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# Bacterial Foraging Optimization Algorithm | |
# (c) Copyright 2013 Max Nanis [max@maxnanis.com]. | |
import os, random, math, csv | |
class BFOA(): | |
def __init__(self, pop_size = 100, problem_size = 2, dimension = [-1, 1], elim_disp_steps = 1, repro_steps = 4, chem_steps = 30): | |
self.step_index = 0 | |
self.run_id = os.urandom(6).encode('hex') |
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var user = [0,1,0,0,1,0,0,1,1,0,0,0,1,0], | |
truth = [0,1,1,1,0,0,0,0,1,1,0,0,1,1]; | |
function compare(user, truth) { | |
var a = 0, b = 0, c = 0, d = 0, fpr, fnr; | |
if( truth.length !== user.length ) return; | |
for (var i = 0; i < truth.length; i++) { | |
switch(user[i] + truth[i]) { | |
case 0: ++d; break; | |
case 2: ++a; break; |
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#!/usr/bin/env python3.1 | |
import math as m, random as r, rhinoscriptsyntax as rs | |
# 1UBQ, 1F9J, 1R4N, 1FXT, 1LDK, 1FQK, 1FNT | |
ubiquitin = "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG" | |
tetraubiquitin = "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG" | |
eone = "MAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQLDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFL |
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#!/usr/bin/env python3.1 | |
# cc attribution-sharealike // max [@] maxnanis.com | |
#transmembrane | |
import re | |
def tmpred(aa): | |
aa = aa.upper() | |
engine = re.compile("[^A-Z]") | |
aa = engine.sub("", aa) | |
ruler = '' | |
count = 1 |
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#!/usr/bin/env python3 | |
# cc attribution-sharealike // max [@] maxnanis.com | |
import re | |
from bio import fastad, fastac, rc | |
# set up a standard code table (as a Python dictionary) | |
# takes in a nucleotide string and returns the amino acid string | |
stdcode = {} | |
stdcode["TTT"] = stdcode["TTC"] = "F" |