roadmapConstruction.C


o initNativeStructure
reads native structure, stores it in allNodes[endNodeIndex], and calls necessary methods for initial setup.
o initExtendedStructure
creates the extended structure.
o kNNLinkNode
o linkNodes
connects each node to k-NN
o makeLinkBetweenNodes
connects n1 and n2 with the given pathweights.
o joinTheTreesForNodes
does join the trees.
o makeOneWayLink
simply connects the node n1 to node n2.
o addNode2Forest
adds allNodes[count] to the global forest.
o completeTreeGeneration
creates trees for the nodes that are not connected to any other node
o sampleAroundProtein
samples (numToCreate) conformations around node # origIndex.
o createNodes
I take samples w/ parameters either gaussianly distributed around the origin or randomly sampled values.
o mycompare
o findTransitionProbability
assigns tr.
o assignTransitionProbability
o computeTransitionProbabilities
returns maxNumNeighbors of any node
o connect
connects if they are not already connected

Alphabetic index



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