x0xMaximus

# 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')

x0xMaximus

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;

x0xMaximus

#!/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

x0xMaximus

#!/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

x0xMaximus

#!/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"