Package denoptim.graph.rings

Classes
class	ChainLink
	ChainLink represents a vertex in a closable chain. More...
class	ClosableChain
	ClosableChain represents a chain of fragments (chain links) that is closable (or candidate closable). More...
class	CyclicGraphHandler
	This is a tool to identify and manage vertices' connections not included in the DGraph, which is a spanning tree, thus connections that identify cyclic paths in the graph. More...
class	PathClosabilityTools
	Tool box for determining whether a chain of atoms, i.e., a path, can be folded as to form a ring-closing bond that transforms the open chain in a ring. More...
class	PathClosabilityToolsTest
	Unit test for path closability tools. More...
class	PathSubGraph
	This object represents a path in a DGraph. More...
class	PathSubGraphTest
	Unit test for PathSubGraph. More...
class	RandomCombOfRingIteratorTest
	Unit test for the iterator over random combination of rings. More...
class	RandomCombOfRingsIterator
	A class for iterating over sets of ring combinations generated by considering any constrain and setting defined in the fragment space and ring-closure settings and by randomly picking candidates when no criterion can be used to take an informed decision. More...
class	RingClosingAttractor
	The RingClosingAttractor represent the available valence/connection that allows to close a ring. More...
class	RingClosingConformations
	Serializable object to store/get a list of conformations that allow to close a ring from an open chain of atoms. More...
class	RingClosure
	RingClosure represents the arrangement of atoms and PseudoAtoms identifying the head and tail of a chain of atoms. More...
class	RingClosureFinder
	Tool to explore the conformational space of chains of atoms and identify ring closing conformations. More...
class	RingClosureParameters
	Parameters and setting related to handling ring closures. More...
class	RingClosuresArchive
	Data structure to store and handle information about sub-structures (i.e., chains of fragments) and ring closure capability. More...
class	RingSizeManager
	Utility class to calculate and manage the alternative ring sizes achievable by formation of Rings. More...
class	RingSizeManagerTest
	Unit test for ring size manager. More...