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 69 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 177 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 164 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 123 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 108 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 74 of file solutions_io.py.
| def IMP.em2d.solutions_io.ResultsDB.get_ccc | ( | self, | |
| solution_id | |||
| ) |
- Parameters
-
solution_id
Definition at line 141 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 219 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 159 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 192 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 94 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 200 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 238 of file solutions_io.py.
Here is the call graph for this function:| 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.
Definition at line 89 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 187 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 81 of file solutions_io.py.
The documentation for this class was generated from the following file: