Notebooks/A5-Modeling - analysis of 3D models.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Descriptive statisitcs on a single model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pytadbit import load_structuralmodels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "models_B = load_structuralmodels('results/models_B/B.models')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "model=  models_B[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Calculate the radius of gyration of a model (median distance of all particles from the center of mass of the model):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "306.368473228\n"
     ]
    }
   ],
   "source": [
    "print model.radius_of_gyration()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Calculate the length of a model, the sum of all distances between consecutive particles:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "14446.0659022\n"
     ]
    }
   ],
   "source": [
    "print model.contour()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Calculate the minimum rectangular space in which to fit the model:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "979.274146923\n",
      "88.5745849916\n"
     ]
    }
   ],
   "source": [
    "print model.longest_axe()\n",
    "print model.shortest_axe()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The minimum cube:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1314.37787457\n",
      "2270705017.11\n"
     ]
    }
   ],
   "source": [
    "print model.cube_side()\n",
    "print model.cube_volume()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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