Task that calls the fitness provider. More...
Public Member Functions | |
| FitnessEvaluationTask (FRParameters settings, DGraph molGraph, IAtomContainer iac, String workDir, String outFileName) | |
| Object | call () throws DENOPTIMException, Exception |
 Public Member Functions inherited from denoptim.task.FitnessTask | |
| FitnessTask (FitnessParameters settings, Candidate c) | |
| Public Member Functions inherited from denoptim.task.Task | |
| Task (final int id) | |
| int | getId () |
| void | setVerbosity (int verbosity) |
| Set the verbosity: i.e., amount of log printed by this class. More... | |
| void | setWorkSpace (File workDir) |
| Sets the pathname of the work space, i.e., the location where the task is supposed to use move to or to threat as the result of "pwd" at runtime. More... | |
| boolean | isCompleted () |
| boolean | foundException () |
| Throwable | getException () |
| String | getErrorMessage () |
| void | stopTask () |
| Stop the task if not already completed. More... | |
| String | toString () |
| Returns a string identifying this task by its ID and reporting whether an exception has been thrown and if the tasks is completed. More... | |
| void | setNotify (boolean notify) |
Private Attributes | |
| FRParameters | frSettings = null |
| Collection of settings controlling the execution of the task. More... | |
| FragmentSpace | fragSpace |
| Fragment space in use. More... | |
Additional Inherited Members | |
| Public Attributes inherited from denoptim.task.Task | |
| Object | lock = new Object() |
| Lock for addressing synchronization issues. More... | |
| Protected Member Functions inherited from denoptim.task.FitnessTask | |
| void | runFitnessProvider () throws DENOPTIMException |
| This method runs the actual evaluation of the fitness, whether that is run internally (i.e., within this instance of the JAVA VM), or delegated to an external child process. More... | |
| Protected Attributes inherited from denoptim.task.FitnessTask | |
| DGraph | dGraph |
| The graph representation of the entity to evaluate. More... | |
| IAtomContainer | fitProvMol = null |
| The chemical representation of the entity to evaluate. More... | |
| Candidate | result |
| The data structure holding the results of this task. More... | |
| String | fitProvInputFile |
| The file where we store the input to the fitness provider. More... | |
| String | fitProvOutFile |
| The file where we store the final output from the fitness provider. More... | |
| String | fitProvPNGFile |
| The file where we store the graphical representation of the candidate (i.e., a picture). More... | |
| String | fitProvUIDFile = null |
| The file where we store the list of unique identifiers or previously evaluated candidates. More... | |
| boolean | fitnessIsRequired = false |
| Flag specifying if a valid fitness value is required to consider the task successfully completed. More... | |
| FitnessParameters | fitnessSettings |
| Settings for the calculation of the fitness. More... | |
| Protected Attributes inherited from denoptim.task.Task | |
| boolean | notifyGlobalTaskManager = false |
| Flag controlling whether this task is expected to notify the static task manager. More... | |
| boolean | completed = false |
| Flag about completion. More... | |
| boolean | hasException = false |
| Flag about exception. More... | |
| String | errMsg = "" |
| Error message produced by any subtask. More... | |
| Throwable | thrownExc |
| Exception thrown. More... | |
| int | id |
| A user-assigned id for this task. More... | |
| ProcessHandler | processHandler |
| Executor for external bash script. More... | |
| File | workDir |
| The file system location where we want to be placed when doing the work. More... | |
| int | verbosity = 0 |
| Verbosity level. More... | |
| final String | SEP = System.getProperty("file.separator") |
| System-dependent file separator. More... | |
| final String | NL = System.getProperty("line.separator") |
| System-dependent line separator (newline) More... | |
Detailed Description
Task that calls the fitness provider.
Definition at line 40 of file FitnessEvaluationTask.java.
Constructor & Destructor Documentation
◆ FitnessEvaluationTask()
| denoptim.programs.fitnessevaluator.FitnessEvaluationTask.FitnessEvaluationTask | ( | FRParameters | settings, |
| DGraph | molGraph, | ||
| IAtomContainer | iac, | ||
| String | workDir, | ||
| String | outFileName | ||
| ) |
- Parameters
-
molGraph the DENOPTIM representation of the entity to evaluate iac the molecular representation of the entity to evaluate workDir where files will be placed. outFileName filename of the output file.
Definition at line 60 of file FitnessEvaluationTask.java.
References denoptim.programs.RunTimeParameters.containsParameters(), denoptim.programs.RunTimeParameters.ParametersType.FIT_PARAMS, denoptim.task.FitnessTask.fitProvMol, denoptim.task.FitnessTask.fitProvOutFile, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getParameters(), and denoptim.task.Task.workDir.
Member Function Documentation
◆ call()
| Object denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call | ( | ) | throws DENOPTIMException, Exception |
Definition at line 82 of file FitnessEvaluationTask.java.
References denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.programs.fitnessevaluator.FRParameters.addTemplatesToLibraries, denoptim.graph.DGraph.clone(), denoptim.task.Task.completed, denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.task.FitnessTask.dGraph, denoptim.task.Task.errMsg, denoptim.task.FitnessTask.fitnessSettings, denoptim.task.FitnessTask.fitProvMol, denoptim.programs.fitnessevaluator.FitnessEvaluationTask.fragSpace, denoptim.programs.fitnessevaluator.FitnessEvaluationTask.frSettings, denoptim.graph.Candidate.getGraph(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.task.Task.hasException, denoptim.fitness.FitnessParameters.make3dTree(), denoptim.graph.DGraph.replaceUnusedRCVsWithCapps(), denoptim.task.FitnessTask.result, denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.task.Task.thrownExc.
Member Data Documentation
◆ fragSpace
|
private |
Fragment space in use.
Definition at line 50 of file FitnessEvaluationTask.java.
Referenced by denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call().
◆ frSettings
|
private |
Collection of settings controlling the execution of the task.
Definition at line 45 of file FitnessEvaluationTask.java.
Referenced by denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call().
The documentation for this class was generated from the following file:
- /github/workspace/src/main/java/denoptim/programs/fitnessevaluator/FitnessEvaluationTask.java
