Pep mass

pepmass.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from random import choice"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "MASS = {\n",
    "    'G':57,\n",
    "    'A':71,\n",
    "    'S':87,\n",
    "    'P':97,\n",
    "    'V':99,\n",
    "    'T':101,\n",
    "    'C':103,\n",
    "    'I':113,\n",
    "    'L':113,\n",
    "    'N':114,\n",
    "    'D':115,\n",
    "    'Q':128,\n",
    "    'K':128,\n",
    "    'E':129,\n",
    "    'M':131,\n",
    "    'H':137,\n",
    "    'F':147,\n",
    "    'R':156,\n",
    "    'Y':163,\n",
    "    'W':186,\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "ALPHA='GASPVTCLNDKEMHFRYW'  # remove I and Q"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def random_peptide(length=10):\n",
    "    return ''.join([choice(ALPHA) for i in range(length)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def weight(peptide):\n",
    "    return sum([MASS[p] for p in peptide])\n",
    "\n",
    "def compute_spectrum(peptide):\n",
    "    mset = set()\n",
    "    n = len(peptide)\n",
    "    for i in range(n):\n",
    "        for j in range(n - i):\n",
    "            s = peptide[i:i+j+1]\n",
    "            mset.add(weight(s))\n",
    "    return mset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LPAAS\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{71, 87, 97, 113, 142, 158, 168, 210, 229, 239, 281, 326, 352, 439}"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p = random_peptide(5)\n",
    "print(p)\n",
    "compute_spectrum(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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