From 4bbfab5aa43acc3efb2b7a3cb78907bbe64a2ed9 Mon Sep 17 00:00:00 2001
From: Anton Oresten <anton.oresten42@gmail.com>
Date: Sun, 1 Sep 2024 23:12:16 +0200
Subject: [PATCH] Delete kd.ipynb

---
 kd.ipynb | 111 -------------------------------------------------------
 1 file changed, 111 deletions(-)
 delete mode 100644 kd.ipynb

diff --git a/kd.ipynb b/kd.ipynb
deleted file mode 100644
index 9aa49b2..0000000
--- a/kd.ipynb
+++ /dev/null
@@ -1,111 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\u001b[32m\u001b[1m  Activating\u001b[22m\u001b[39m project at `c:\\Users\\anton\\.julia\\dev\\AssigningSecondaryStructure`\n"
-     ]
-    }
-   ],
-   "source": [
-    "using Pkg; Pkg.activate(\".\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 81,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "WARNING: using LinearAlgebra.I in module Main conflicts with an existing identifier.\n"
-     ]
-    }
-   ],
-   "source": [
-    "using AssigningSecondaryStructure\n",
-    "import AssigningSecondaryStructure as ASS\n",
-    "\n",
-    "using Backboner, NearestNeighbors\n",
-    "using LinearAlgebra"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 99,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "10-element Vector{Bool}:\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0\n",
-       " 0"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "coords = reshape(Protein.readpdb(\"test/data/1ASS.pdb\")[1].backbone.coords, 3, 3, :)\n",
-    "L = size(coords, 3)\n",
-    "\n",
-    "Ca_pos = coords[:, 2, :]\n",
-    "\n",
-    "pad_pos = fill(NaN, 3)\n",
-    "C_pos = coords[:, 3, :]\n",
-    "O_pos = [ASS.get_oxygen_positions(coords) pad_pos]\n",
-    "N_pos = coords[:, 1, :]\n",
-    "H_pos = [pad_pos ASS.get_hydrogen_positions(coords)]\n",
-    "\n",
-    "kdtree = KDTree(Ca_pos, Euclidean())\n",
-    "\n",
-    "for i in axes(coords, 3)[[4]]\n",
-    "    js, dists = knn(kdtree, view(Ca_pos, :, 1), 10, true)\n",
-    "    Hbonds = map(js) do j\n",
-    "        i <= j <= i+2 && return false\n",
-    "        r_ON = norm(O_pos[:, i] - N_pos[:, j])\n",
-    "        r_CH = norm(C_pos[:, i] - H_pos[:, j])\n",
-    "        r_OH = norm(O_pos[:, i] - H_pos[:, j])\n",
-    "        r_CN = norm(C_pos[:, i] - N_pos[:, j])\n",
-    "        E = ASS.Q1Q2 * ASS.F * (1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)\n",
-    "        return E < ASS.CUTOFF\n",
-    "    end\n",
-    "    display(Hbonds)\n",
-    "end"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Julia 1.10.0",
-   "language": "julia",
-   "name": "julia-1.10"
-  },
-  "language_info": {
-   "file_extension": ".jl",
-   "mimetype": "application/julia",
-   "name": "julia",
-   "version": "1.10.0"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}