Builder of molecular models. More...
Public Member Functions | |
| MolecularModelBuilder (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) |
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.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 |
| 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
Builder of molecular models.
This program constructs a three-dimensional molecular model by converting a given DENOPTIM Candidate.
Definition at line 44 of file MolecularModelBuilder.java.
Constructor & Destructor Documentation
◆ MolecularModelBuilder()
| denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.MolecularModelBuilder | ( | 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 54 of file MolecularModelBuilder.java.
References denoptim.task.Task.workDir.
Member Function Documentation
◆ runProgram()
| void denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram | ( | ) | throws Throwable |
Reimplemented from denoptim.task.ProgramTask.
Definition at line 62 of file MolecularModelBuilder.java.
References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.task.ProgramTask.configFilePathName, denoptim.graph.Candidate.getChemicalRepresentation(), denoptim.graph.Candidate.getGraph(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getInputSDFFile(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.Candidate.getName(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getOutputSDFFile(), denoptim.task.ProgramTask.loggerIdentifier, denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.task.Task.NL, denoptim.programs.RunTimeParameters.printParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters(), denoptim.io.DenoptimIO.readCandidates(), denoptim.programs.RunTimeParameters.readParameterFile(), denoptim.programs.RunTimeParameters.setWorkDirectory(), denoptim.integration.tinker.TinkerException.solution, denoptim.programs.RunTimeParameters.startProgramSpecificLogger(), denoptim.task.Task.workDir, and denoptim.io.DenoptimIO.writeSDFFile().
The documentation for this class was generated from the following file:
- /github/workspace/src/main/java/denoptim/programs/moldecularmodelbuilder/MolecularModelBuilder.java
