Parameters for the conformer generator (3D builder). More...

Inheritance diagram for denoptim.programs.moldecularmodelbuilder.MMBuilderParameters:

Collaboration diagram for denoptim.programs.moldecularmodelbuilder.MMBuilderParameters:

Public Member Functions
	MMBuilderParameters ()
	Constructor. More...

int	getTaskID ()

String	getInputSDFFile ()

String	getOutputSDFFile ()

String	getPSSROTTool ()

String	getXYZINTTool ()

String	getINTXYZTool ()

String	getParamFile ()

ArrayList< String >	getInitPSSROTParams ()

ArrayList< String >	getRSInitPSSROTParams ()

ArrayList< String >	getRestPSSROTParams ()

ArrayList< String >	getRSRestPSSROTParams ()

ArrayList< String >	getKeyFileParams ()

boolean	getKeepDummyFlag ()

ArrayList< String >	getRSKeyFileParams ()

boolean	debug ()

int	getAtomOrderingScheme ()

HashMap< String, Integer >	getTinkerMap ()

String	getWorkingDirectory ()

void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

void	checkParameters () throws DENOPTIMException
	Check all parameters. More...

String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

Public Member Functions inherited from denoptim.programs.RunTimeParameters
	RunTimeParameters (ParametersType paramType)
	Constructor. More...

String	paramTypeName ()
	Returns a string defining the type the parameters collected here. More...

String	getWorkDirectory ()
	Gets the pathname to the working directory. More...

void	setWorkDirectory (String pathname)
	Gets the pathname to the working directory. More...

String	getLogFilePathname ()
	Gets the pathname to the log file. More...

void	setLogFilePathname (String pathname)
	Sets the pathname to the log file. More...

Logger	getLogger ()
	Get the name of the program specific logger. More...

Logger	startProgramSpecificLogger (String loggerIdentifier) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startProgramSpecificLogger (String loggerIdentifier, boolean toLogFile) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startConsoleLogger (String loggerIdentifier)
	Starts a program-specific logger that prints to System.err stream. More...

int	getVerbosity ()
	Returns the level of verbosity, i.e., the amount of log that we want to print. More...

void	setVerbosity (int l)
	Set the level of verbosity. More...

Randomizer	getRandomizer ()
	Returns the current program-specific randomizer. More...

long	getRandomSeed ()
	Returns the seed. More...

void	setRandomizer (Randomizer rng)
	Sets the randomizer. More...

Randomizer	startRandomizer ()
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

Randomizer	startRandomizer (long seed)
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

void	readParameterFile (String infile) throws DENOPTIMException
	Read the parameter TXT file line by line and interpret its content. More...

void	readParameterLine (String line) throws DENOPTIMException

boolean	containsParameters (ParametersType type)

RunTimeParameters	getParameters (ParametersType type)

void	setParameters (RunTimeParameters otherParams)

void	interpretKeyword (String line) throws DENOPTIMException
	Processes a string looking for keyword and a possibly associated value. More...

abstract void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

abstract void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

abstract void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

abstract String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

void	printParameters ()
	Print all parameters. More...

Protected Attributes
boolean	debug = false
	Flag controlling debug verbosity. More...

String	toolPSSROT
	Pathname to Tinker's pssrot executable. More...

String	toolXYZINT
	Pathname to Tinker's xyzint executable. More...

String	toolINTXYZ
	Pathname to Tinker's intxyz executable. More...

boolean	keepDummy = false
	Flag controlling removal of dummy atoms from output geometry. More...

String	forceFieldFile
	Pathname to force field parameters file for Tinker. More...

String	pssrotFile
	Pathname to parameters file for PSS part of Tinker's PSSROT. More...

String	rsPssrotFile
	Pathname to parameters file for PSS part of Tinker's ring-closing PSSROT. More...

String	keyFile
	Pathname to keywords file for Tinker's conformational search. More...

String	rsKeyFile
	Pathname to keywords file for Tinker's ring-closing conformational search. More...

ArrayList< String >	pssrotParams_Init
	Parameters for PSS part of Tinker's PSSROT step. More...

ArrayList< String >	pssrotParams_Rest
	Parameters for linear search part of Tinker's PSSROT step. More...

ArrayList< String >	keyFileParams
	Keywords for Tinker's conformational search. More...

ArrayList< String >	rsPssrotParams_Init
	Parameters for PSS part of Tinker's ring-closing PSSROT step. More...

ArrayList< String >	rsPssrotParams_Rest
	Parameters for linear search part of Tinker's ring-closing PSSROT step. More...

ArrayList< String >	rsKeyFileParams
	Keywords for Tinker's ring-closing conformational search. More...

int	atomOrderingScheme = 1
	Flag controlling the criterion used to reorder atom lists. More...

HashMap< String, Integer >	TINKER_MAP
	Atom type map. More...

int	taskID
	Unique task identifier. More...

String	inpSDFFile
	Pathname of input SDF file. More...

String	outSDFFile
	Pathname of ouput SDF file. More...

Protected Attributes inherited from denoptim.programs.RunTimeParameters
boolean	isMaster = true
	Flag signaling this is the master collection of parameters. More...

String	workDir = System.getProperty("user.dir")
	Working directory. More...

String	logFile = "unset"
	Log file. More...

int	verbosity = 0
	Verbosity level for logger. More...

Map< ParametersType, RunTimeParameters >	otherParameters
	Collection of other parameters by type. More...

Additional Inherited Members
Static Public Member Functions inherited from denoptim.programs.RunTimeParameters
static boolean	readYesNoTrueFalse (String s)
	Reads a string searching for any common way to say either yes/true (including shorthand t/y) or no/false (including shorthand f/n either). More...

Public Attributes inherited from denoptim.programs.RunTimeParameters
final String	NL = System.getProperty("line.separator")
	New line character. More...

Protected Member Functions inherited from denoptim.programs.RunTimeParameters
void	checkOtherParameters () throws DENOPTIMException
	Checks any of the parameter collections contained in this instance. More...

void	processOtherParameters () throws DENOPTIMException
	Processes any of the parameter collections contained in this instance. More...

void	ensureFileExistsIfSet (String pathname)
	Ensures a pathname is not empty nor null and that it does lead to an existing file or triggers an error. More...

void	ensureFileExists (String pathname)
	Ensures a pathname does lead to an existing file or triggers an error. More...

void	ensureNotNull (String paramName, String param, String paramKey)
	Ensures that a parameter is not null or triggers an error. More...

void	ensureIsPositive (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureIsPositiveOrZero (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureInRange (String paramName, int value, int min, int max, String paramKey)
	Ensures that a parameter is within a range or triggers an error. More...

Detailed Description

Parameters for the conformer generator (3D builder).

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 37 of file MMBuilderParameters.java.

Constructor & Destructor Documentation

◆ MMBuilderParameters()

denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.MMBuilderParameters ( )

Constructor.

Definition at line 152 of file MMBuilderParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.MMB_PARAM.

Member Function Documentation

◆ checkParameters()

void denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters ( ) throws DENOPTIMException

Check all parameters.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 378 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ debug()

boolean denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.debug ( )

Definition at line 257 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.debug.

◆ getAtomOrderingScheme()

int denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getAtomOrderingScheme ( )

Definition at line 264 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.atomOrderingScheme.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree().

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◆ getInitPSSROTParams()

ArrayList< String > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getInitPSSROTParams ( )

Definition at line 208 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.pssrotParams_Init.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getInputSDFFile()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getInputSDFFile ( )

Definition at line 166 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.inpSDFFile.

Referenced by denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ getINTXYZTool()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getINTXYZTool ( )

Definition at line 194 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.toolINTXYZ.

◆ getKeepDummyFlag()

boolean denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getKeepDummyFlag ( )

Definition at line 243 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.keepDummy.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getKeyFileParams()

ArrayList< String > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getKeyFileParams ( )

Definition at line 236 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.keyFileParams.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getOutputSDFFile()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getOutputSDFFile ( )

Definition at line 173 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.outSDFFile.

Referenced by denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ getParamFile()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getParamFile ( )

Definition at line 201 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.forceFieldFile.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getPrintedList()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getPrintedList ( )

Returns the list of parameters in a string with newline characters as delimiters.

Returns: the list of parameters in a string with newline characters as delimiters.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 423 of file MMBuilderParameters.java.

References denoptim.programs.RunTimeParameters.NL, denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.paramTypeName().

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◆ getPSSROTTool()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getPSSROTTool ( )

Definition at line 180 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.toolPSSROT.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getRestPSSROTParams()

ArrayList< String > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRestPSSROTParams ( )

Definition at line 222 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.pssrotParams_Rest.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getRSInitPSSROTParams()

ArrayList< String > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRSInitPSSROTParams ( )

Definition at line 215 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsPssrotParams_Init.

◆ getRSKeyFileParams()

ArrayList< String > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRSKeyFileParams ( )

Definition at line 250 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsKeyFileParams.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure().

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◆ getRSRestPSSROTParams()

ArrayList< String > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRSRestPSSROTParams ( )

Definition at line 229 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsPssrotParams_Rest.

◆ getTaskID()

int denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTaskID ( )

Definition at line 159 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.taskID.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getTinkerMap()

HashMap< String, Integer > denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTinkerMap ( )

Definition at line 271 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.TINKER_MAP.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), and denoptim.molecularmodeling.RingClosureTool.setTinkerTypes().

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◆ getWorkingDirectory()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getWorkingDirectory ( )

Definition at line 278 of file MMBuilderParameters.java.

References denoptim.programs.RunTimeParameters.workDir.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ getXYZINTTool()

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getXYZINTTool ( )

Definition at line 187 of file MMBuilderParameters.java.

References denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.toolXYZINT.

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosure(), and denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

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◆ interpretKeyword()

void denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword	(	String	key,
		String	value
	)		throws DENOPTIMException

Processes a keyword/value pair and assign the related parameters.

Parameters

key	the keyword as string
value	the value as a string

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 292 of file MMBuilderParameters.java.

◆ processParameters()

void denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 450 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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Member Data Documentation

◆ atomOrderingScheme

int denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.atomOrderingScheme = 1

protected

Flag controlling the criterion used to reorder atom lists.

1: branch-oriented (completes a branch before moving to the next one). 2: layer-oriented) completes a layer before moving to the next one).

Definition at line 124 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getAtomOrderingScheme(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ debug

boolean denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.debug = false

protected

Flag controlling debug verbosity.

Definition at line 42 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.debug(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ forceFieldFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.forceFieldFile

protected

Pathname to force field parameters file for Tinker.

Definition at line 67 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getParamFile(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ inpSDFFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.inpSDFFile

protected

Pathname of input SDF file.

Definition at line 139 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getInputSDFFile(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ keepDummy

boolean denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.keepDummy = false

protected

Flag controlling removal of dummy atoms from output geometry.

Definition at line 62 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getKeepDummyFlag(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ keyFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.keyFile

protected

Pathname to keywords file for Tinker's conformational search.

Definition at line 82 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ keyFileParams

ArrayList<String> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.keyFileParams

protected

Keywords for Tinker's conformational search.

Definition at line 102 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getKeyFileParams(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ outSDFFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.outSDFFile

protected

Pathname of ouput SDF file.

Definition at line 144 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getOutputSDFFile(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ pssrotFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.pssrotFile

protected

Pathname to parameters file for PSS part of Tinker's PSSROT.

Definition at line 72 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ pssrotParams_Init

ArrayList<String> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.pssrotParams_Init

protected

Parameters for PSS part of Tinker's PSSROT step.

Definition at line 92 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getInitPSSROTParams(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ pssrotParams_Rest

ArrayList<String> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.pssrotParams_Rest

protected

Parameters for linear search part of Tinker's PSSROT step.

Definition at line 97 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRestPSSROTParams(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ rsKeyFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsKeyFile

protected

Pathname to keywords file for Tinker's ring-closing conformational search.

Definition at line 87 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ rsKeyFileParams

ArrayList<String> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsKeyFileParams

protected

Keywords for Tinker's ring-closing conformational search.

Definition at line 117 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRSKeyFileParams(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ rsPssrotFile

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsPssrotFile

protected

Pathname to parameters file for PSS part of Tinker's ring-closing PSSROT.

Definition at line 77 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ rsPssrotParams_Init

ArrayList<String> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsPssrotParams_Init

protected

Parameters for PSS part of Tinker's ring-closing PSSROT step.

Definition at line 107 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRSInitPSSROTParams(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ rsPssrotParams_Rest

ArrayList<String> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.rsPssrotParams_Rest

protected

Parameters for linear search part of Tinker's ring-closing PSSROT step.

Definition at line 112 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getRSRestPSSROTParams(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ taskID

int denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.taskID

protected

Unique task identifier.

Definition at line 134 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTaskID().

◆ TINKER_MAP

HashMap<String, Integer> denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.TINKER_MAP

protected

Atom type map.

Definition at line 129 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getTinkerMap(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

◆ toolINTXYZ

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.toolINTXYZ

protected

Pathname to Tinker's intxyz executable.

Definition at line 57 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getINTXYZTool(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ toolPSSROT

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.toolPSSROT

protected

Pathname to Tinker's pssrot executable.

Definition at line 47 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getPSSROTTool(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

◆ toolXYZINT

String denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.toolXYZINT

protected

Pathname to Tinker's xyzint executable.

Definition at line 52 of file MMBuilderParameters.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.checkParameters(), denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.getXYZINTTool(), and denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.interpretKeyword().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/programs/moldecularmodelbuilder/MMBuilderParameters.java

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MMBuilderParameters()

Member Function Documentation

◆ checkParameters()

◆ debug()

◆ getAtomOrderingScheme()

◆ getInitPSSROTParams()

◆ getInputSDFFile()

◆ getINTXYZTool()

◆ getKeepDummyFlag()

◆ getKeyFileParams()

◆ getOutputSDFFile()

◆ getParamFile()

◆ getPrintedList()

◆ getPSSROTTool()

◆ getRestPSSROTParams()

◆ getRSInitPSSROTParams()

◆ getRSKeyFileParams()

◆ getRSRestPSSROTParams()

◆ getTaskID()

◆ getTinkerMap()

◆ getWorkingDirectory()

◆ getXYZINTTool()

◆ interpretKeyword()

◆ processParameters()

Member Data Documentation

◆ atomOrderingScheme

◆ debug

◆ forceFieldFile

◆ inpSDFFile

◆ keepDummy

◆ keyFile

◆ keyFileParams

◆ outSDFFile

◆ pssrotFile

◆ pssrotParams_Init

◆ pssrotParams_Rest

◆ rsKeyFile

◆ rsKeyFileParams

◆ rsPssrotFile

◆ rsPssrotParams_Init

◆ rsPssrotParams_Rest

◆ taskID

◆ TINKER_MAP

◆ toolINTXYZ

◆ toolPSSROT

◆ toolXYZINT