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Protein::Protein - samples a new config, and guarantees it is not of energy > maxEnergy
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Protein::Protein - samples around original node.
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Protein::Protein - creates a node located at coords.
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Protein::computeParams - sets params array of the protein, which determines the relative location of the node on the landscape
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Protein::computeEnergy - computes energy of protein
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Protein::probabilisticAcceptConformation - returns true if configuration does not collide with itself, and is low than a probabilistically generated energy threshold
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Protein::computeDistance - returns the L2 distance between 2 proteins
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Protein::computeDistance - returns L2 distance between 2 configs
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Protein::getNumLinks - returns num.
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Protein::getCoords-
Protein::setXY - only sets x and y
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Protein::getMyNode - accessor
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computeConfigEnergy - returns energy.
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energyTerm - xI and yI corresponds to the location of the node, x and y.
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sampleAroundCoords - generates a random config.
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sampleRandomCoords - returns coordinates within the boundaries of the landscape, but not necessarily collision-free
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generateRandomConfig - returns a vector st.
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coords2Params-
params2Coords-
midConfig - just average of the start and end.
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configsClose - returns true if the distance between configs < epsilon
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configsClose - returns true if the distance between configs < epsilon
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checkCollision - returns true if collision free
Alphabetic index
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