From 438176d3d328ddf85e0033f7b58d6a935772ef29 Mon Sep 17 00:00:00 2001
From: Tapasweni Pathak <tapaswenipathak@gmail.com>
Date: Sat, 25 Feb 2023 22:29:51 +0530
Subject: [PATCH] Add base for c++ xeus-cling google collab mybinder.org
 notebooks

---
 README.md                 | 28 ++++++++++++++++-
 Tutorial_AASequence.ipynb | 66 +++++++++++++++++++++++++++++++++++++++
 environment.yml           |  7 +++++
 3 files changed, 100 insertions(+), 1 deletion(-)
 create mode 100644 Tutorial_AASequence.ipynb
 create mode 100644 environment.yml

diff --git a/README.md b/README.md
index 4db827c..1e77450 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,27 @@
-# cling-notebooks
\ No newline at end of file
+# cling-notebooks
+
+This repository contains xeus-cling notebooks of OpenMS C++ code example files.
+
+Users can run in local or try it online on mybinder.org.
+
+## To run in local
+
+1. Create conda environment `cling-notebooks` using: `conda create -n cling-notebooks`.
+2. Activate conda environment using: `conda activate cling-notebooks`.
+3. Install xeus-cling using: `conda install xeus-cling -c conda-forge`.
+4. Install jupyterlab using: `conda install jupyterlab -c conda-forge`.
+5. Install openms using conda or bioconda following the instructions given [here](https://openms.readthedocs.io/en/latest/installations/installation-on-macos.html#install-via-conda-or-bioconda).
+6. Browse for the `.ipynb` notebooks and click on run.
+
+## Browse the C++ notebooks online on mybinder.org
+
+https://mybinder.org/v2/gh/OpenMS/OpenMS/develop?urlpath=https%3A%2F%2Fgithub.com%2Ftapaswenipathak%2FOpenMS%2Fblob%2Fdevelop%2FTutorial_AASequence.ipynb
+
+## Browse the C++ notebooks on Google Collab
+
+## Troubleshooting
+
+Please read the issues having documentation on common errors you might get and how
+to resolve them.
+
+Let us know if you get errors not already mentioned.
diff --git a/Tutorial_AASequence.ipynb b/Tutorial_AASequence.ipynb
new file mode 100644
index 0000000..a39b2ff
--- /dev/null
+++ b/Tutorial_AASequence.ipynb
@@ -0,0 +1,66 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "182ebb96",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#include <iostream>\n",
+    "#pragma base add_include_path(\"/Users/tapaswenipathak/miniconda3/envs/cling/include/OpenMS/\")\n",
+    "#include \"OpenMS/CHEMISTRY/AASequence.h\"\n",
+    "\n",
+    "using namespace OpenMS;\n",
+    "using namespace std;\n",
+    "\n",
+    "\n",
+    "  // generate AASequence object from String\n",
+    "  const String s = \"DEFIANGER\";\n",
+    "  AASequence peptide1 = AASequence::fromString(s);\n",
+    "\n",
+    "  // generate AASequence object from string literal\n",
+    "  AASequence peptide2 = AASequence::fromString(\"PEPTIDER\");\n",
+    "\n",
+    "  // extract prefix and suffix\n",
+    "  AASequence prefix(peptide1.getPrefix(2));\n",
+    "  AASequence suffix(peptide1.getSuffix(3));\n",
+    "  cout << peptide1.toString() << \" \"\n",
+    "       << prefix << \" \"\n",
+    "       << suffix << endl;\n",
+    "  \n",
+    "  // create chemically modified peptide\n",
+    "  AASequence peptide_meth_ox = AASequence::fromString(\"PEPTIDESEKUEM(Oxidation)CER\");\n",
+    "  cout << peptide_meth_ox.toString() << \" \"\n",
+    "       << peptide_meth_ox.toUnmodifiedString()\n",
+    "       << endl;\n",
+    "\n",
+    "  // mass of the full, uncharged peptide\n",
+    "  double peptide_mass_mono = peptide_meth_ox.getMonoWeight();\n",
+    "  cout << \"Monoisotopic mass of the uncharged, full peptide: \" << peptide_mass_mono << endl;\n",
+    "\n",
+    "  double peptide_mass_avg = peptide_meth_ox.getAverageWeight();\n",
+    "  cout << \"Average mass of the uncharged, full peptide: \" << peptide_mass_avg << endl;\n",
+    "\n",
+    "  // mass of the 2+ charged b-ion with the given sequence\n",
+    "  double ion_mass_2plus = peptide_meth_ox.getMonoWeight(Residue::BIon, 2);\n",
+    "  cout << \"Mass of the doubly positively charged b-ion: \" << ion_mass_2plus << endl;\n",
+    "\n",
+    "  // mass-to-charge ratio (m/z) of the 2+ charged b-ion and full peptide with the given sequence\n",
+    "  cout << \"Mass-to-charge of the doubly positively charged b-ion: \" << peptide_meth_ox.getMZ(2, Residue::BIon) << endl;\n",
+    "  cout << \"Mass-to-charge of the doubly positively charged peptide: \" << peptide_meth_ox.getMZ(2) << endl;\n",
+    "\n",
+    "  // ... many more\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "C++17",
+   "language": "C++17",
+   "name": "xeus-cling-cpp17"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..4220173
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,7 @@
+name: openms
+channels:
+    - openms
+    - conda-forge
+dependencies:
+    - xeus-cling
+    - openms