Sends the request to produce a socket server running the RingClosingMM service. More...

Collaboration diagram for denoptim.integration.rcoserver.RCOSocketServerClient:

Public Member Functions
void	setHostname (String hostname)
	Sets the hostname for the socket server connection. More...

void	setPort (Integer port)
	Sets the port for the socket server connection. More...

String	getHostname ()
	Gets the currently configured hostname. More...

Integer	getPort ()
	Gets the currently configured port. More...

void	runConformationalOptimization (ChemicalObjectModel chemObj, Logger logger) throws IOException, JsonSyntaxException, DENOPTIMException
	Runs a conformational optimization using the services provided by the socket server configured for this instance. More...

void	runConformationalOptimization (ChemicalObjectModel chemObj, Set< ObjectPair > rcaCombination, Logger logger) throws IOException, JsonSyntaxException, DENOPTIMException
	Runs a conformational optimization using the services provided by the socket server configured for this instance. More...

String	formulateRequest (ZMatrix zmat, List< int[]> rcpTerms, List< int[]> rotatableBonds, List< int[]> allBonds) throws IOException
	Formulates the request to be sent to the socket server. More...

JsonObject	sendRequest (String requestAsJSONString) throws IOException, JsonSyntaxException
	Sends the given request to the socket server and waits for the answer, which is then processed and returned. More...

Static Public Member Functions
static synchronized RCOSocketServerClient	getInstance (String hostname, Integer port)
	Gets the singleton instance of RCOSocketServerClient. More...

static RCOSocketServerClient	getInstance ()
	Gets the singleton instance of RCOSocketServerClient if it has been initialized. More...

static JsonArray	getZMatrixAsJsonArray (ZMatrix zmat)
	Gets a JsonArray representation of the Z-matrix. More...

Private Member Functions
	RCOSocketServerClient (String hostname, Integer port)
	Private constructor for singleton pattern. More...

Static Private Member Functions
static JsonArray	convertIntArrayListToJsonArray (List< int[]> intArrayList)
	Converts a List of 0-based int arrays to a JsonArray containing 1-based ints. More...

Private Attributes
final int	version = 1
	Version identifier. More...

String	hostname
	The name of the host or ID address used to communicate with the socket server. More...

Integer	port
	The identifier of the port used to communicate with the socket server. More...

Gson	jsonConverter = new GsonBuilder().create()
	Converter to and from JSON/Java objects. More...

Static Private Attributes
static RCOSocketServerClient	instance = null
	Singleton instance. More...

Detailed Description

Sends the request to produce a socket server running the RingClosingMM service.

This performs conformational search, possibly biased to induce ring-closing conformations. The service is provided by the RingClosingMM socket server, which we assume to be running. This class follows the singleton pattern.

Definition at line 59 of file RCOSocketServerClient.java.

Constructor & Destructor Documentation

◆ RCOSocketServerClient()

denoptim.integration.rcoserver.RCOSocketServerClient.RCOSocketServerClient	(	String	hostname,
		Integer	port
	)

private

Private constructor for singleton pattern.

Definition at line 92 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.hostname, and denoptim.integration.rcoserver.RCOSocketServerClient.port.

Referenced by denoptim.integration.rcoserver.RCOSocketServerClient.getInstance().

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Member Function Documentation

◆ convertIntArrayListToJsonArray()

static JsonArray denoptim.integration.rcoserver.RCOSocketServerClient.convertIntArrayListToJsonArray ( List< int[]> intArrayList )

staticprivate

Converts a List of 0-based int arrays to a JsonArray containing 1-based ints.

Parameters

intArrayList The list of int arrays to convert

Returns: A JsonArray where each element is a JsonArray of integers

Definition at line 398 of file RCOSocketServerClient.java.

Referenced by denoptim.integration.rcoserver.RCOSocketServerClient.formulateRequest().

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◆ formulateRequest()

String denoptim.integration.rcoserver.RCOSocketServerClient.formulateRequest	(	ZMatrix	zmat,
		List< int[]>	rcpTerms,
		List< int[]>	rotatableBonds,
		List< int[]>	allBonds
	)		throws IOException

Formulates the request to be sent to the socket server.

Since the socket works with chemical conventions, not with Java or Python conventions, the request has to be formulated with 1-based indexing. This method takes care of

Parameters

zmat	the zMatrix representation
rcpTerms	The list of ring-closing potential energy terms (RCP terms) (0-based)
rotatableBonds	The list of bonds that can be twisted. Each bond is defined by the two 0-based indexes of the bonded atoms.
allBonds	The list of all bonds. Each bond is defined by the two 0-based indexes of the bonded atoms.

Returns: The request as a JSON string.

Definition at line 327 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.convertIntArrayListToJsonArray(), denoptim.integration.rcoserver.RCOSocketServerClient.getZMatrixAsJsonArray(), denoptim.integration.rcoserver.RCOSocketServerClient.jsonConverter, and denoptim.integration.rcoserver.RCOSocketServerClient.version.

Referenced by denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization().

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◆ getHostname()

String denoptim.integration.rcoserver.RCOSocketServerClient.getHostname ( )

Gets the currently configured hostname.

Returns: The hostname

Definition at line 160 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.hostname.

◆ getInstance() [1/2]

static RCOSocketServerClient denoptim.integration.rcoserver.RCOSocketServerClient.getInstance ( )

static

Gets the singleton instance of RCOSocketServerClient if it has been initialized.

Returns: The singleton instance

Exceptions

IllegalStateException if the instance has not been initialized yet.

Definition at line 123 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.instance.

◆ getInstance() [2/2]

static synchronized RCOSocketServerClient denoptim.integration.rcoserver.RCOSocketServerClient.getInstance	(	String	hostname,
		Integer	port
	)

static

Gets the singleton instance of RCOSocketServerClient.

Parameters

hostname	The hostname or IP address of the socket server
port	The port number of the socket server

Returns: The singleton instance

Definition at line 105 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.hostname, denoptim.integration.rcoserver.RCOSocketServerClient.instance, denoptim.integration.rcoserver.RCOSocketServerClient.port, and denoptim.integration.rcoserver.RCOSocketServerClient.RCOSocketServerClient().

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

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◆ getPort()

Integer denoptim.integration.rcoserver.RCOSocketServerClient.getPort ( )

Gets the currently configured port.

Returns: The port number

Definition at line 170 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.port.

◆ getZMatrixAsJsonArray()

static JsonArray denoptim.integration.rcoserver.RCOSocketServerClient.getZMatrixAsJsonArray ( ZMatrix zmat )

static

Gets a JsonArray representation of the Z-matrix.

Note that this is meant to produce 1-based indices for the atoms.

Parameters

zmat	The TinkerMolecule object to be processed.

Returns: the Z-matrix as a JsonArray.

Definition at line 348 of file RCOSocketServerClient.java.

Referenced by denoptim.integration.rcoserver.RCOSocketServerClient.formulateRequest(), and denoptim.integration.rcoserver.RCOSocketServerClientTest.testGetZMatrixAsJsonArray().

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◆ runConformationalOptimization() [1/2]

void denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization	(	ChemicalObjectModel	chemObj,
		Logger	logger
	)		throws IOException, JsonSyntaxException, DENOPTIMException

Runs a conformational optimization using the services provided by the socket server configured for this instance.

This wrapper does not consider the possibility to close rings defined by RingClosingAttractor combinations.

Parameters

chemObj	the definition of the chemical system to work with.
logger	logging tool

Exceptions

IOException
JsonSyntaxException
DENOPTIMException

Definition at line 187 of file RCOSocketServerClient.java.

References denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization().

Referenced by denoptim.molecularmodeling.RingClosureTool.attemptRingClosureWithRCOServer(), denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), and denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization().

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◆ runConformationalOptimization() [2/2]

void denoptim.integration.rcoserver.RCOSocketServerClient.runConformationalOptimization	(	ChemicalObjectModel	chemObj,
		Set< ObjectPair >	rcaCombination,
		Logger	logger
	)		throws IOException, JsonSyntaxException, DENOPTIMException

Runs a conformational optimization using the services provided by the socket server configured for this instance.

Parameters

chemObj	the definition of the chemical system to work with.
rcaCombination	if not `null` and not empty, biases the conformational search towards conformations closing the rings defined by each given pair of `RingClosingAttractor`s.
logger	logging tool

Exceptions