Tool to explore the conformational space of chains of atoms and identify ring closing conformations. More...

Static Public Member Functions
static boolean	evaluateClosability (List< IAtom > path, ArrayList< Boolean > rotatability, ArrayList< ArrayList< Point3d > > dihRefs, ArrayList< ArrayList< Double > > closableConfs, RingClosureParameters settings)
	Giving a list of points in 3D space (the path) this method evaluates whether it exists at least one conformation of the chain that allows to form ring by connecting the head and the tail of the chain. More...

static boolean	hasClosableRotamer (List< Point3d > chain, ArrayList< Boolean > rotatability, ArrayList< Double > dihedrals, ArrayList< Double > dihIncement, int activeRot, double step, int h1, int h2, int t1, int t2, ArrayList< Double > clsablConds, ArrayList< ArrayList< Double > > closableConfs, boolean doExhaustiveSearch, boolean writeAllConfs, Logger logger, int rec)
	Scan rotatable space looking for conformations that satisfy closability condition. More...

Static Private Member Functions
static void	reportForDebug (String filename, List< Point3d > chain)
	Method for reporting a path of atoms (list of points) as SDF file. More...

Static Private Attributes
static final String	NL = DENOPTIMConstants.EOL

Detailed Description

Tool to explore the conformational space of chains of atoms and identify ring closing conformations.

Author: Marco Foscato

Definition at line 49 of file RingClosureFinder.java.

Member Function Documentation

◆ evaluateClosability()

static boolean denoptim.graph.rings.RingClosureFinder.evaluateClosability	(	List< IAtom >	path,
		ArrayList< Boolean >	rotatability,
		ArrayList< ArrayList< Point3d > >	dihRefs,
		ArrayList< ArrayList< Double > >	closableConfs,
		RingClosureParameters	settings
	)

static

Giving a list of points in 3D space (the path) this method evaluates whether it exists at least one conformation of the chain that allows to form ring by connecting the head and the tail of the chain.

Parameters

path	the chain of atoms
rotatability	list of flags defining which bond is rotatable

Returns: true is a closable conformation is found

Definition at line 65 of file RingClosureFinder.java.

References denoptim.utils.MathUtils.angle(), denoptim.utils.MathUtils.computeDihedralAngle(), denoptim.graph.rings.RingClosureParameters.doExhaustiveConfSrch(), denoptim.graph.rings.RingClosure.getClosabilityConditions(), denoptim.graph.rings.RingClosureParameters.getConfPathExtraTolerance(), denoptim.graph.rings.RingClosureParameters.getLinearityLimit(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.rings.RingClosureParameters.getMaxNumberRotatableBonds(), denoptim.graph.rings.RingClosureParameters.getPathConfSearchStep(), and denoptim.graph.rings.RingClosureFinder.hasClosableRotamer().

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ hasClosableRotamer()

static boolean denoptim.graph.rings.RingClosureFinder.hasClosableRotamer	(	List< Point3d >	chain,
		ArrayList< Boolean >	rotatability,
		ArrayList< Double >	dihedrals,
		ArrayList< Double >	dihIncement,
		int	activeRot,
		double	step,
		int	h1,
		int	h2,
		int	t1,
		int	t2,
		ArrayList< Double >	clsablConds,
		ArrayList< ArrayList< Double > >	closableConfs,
		boolean	doExhaustiveSearch,
		boolean	writeAllConfs,
		Logger	logger,
		int	rec
	)

static

Scan rotatable space looking for conformations that satisfy closability condition.

Parameters

chain	the chain of atoms as a list of points in 3D space
rotatability	flags defining which bond is rotatable
dihedrals	the current value of the dihedral angles
activeRot	index of the currently active (rotating) bond
step	the step taken by each sequential rotation of the bond
h1	the index of the first point defining the head vector
h2	the index of the second point defining the head vector
t1	the index of the first point defining the tail vector
t2	the index of the second point defining the tail vector
clsablConds	the closability condition vector meant to feed `RingClosure`