# Pastebin sfy0C9ML
{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Load a PDB file and visualize it"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Set up the AMBER paths."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(setf (logical-pathname-translations \"amber\") \n",
    "      (list (list \"**;*.*\" (concatenate 'string (ext:getenv \"AMBERHOME\") \"/**/*.*\"))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "(leap.core:clear-path)\n",
    "(leap.core:add-path \"amber:dat;leap;prep;\")\n",
    "(leap.core:add-path \"amber:dat;leap;lib;\")\n",
    "(leap.core:add-path \"amber:dat;leap;parm;\")\n",
    "(leap.core:add-path \"amber:dat;leap;cmd;\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Cando reads Leap scripts."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "(source #P\"leaprc.protein.ff14SB\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Load a PDB file - warn if there are any unbuilt heavy atoms and unbuilt hydrogens. Put the result in the global variable \\*pdb\\*."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "(:= *pdb* (load-pdb \"data/pdbload/5t6o.pdb\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use a simple builder that builds unbuilt atoms by building them a random direction and 1A away from their bonded neighbor."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(simple-build-unbuilt-atoms *pdb*)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "(count-unbuilt-atoms *pdb*)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Show the structure. Rotate using the left mouse button, scale using two finger dragging."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(nglv:show-aggregate *pdb*)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "cando",
   "language": "lisp",
   "name": "cando"
  },
  "language_info": {
   "codemirror_mode": "text/x-common-lisp",
   "file_extension": ".lisp",
   "mimetype": "text/x-common-lisp",
   "name": "common-lisp",
   "pygments_lexer": "common-lisp",
   "version": "X3J13"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}