Combinatorial exploration of the fragment space. More...
Public Member Functions | |
| FragSpaceExplorer (File configFile, File workDir) | |
| Creates and configures the program task. More... | |
| void | runProgram () throws Throwable |
 Public Member Functions inherited from denoptim.task.ProgramTask | |
| ProgramTask (File configFile, File workDir) | |
| Creates and configures the program task. More... | |
| Object | call () |
This method redirects the callable functionality to an abstract method (namely ProgramTask#runProgram()) to be specified by the implementations of this abstract class. More... | |
| void | printErrorToFile () |
Method that can be called to create a text file with the error triggered by any Throwable that can be thrown by the execution of the program. More... | |
| 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) |
Protected Member Functions | |
| void | handleThrowable () |
Method to handle any Throwable originated from the runProgram() method. More... | |
| Protected Member Functions inherited from denoptim.task.ProgramTask | |
| void | handleThrowable () |
Method to handle any Throwable originated from the runProgram() method. More... | |
| void | stopLogger () |
| Stops the program-specific logger and releases the lock file on the logfile. More... | |
| abstract void | runProgram () throws Throwable |
Private Attributes | |
| CombinatorialExplorerByLayer | combinatorialAlgorithm = null |
Additional Inherited Members | |
| Public Attributes inherited from denoptim.task.Task | |
| Object | lock = new Object() |
| Lock for addressing synchronization issues. More... | |
| Protected Attributes inherited from denoptim.task.ProgramTask | |
| File | configFilePathName |
| File containing configuration parameters for the program task. More... | |
| String | loggerIdentifier = "none" |
| Identifier of this program's logger. 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
Combinatorial exploration of the fragment space.
Graphs are built stepwise layer by layer. Each layer of new graphs is stored in text files and, if a graph is complete (i.e., it corresponds to a finished chemical entity), optionally submitted to further processing, which is controlled by external bash script. Combinations of building blocks (i.e., used defined root graphs or scaffold fragments, proper fragments, and capping groups) are generated serially while each new graph is handled by a dedicated, asynchronous task, thus parallelizing the construction, evaluation, and post-processing of each new graph. The exploration of a fragment space generated all combination of building blocks according to the definition of the fragment space. Symmetry may be enforced in the fragment space (see FragmentSpaceParameters). In such case, if symmetric attachment points are found on a scaffold/fragment/graph, then the exploration is restricted to such combinations respecting the constitutional symmetry of the APs.
Definition at line 52 of file FragSpaceExplorer.java.
Constructor & Destructor Documentation
◆ FragSpaceExplorer()
| denoptim.programs.combinatorial.FragSpaceExplorer.FragSpaceExplorer | ( | File | configFile, |
| File | workDir | ||
| ) |
Creates and configures the program task.
- Parameters
-
configFile the file containing the configuration parameters. workDir the file system location from which to run the program.
Definition at line 63 of file FragSpaceExplorer.java.
References denoptim.task.Task.workDir.
Member Function Documentation
◆ handleThrowable()
|
protected |
Method to handle any Throwable originated from the runProgram() method.
This method can be overwritten to alter the behavior in case of specific needs.
Reimplemented from denoptim.task.ProgramTask.
Definition at line 90 of file FragSpaceExplorer.java.
References denoptim.programs.combinatorial.FragSpaceExplorer.combinatorialAlgorithm, and denoptim.combinatorial.CombinatorialExplorerByLayer.stopRun().
◆ runProgram()
| void denoptim.programs.combinatorial.FragSpaceExplorer.runProgram | ( | ) | throws Throwable |
Reimplemented from denoptim.task.ProgramTask.
Definition at line 71 of file FragSpaceExplorer.java.
References denoptim.programs.combinatorial.CEBLParameters.checkParameters(), denoptim.programs.combinatorial.FragSpaceExplorer.combinatorialAlgorithm, denoptim.task.ProgramTask.configFilePathName, denoptim.task.ProgramTask.loggerIdentifier, denoptim.programs.RunTimeParameters.printParameters(), denoptim.programs.combinatorial.CEBLParameters.processParameters(), denoptim.programs.RunTimeParameters.readParameterFile(), denoptim.combinatorial.CombinatorialExplorerByLayer.run(), denoptim.programs.RunTimeParameters.setWorkDirectory(), denoptim.programs.RunTimeParameters.startProgramSpecificLogger(), and denoptim.task.Task.workDir.
Member Data Documentation
◆ combinatorialAlgorithm
|
private |
Definition at line 54 of file FragSpaceExplorer.java.
Referenced by denoptim.programs.combinatorial.FragSpaceExplorer.handleThrowable(), and denoptim.programs.combinatorial.FragSpaceExplorer.runProgram().
The documentation for this class was generated from the following file:
- /github/workspace/src/main/java/denoptim/programs/combinatorial/FragSpaceExplorer.java
