutions. plca_mean - Average of the placement angle for the entire complex over all the solutions. plca_std - Standard deviation of the placement angle for the entire complex over all the solutions.

Definition at line 671 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_solutions	(		self,
			fields = False,
			max_number = None,
			orderby = False
	)

Parameters

fields	Fields requested. If the fields are in different tables, a left join is done. Otherwise get_solutions_results_table() is called. See get_solutions_results_table() for the meaning of the parameters.
max_number
orderby

Definition at line 332 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_solutions_from_list	(		self,
			fields = False,
			solutions_ids = []
	)

Parameters

fields	Fields to recover fro the database
solutions_ids	A list with the desired solutions. E.g. [0,3,6]

Definition at line 587 of file solutions_io.py.

def IMP.em2d.solutions_io.ResultsDB.get_solutions_results_table	(		self,
			fields = False,
			max_number = None,
			orderby = False
	)

Parameters

fields	Fields to recover from the table
max_number	Maximum number of solutions to recover
orderby	Name of the restraint used for sorting the states

Definition at line 312 of file solutions_io.py.

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The documentation for this class was generated from the following file:

• solutions_io.py