ModelSystems.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import random\n",
    "import amino"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def gen_two():\n",
    "    traj = []\n",
    "    for i in range(5000):\n",
    "        tmp = random.random()\n",
    "        tmp = 1 - (tmp * tmp * tmp * tmp)\n",
    "        if random.random() < 0.5:\n",
    "            tmp = -1 * tmp\n",
    "        traj.append(tmp)\n",
    "    return traj"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "def gen_three():\n",
    "    traj = []\n",
    "    for i in range(5000):\n",
    "        tmp = random.random()\n",
    "        tmp = (tmp * tmp * tmp * tmp)/2\n",
    "        if random.random() < 0.5:\n",
    "            tmp = 1 - tmp\n",
    "        if random.random() < 0.5:\n",
    "            tmp = -1 * tmp\n",
    "        traj.append(tmp)\n",
    "    return traj"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def add_noise(traj):\n",
    "    new_traj = []\n",
    "    for i in traj:\n",
    "        new_traj.append(i + (random.random() / 10) - 0.05)\n",
    "    return new_traj"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def rand_insert(lst, ele):\n",
    "    lst.insert(random.randrange(len(lst) + 1), ele)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def make_OP(name, num, num_wells, ops):\n",
    "    \n",
    "    original = None\n",
    "    if num_wells == 2:\n",
    "        original = gen_two()\n",
    "    elif num_wells == 3:\n",
    "        original = gen_three()\n",
    "    else:\n",
    "        raise Exception(\"I've only built in distribution generators for 2 and 3 well OP's.\")\n",
    "        \n",
    "    rand_insert(ops, amino.OrderParameter(name, original))\n",
    "    \n",
    "    for i in range(num - 1):\n",
    "        rand_insert(ops, amino.OrderParameter(name + str(i + 1), add_noise(original)))\n",
    "        \n",
    "    return None\n",
    "        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "ten_ops = []\n",
    "make_OP(\"A\", 14, 2, ten_ops)\n",
    "make_OP(\"B\", 10, 2, ten_ops)\n",
    "make_OP(\"C\", 14, 3, ten_ops)\n",
    "make_OP(\"D\", 10, 3, ten_ops)\n",
    "make_OP(\"E\", 14, 2, ten_ops)\n",
    "make_OP(\"F\", 10, 2, ten_ops)\n",
    "make_OP(\"G\", 14, 2, ten_ops)\n",
    "make_OP(\"H\", 10, 3, ten_ops)\n",
    "make_OP(\"I\", 14, 3, ten_ops)\n",
    "make_OP(\"J\", 10, 2, ten_ops)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Building dissimilarity matrix...\n",
      "Done dissimilarity matrix construction...\n",
      "Checking 30 order parameters...\n",
      "Checking 29 order parameters...\n",
      "Checking 28 order parameters...\n",
      "Checking 27 order parameters...\n",
      "Checking 26 order parameters...\n",
      "Checking 25 order parameters...\n",
      "Checking 24 order parameters...\n",
      "Checking 23 order parameters...\n",
      "Checking 22 order parameters...\n",
      "Checking 21 order parameters...\n",
      "Checking 20 order parameters...\n",
      "Checking 19 order parameters...\n",
      "Checking 18 order parameters...\n",
      "Checking 17 order parameters...\n",
      "Checking 16 order parameters...\n",
      "Checking 15 order parameters...\n",
      "Checking 14 order parameters...\n",
      "Checking 13 order parameters...\n",
      "Checking 12 order parameters...\n",
      "Checking 11 order parameters...\n",
      "Checking 10 order parameters...\n",
      "Checking 9 order parameters...\n",
      "Checking 8 order parameters...\n",
      "Checking 7 order parameters...\n",
      "Checking 6 order parameters...\n",
      "Checking 5 order parameters...\n",
      "Checking 4 order parameters...\n",
      "Checking 3 order parameters...\n",
      "Checking 2 order parameters...\n",
      "Checking 1 order parameters...\n"
     ]
    }
   ],
   "source": [
    "final_ten_ops = amino.find_ops(ten_ops, 30, 80)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of Order Parameters: 10\n",
      "D\n",
      "H\n",
      "F\n",
      "I\n",
      "C\n",
      "B\n",
      "G\n",
      "E\n",
      "J\n",
      "A\n",
      "\n",
      "All order Parmeters:\n",
      "D6\n",
      "E8\n",
      "B7\n",
      "I13\n",
      "C9\n",
      "G12\n",
      "H6\n",
      "G9\n",
      "F4\n",
      "H\n",
      "A5\n",
      "F7\n",
      "C6\n",
      "I2\n",
      "C3\n",
      "A1\n",
      "B2\n",
      "D8\n",
      "J9\n",
      "G4\n",
      "G2\n",
      "F1\n",
      "C7\n",
      "G7\n",
      "F\n",
      "B6\n",
      "J7\n",
      "D5\n",
      "E6\n",
      "A10\n",
      "C4\n",
      "D1\n",
      "C5\n",
      "J5\n",
      "F5\n",
      "I5\n",
      "E7\n",
      "E\n",
      "I8\n",
      "H4\n",
      "J8\n",
      "C10\n",
      "F3\n",
      "C\n",
      "I4\n",
      "E1\n",
      "I9\n",
      "J3\n",
      "C2\n",
      "G13\n",
      "G6\n",
      "E11\n",
      "J6\n",
      "B5\n",
      "C8\n",
      "G\n",
      "A\n",
      "H5\n",
      "E9\n",
      "H2\n",
      "B9\n",
      "B4\n",
      "E13\n",
      "A7\n",
      "D7\n",
      "I10\n",
      "C11\n",
      "G1\n",
      "E5\n",
      "C1\n",
      "E2\n",
      "F8\n",
      "E10\n",
      "D4\n",
      "G10\n",
      "A3\n",
      "A11\n",
      "F9\n",
      "J1\n",
      "H3\n",
      "H8\n",
      "I7\n",
      "I\n",
      "B\n",
      "I1\n",
      "C12\n",
      "J4\n",
      "E12\n",
      "I6\n",
      "H7\n",
      "A6\n",
      "A4\n",
      "J\n",
      "B1\n",
      "A2\n",
      "F6\n",
      "B8\n",
      "E3\n",
      "J2\n",
      "G11\n",
      "G5\n",
      "A13\n",
      "H1\n",
      "A8\n",
      "D2\n",
      "B3\n",
      "D\n",
      "A9\n",
      "E4\n",
      "G3\n",
      "G8\n",
      "I3\n",
      "I12\n",
      "D9\n",
      "H9\n",
      "D3\n",
      "A12\n",
      "I11\n",
      "C13\n",
      "F2\n"
     ]
    }
   ],
   "source": [
    "print(\"Number of Order Parameters: \" + str(len(final_ten_ops)))\n",
    "for i in final_ten_ops:\n",
    "    print(i.name)\n",
    "print(\"\\nAll order Parmeters:\")\n",
    "for i in ten_ops:\n",
    "    print(i.name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "five_ops = []\n",
    "make_OP(\"A\", 14, 2, five_ops)\n",
    "make_OP(\"B\", 10, 2, five_ops)\n",
    "make_OP(\"C\", 14, 3, five_ops)\n",
    "make_OP(\"D\", 10, 3, five_ops)\n",
    "make_OP(\"E\", 14, 2, five_ops)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Building dissimilarity matrix...\n",
      "Done dissimilarity matrix construction...\n",
      "Checking 30 order parameters...\n",
      "Checking 29 order parameters...\n",
      "Checking 28 order parameters...\n",
      "Checking 27 order parameters...\n",
      "Checking 26 order parameters...\n",
      "Checking 25 order parameters...\n",
      "Checking 24 order parameters...\n",
      "Checking 23 order parameters...\n",
      "Checking 22 order parameters...\n",
      "Checking 21 order parameters...\n",
      "Checking 20 order parameters...\n",
      "Checking 19 order parameters...\n",
      "Checking 18 order parameters...\n",
      "Checking 17 order parameters...\n",
      "Checking 16 order parameters...\n",
      "Checking 15 order parameters...\n",
      "Checking 14 order parameters...\n",
      "Checking 13 order parameters...\n",
      "Checking 12 order parameters...\n",
      "Checking 11 order parameters...\n",
      "Checking 10 order parameters...\n",
      "Checking 9 order parameters...\n",
      "Checking 8 order parameters...\n",
      "Checking 7 order parameters...\n",
      "Checking 6 order parameters...\n",
      "Checking 5 order parameters...\n",
      "Checking 4 order parameters...\n",
      "Checking 3 order parameters...\n",
      "Checking 2 order parameters...\n",
      "Checking 1 order parameters...\n"
     ]
    }
   ],
   "source": [
    "final_five_ops = amino.find_ops(five_ops, 30, 80)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of Order Parameters: 5\n",
      "A\n",
      "C\n",
      "B\n",
      "E\n",
      "D\n",
      "\n",
      "All order Parmeters:\n",
      "B4\n",
      "C11\n",
      "E12\n",
      "A3\n",
      "C3\n",
      "C2\n",
      "C13\n",
      "E5\n",
      "A4\n",
      "E3\n",
      "A1\n",
      "E7\n",
      "D1\n",
      "C6\n",
      "E2\n",
      "A7\n",
      "D8\n",
      "A6\n",
      "C7\n",
      "B5\n",
      "A5\n",
      "D9\n",
      "E8\n",
      "E11\n",
      "D7\n",
      "A8\n",
      "A12\n",
      "D3\n",
      "D6\n",
      "D5\n",
      "E13\n",
      "B9\n",
      "E\n",
      "D2\n",
      "B3\n",
      "E4\n",
      "B7\n",
      "A10\n",
      "A2\n",
      "C\n",
      "B\n",
      "B1\n",
      "E1\n",
      "D4\n",
      "C8\n",
      "E6\n",
      "A11\n",
      "D\n",
      "B8\n",
      "C12\n",
      "B2\n",
      "C4\n",
      "C1\n",
      "C10\n",
      "A\n",
      "C5\n",
      "B6\n",
      "A13\n",
      "A9\n",
      "C9\n",
      "E10\n",
      "E9\n"
     ]
    }
   ],
   "source": [
    "print(\"Number of Order Parameters: \" + str(len(final_five_ops)))\n",
    "for i in final_five_ops:\n",
    "    print(i.name)\n",
    "print(\"\\nAll order Parmeters:\")\n",
    "for i in five_ops:\n",
    "    print(i.name)"
   ]
  }
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