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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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Class for managing the results of the experiments. More...
Inheritance diagram for IMP.EMageFit.solutions_io.ResultsDB:Class for managing the results of the experiments.
Definition at line 239 of file solutions_io.py.
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. More... | |
| 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. More... | |
| 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 record 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. More... | |
| def | format_placement_record |
| both distances and angles are expected to be a list of floats More... | |
| 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 fields 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. More... | |
| 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. More... | |
| Public Member Functions inherited from IMP.EMageFit.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. More... | |
| def | close |
| Closes the database. More... | |
| def | connect |
| Connects to the database in filename. More... | |
| def | create |
| Creates a database by simply connecting to the file. More... | |
| 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. More... | |
| def | drop_view |
| Removes a view from the database. More... | |
| def | get_condition_string |
| creates a condition applying each value to each field More... | |
| def | get_table |
| Returns th fields requested from the table. More... | |
| def | get_table_column_names |
| Get the names of the columns for a given table. More... | |
| def | get_table_types |
| Gets info about a table and retuns all the types in it. More... | |
| def | retrieve_data |
| Retrieves data from the database using the sql_command returns the records as a list of tuples. More... | |
| def | select_table |
| Prompt for tables so the user can choose one. More... | |
| 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 More... | |
| def IMP.EMageFit.solutions_io.ResultsDB.add_ccc_table | ( | self | ) |
Add a table to the database for store the values of the cross correlation coefficient between a model and the native configuration.
Definition at line 440 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.add_cluster_record | ( | self, | |
| cluster_id, | |||
| n_elements, | |||
| representative, | |||
| elements, | |||
| solutions_ids | |||
| ) |
Add a record to the cluster database.
Actually, only stores it in a list (that will be added later)
| 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 532 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.add_clusters_table | ( | self, | |
| name | |||
| ) |
Add a table to store information about the clusters of structures.
| name | Name of the table |
Definition at line 519 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.add_native_record | ( | self, | |
| assignment, | |||
| RFs, | |||
| total_score, | |||
| restraints_scores | |||
| ) |
Add a record for the native structure to the database see add_record() for the meaning of the parameters.
Definition at line 385 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.add_placement_scores_table | ( | self, | |
| names | |||
| ) |
Creates a table to store the values of the placement scores for the models.
| names | Names of the components of the assembly |
Definition at line 408 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.add_record | ( | self, | |
| solution_id, | |||
| assignment, | |||
| RFs, | |||
| total_score, | |||
| restraints_scores, | |||
| measures | |||
| ) |
Add a record to the database.
| solution_id | The key for the solution |
| assignment | The assignment 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 364 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.add_results_table | ( | self, | |
| restraints_names, | |||
add_measures = False |
|||
| ) |
Build the table of results.
| 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 261 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.format_ccc_record | ( | self, | |
| solution_id, | |||
| ccc | |||
| ) |
Format for the record to store in the ccc table.
Definition at line 457 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.format_placement_record | ( | self, | |
| solution_id, | |||
| distances, | |||
| angles | |||
| ) |
both distances and angles are expected to be a list of floats
Definition at line 403 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_ccc | ( | self, | |
| solution_id | |||
| ) |
Recover the cross-correlation coefficient for a solution.
| solution_id |
Definition at line 461 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_individual_placement_statistics | ( | self, | |
| solutions_ids | |||
| ) |
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.
This function will be typical used to compute the variation of the placement of each component within a cluster of solutions
| solutions_ids | The ids of the solutions used to compute the statistics |
Definition at line 607 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_left_join_command | ( | self, | |
| pairs_table_field, | |||
| tables_names | |||
| ) |
Format a left join SQL command that recovers all fields from the tables given.
| 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 479 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_native_rank | ( | self, | |
| orderby | |||
| ) |
Get the position of the native configuration.
| orderby | Criterion used to sort the solutions |
Definition at line 574 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_native_solution | ( | self, | |
fields = False |
|||
| ) |
Recover data for the native solution.
| fields | Fields to recover |
Definition at line 351 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_nth_largest_cluster | ( | self, | |
| position, | |||
table_name = 'clusters' |
|||
| ) |
Recover the the information about the n-th largest cluster.
| 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 589 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_placement_fields | ( | self | ) |
Return the names of the placement score fields in the database.
Definition at line 431 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_placement_statistics | ( | self, | |
| solutions_ids | |||
| ) |
Calculate the placement score and its standard deviation for the complexes in a set of solutions.
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.
| solutions_ids | The ids of the solutions used to compute the statistics |
Definition at line 644 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_solutions | ( | self, | |
fields = False, |
|||
max_number = None, |
|||
orderby = False |
|||
| ) |
Get solutions from the database.
| 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 305 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_solutions_from_list | ( | self, | |
fields = False, |
|||
solutions_ids = [] |
|||
| ) |
Recover solutions for a specific list of results.
| fields | Fields to recover fro the database |
| solutions_ids | A list with the desired solutions. E.g. [0,3,6] |
Definition at line 560 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.get_solutions_results_table | ( | self, | |
fields = False, |
|||
max_number = None, |
|||
orderby = False |
|||
| ) |
Recovers solutions.
| 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 285 of file solutions_io.py.
| def IMP.EMageFit.solutions_io.ResultsDB.store_cluster_data | ( | self | ) |
Store the data for the clusters.
Definition at line 552 of file solutions_io.py.