import(bio3d)
import(rSymPy)
import(rgl)

importFrom(graphics, arrows, lines, plot)
importFrom(methods, is, new, validObject)
importFrom(utils, data, head, tail)
 

exportClasses( "Knot" )


exportMethods(
   getCoordinates, "setCoordinates<-",
   getEnds, "setEnds<-",
   print,
   plot
)

export( 
	#for 'Knot'
	newKnot,
	reduceStructure,
   	computeInvariant,
   	plot3D,
   	makeExampleKnot,
   	makeExampleProtein,
   	closeAndProject,
	
	##for 'general'
	AlexanderBriggs,
	centroidClosure,
	loadProtein,
	findGaps,
	HOMFLYpolynomial,
	HOMFLY2mirror,
	HOMFLY2Alexander,
	HOMFLY2Jones,
	intersectionMatrix,
	linkingNumber,
	mVA,
	msr,
	PCAProjection,
	plotKnot3D,
	plotDiagram,
	rMatrix,
	skeinIterator,
	localize,
	cyclicP,
	auxiliaryAlexander,
	get2D,
	computeFactors,
	escapePath,
	vertexPresentation,
	getKnotType
)