protein.C


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

Alphabetic index



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