Global

Methods

angToCoord(coord)

Converts AB model Angle sequences to Coordinates sequences
Parameters:
Name Type Description
coord Array Length of the desired sequence.
Source:

Ann(seq, ang, l)

Algorithm inspired in Simulated Annealing
Parameters:
Name Type Description
seq String String with the aminoacid's type sequence.
ang Array The angle sequence in radians.
l int The limit of loops (stop criteria).
Source:

C(i, j)

Calculates the coefficient "C" from a AB model pair (AB model energy calculation)
Parameters:
Name Type Description
i String Type of the first aminoacid model ("A" or "B").
j String Type of the second aminoacid model ("A" or "B").
Source:

coordToAng(coord)

Converts AB model Coordinates sequences to Angle sequences
Parameters:
Name Type Description
coord Array Length of the desired sequence.
Source:

distance(Point, Point)

Calculates euclidean distance between two points
Parameters:
Name Type Description
Point i An object with x and y values ({x: Float, y: Float})
Point j Another object with x and y values
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Ela(seq, ang, l, parameter, pop, parent, ang_num, rigs, rigf, rigm, rign, rigx, effs, efff)

Estimated Learning Algorithm
Parameters:
Name Type Description
seq String String with the aminoacid's type sequence.
ang Array The angle sequence in radians.
l int The limit of loops (stop criteria).
parameter Object The parameters object {rigidity: Array, efficiency: Array}.
pop int The size of the population (number of solutions per loop).
parent float The percentage of the population that will be reference to new solutions.
ang_num int Number of angles changed per solution.
rigs string The expression that changes rigidity on successes.
rigf string The expression that changes rigidity on fails.
rigm float Maximum value for rigidity.
rign int Number of neightbors affected by rigidity.
rigx string The expression that changes neightbors rigidity value.
effs string The expression that changes efficiency on successes.
efff string The expression that changes efficiency on fails.
Source:

energy(Protein)

Calculates the energy of a AB model protein
Parameters:
Name Type Description
Protein protein A protein in AB model with a series of aminoacids
Source:

fibonacci(l)

Fibonacci sequence with AB Model
Parameters:
Name Type Description
l Int Length of the desired sequence.
Source:

gaussRandom(e)

Gaussian Random with polar method - Sheldon Ross (pp. 464, 6ed)
Parameters:
Name Type Description
e String Converts a Real Sequence to AB Model. A: [I, V, L, P, C, M, G] B: [D, E, F, H, K, N, Q, R, S, T, W, Y]
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onError(e)

Prints Error events to the debug console
Parameters:
Name Type Description
e Error Object with error degub info.
Source:

realToAb(e)

Converts Real protein sequences to AB Model sequences - A: [I, V, L, P, C, M, G] B: [D, E, F, H, K, N, Q, R, S, T, W, Y]
Parameters:
Name Type Description
e String Converts a Real Sequence to AB Model.
Source: