RingClosure represents the arrangement of atoms and PseudoAtoms identifying the head and tail of a chain of atoms. More...

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Public Member Functions
	RingClosure (RingClosureParameters settings)
	Constructs an empty RingClosure. More...

	RingClosure (Point3d h1, Point3d h2, Point3d t1, Point3d t2)
	Constructs a RingClosure from the involved points. More...

void	calculateDescriptors ()
	Calculate desctiprots (distances and dot product). More...

boolean	isClosable (ArrayList< Double > clsablConds, Logger logger)
	Evaluate closability by comparing the distances and the dot product with the given critera. More...

boolean	isClosable (double minDH1T2, double maxDH1T2, double minDH2T1, double maxDH2T1, double minDH2T2, double maxDH2T2, double maxDotHT, Logger logger)
	Evaluate closability by comparing the distances and the dot product with the given critera (i.e., the closability conditions). More...

double	getRingClosureQuality ()
	Returns the score evaluating the overal closure quality of this ring closure. More...

Point3d	getPoint (int i)
	Returns the point requested. More...

ArrayList< Double >	getClosabilityConditions (double etrxTol)
	Returns the list of min/max values defining the closability conditions. More...

RingClosure	deepCopy ()
	Returns a deep copy of this RingClosure object. More...

String	toString ()

Private Attributes
Point3d	h1
	The firs point defining the head vector. More...

Point3d	h2
	The second point defining the head vector. More...

Point3d	t1
	The firs point defining the tail vector. More...

Point3d	t2
	The second point defining the tail vector. More...

Vector3d	h
	vector head of chain More...

Vector3d	t
	vector tail of chain More...

double	distH1T2
	Distance H1 T2. More...

double	distH2T1
	Distance H2 T1. More...

double	distH2T2
	Distance H2 T2. More...

double	qscore = Double.NaN
	Quality score of the head and tail vectors alignement. More...

RingClosureParameters	settings
	Parameters. More...

Detailed Description

RingClosure represents the arrangement of atoms and PseudoAtoms identifying the head and tail of a chain of atoms.

The chain may have a proper conformation that allows to close a ring by forming a new bond. The four points contained in RingClosure represents (in this order) atom H1, PseudoAtom H2, atom T1, and PseudoAtom T2. keep in mind this scheme:
H2–H1.....rest of chain.....T1–T2

Author: Marco Foscato

Definition at line 42 of file RingClosure.java.

Constructor & Destructor Documentation

◆ RingClosure() [1/2]

denoptim.graph.rings.RingClosure.RingClosure ( RingClosureParameters settings )

Constructs an empty RingClosure.

Definition at line 105 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.settings.

Referenced by denoptim.graph.rings.RingClosure.deepCopy().

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◆ RingClosure() [2/2]

denoptim.graph.rings.RingClosure.RingClosure	(	Point3d	h1,
		Point3d	h2,
		Point3d	t1,
		Point3d	t2
	)

Constructs a RingClosure from the involved points.

Definition at line 116 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.h1, denoptim.graph.rings.RingClosure.h2, denoptim.graph.rings.RingClosure.t1, and denoptim.graph.rings.RingClosure.t2.

Member Function Documentation

◆ calculateDescriptors()

void denoptim.graph.rings.RingClosure.calculateDescriptors ( )

Calculate desctiprots (distances and dot product).

This method is not executed during creation of the object to allow faster handling of the RingClosure object.

Definition at line 132 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.h1, denoptim.graph.rings.RingClosure.h2, denoptim.graph.rings.RingClosure.t1, and denoptim.graph.rings.RingClosure.t2.

◆ deepCopy()

RingClosure denoptim.graph.rings.RingClosure.deepCopy ( )

Returns a deep copy of this RingClosure object.

Definition at line 354 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.h1, denoptim.graph.rings.RingClosure.h2, denoptim.graph.rings.RingClosure.RingClosure(), denoptim.graph.rings.RingClosure.t1, and denoptim.graph.rings.RingClosure.t2.

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◆ getClosabilityConditions()

ArrayList< Double > denoptim.graph.rings.RingClosure.getClosabilityConditions ( double etrxTol )

Returns the list of min/max values defining the closability conditions.

This method is made available to guarantee that only one set of closability conditions is used by whichever tool needs to evaluate ring closability.

Parameters

etrxTol additional factor that multiplies dist. tolerance

Returns

the vector of conditions in this exact order:

minDistH1T2
maxDistH1T2
minDistH2T1
maxDistH2T1
minDistH2T2
maxDistH2T2
maxDotProdHT

Definition at line 316 of file RingClosure.java.

References denoptim.graph.rings.RingClosureParameters.getRCDistTolerance(), denoptim.graph.rings.RingClosureParameters.getRCDotPrTolerance(), denoptim.graph.rings.RingClosure.h1, denoptim.graph.rings.RingClosure.h2, denoptim.graph.rings.RingClosure.settings, denoptim.graph.rings.RingClosure.t1, and denoptim.graph.rings.RingClosure.t2.

Referenced by denoptim.graph.rings.RingClosureFinder.evaluateClosability().

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◆ getPoint()

Point3d denoptim.graph.rings.RingClosure.getPoint ( int i )

Returns the point requested.

Parameters

i	index of the point to return (0,3)

Definition at line 269 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.h1, denoptim.graph.rings.RingClosure.h2, denoptim.graph.rings.RingClosure.t1, and denoptim.graph.rings.RingClosure.t2.

◆ getRingClosureQuality()

double denoptim.graph.rings.RingClosure.getRingClosureQuality ( )

Returns the score evaluating the overal closure quality of this ring closure.

Definition at line 241 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.h1, denoptim.graph.rings.RingClosure.h2, denoptim.graph.rings.RingClosure.qscore, denoptim.graph.rings.RingClosure.t1, and denoptim.graph.rings.RingClosure.t2.

◆ isClosable() [1/2]

boolean denoptim.graph.rings.RingClosure.isClosable	(	ArrayList< Double >	clsablConds,
		Logger	logger
	)

Evaluate closability by comparing the distances and the dot product with the given critera.

Parameters

clsablConds	the closability conditions.
logger	the program-specific logger.

Returns: true is the arrangement of points respect the closability condition

Definition at line 154 of file RingClosure.java.

References denoptim.graph.rings.RingClosure.isClosable().

Referenced by denoptim.molecularmodeling.RingClosureTool.closeRings(), denoptim.graph.rings.RingClosureFinder.hasClosableRotamer(), and denoptim.graph.rings.RingClosure.isClosable().

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◆ isClosable() [2/2]

boolean denoptim.graph.rings.RingClosure.isClosable	(	double	minDH1T2,
		double	maxDH1T2,
		double	minDH2T1,
		double	maxDH2T1,
		double	minDH2T2,
		double	maxDH2T2,
		double	maxDotHT,
		Logger	logger
	)

Evaluate closability by comparing the distances and the dot product with the given critera (i.e., the closability conditions).

Parameters

minDH1T2	minimum threshold value for distance h1-t2
maxDH1T2	maximum threshold value for distance h1-t2
minDH2T1	minimum threshold value for distance h2-t1
maxDH2T1	maximum threshold value for distance h2-t1
minDH2T2	minimum threshold value for distance h2-t2
maxDH2T2	maximum threshold value for distance h2-t2
maxDotHT	maximum value for the dot product
logger	for debugging