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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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Utility functions to store and retrieve solution information. More...
Utility functions to store and retrieve solution information.
Classes | |
| class | ClusterRecord |
| Simple named tuple class. More... | |
| class | HeapRecord |
| The heapq algorithm is a min-heap. More... | |
| class | ResultsDB |
| Class for managing the results of the experiments. More... | |
Functions | |
| def | gather_best_solution_results |
| Reads a set of database files and merge them into a single file. More... | |
| def | gather_solution_results |
| Reads a set of database files and puts them in a single file Makes sure to reorder all column names if neccesary before merging. More... | |
| def | get_best_solution |
| Recover the reference frame of the n-th best solution from a database. More... | |
| def | get_fields_string |
| Get a list of fields and return a string with them. More... | |
| def | get_sorting_indices |
| Return indices that sort the list l. More... | |
| def IMP.em2d.solutions_io.gather_best_solution_results | ( | fns, | |
| fn_output, | |||
max_number = 50000, |
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raisef = 0.1, |
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orderby = 'em2d' |
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| ) |
Reads a set of database files and merge them into a single file.
| fns | List of files with databases |
| fn_output | The database to create |
| max_number | Maximum number of records to keep, sorted according to orderby |
| raisef | Ratio of problematic database files tolerated before raising an error. This option is to tolerate some files of the databases being broken because the cluster fails, fill the disks, etc |
| orderby | Criterium used to sort the the records NOTE: Makes sure to reorder all column names if neccesary before merging The record for the native solution is only added once (from first file). |
Definition at line 94 of file solutions_io.py.
| def IMP.em2d.solutions_io.gather_solution_results | ( | fns, | |
| fn_output, | |||
raisef = 0.1 |
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| ) |
Reads a set of database files and puts them in a single file Makes sure to reorder all column names if neccesary before merging.
| fns | List of database files |
| fn_output | Name of the output database |
| raisef | See help for gather_best_solution_results() |
Definition at line 177 of file solutions_io.py.
| def IMP.em2d.solutions_io.get_best_solution | ( | fn_database, | |
| Nth, | |||
fields = False, |
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orderby = False, |
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tbl = 'results' |
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| ) |
Recover the reference frame of the n-th best solution from a database.
The index Nth stars at 0
Definition at line 229 of file solutions_io.py.
| def IMP.em2d.solutions_io.get_fields_string | ( | fields | ) |
Get a list of fields and return a string with them.
If there are no fields, return an *, indicating SQL that all the fields are requested
| fields | A list of strings |
Definition at line 253 of file solutions_io.py.
| def IMP.em2d.solutions_io.get_sorting_indices | ( | l | ) |
Return indices that sort the list l.
Definition at line 222 of file solutions_io.py.