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