Notebooks/A5-Modeling_-_analysis_of_3D_models.ipynb

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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Descriptive statisitcs on a sinlge model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from pytadbit import load_structuralmodels"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "models_t0 = load_structuralmodels('T0.models')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "model=  models_t0[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": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1580.39291117\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": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "63287.0216901\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": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4586.20202907\n",
      "462.094110797\n"
     ]
    }
   ],
   "source": [
    "print model.longest_axe()\n",
    "print model.shortest_axe()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The minimum cube:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6565.19462149\n",
      "2.82971576977e+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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