Merge branch 'vanilla-ssg' into dependabot/pip/jinja2-3.1.3

12 files changed, 1104 insertions, 4 deletions

diff --git a/Content/3D-Designs/2024-02-17-Can-Holder-Mountain-Bike.md b/Content/3D-Designs/2024-02-17-Can-Holder-Mountain-Bike.md
new file mode 100644
index 0000000..49378ca
--- /dev/null
+++ b/Content/3D-Designs/2024-02-17-Can-Holder-Mountain-Bike.md
@@ -0,0 +1,38 @@
+---
+date: 2024-02-17 18:42
+description: Carry your favourite soda (or beer) can with you while you ride
+tags: Mountain Biking, OpenSCAD
+---
+
+# Bike Soda Can Holder
+
+Ever wanted a nice craft soda, or a natty light during your ride? Mounts to the standard bottle cage holes on your bike.
+
+Printed on an Anycubic Kobra 2 (0.20mm resolution w/ 0.40mm nozzle at 40% Infill) 
+
+Download Link: [Github](https://github.com/navanchauhan/3D-Designs/tree/master/MTBCanHolder)
+
+<script type="module" src="https://ajax.googleapis.com/ajax/libs/model-viewer/3.4.0/model-viewer.min.js"></script>
+
+<div class="wrapper">
+<model-viewer alt="Holder for standard 12oz can" src="https://raw.githubusercontent.com/navanchauhan/3D-Designs/master/MTBCanHolder/12ozCanHolder.glb" shadow-intensity="1" ar ar-scale="auto" camera-controls touch-action="pan-y" camera-orbit="90deg 45def auto" auto-rotate xr-environment>
+</div>
+
+<style>
+.wrapper {
+    width: 100%
+}
+
+model-viewer {
+    height: 600px;
+    width: auto;
+}
+</style>
+
+## Current Variations
+
+* Standard 12oz Can
+* 8.4 oz Red Bull holder
+
+
+The OpenSCAD code can be modified to support tall boys and stovepipe cans. Email me if you need help generating more variations
diff --git a/Content/3D-Designs/index.md b/Content/3D-Designs/index.md
new file mode 100644
index 0000000..0375031
--- /dev/null
+++ b/Content/3D-Designs/index.md
@@ -0,0 +1,3 @@
+# 3D Designs
+
+I refuse to learn how to use a normal CAD software like SolidWorks. I use OpenSCAD. All of the code and exported models are stored in my GitHub Repository: [navanchauhan/3D-Designs](https://github.com/navanchauhan/3D-Designs).
diff --git a/Content/about/index.md b/Content/about/index.md
index 55fc7a5..162f311 100644
--- a/Content/about/index.md
+++ b/Content/about/index.md
@@ -1,6 +1,6 @@
 ---
 date: 2003-12-21 22:32
-description: About Me!
+description: About Me
 tags: Personal
 ---
 
@@ -8,7 +8,11 @@ tags: Personal
 
 Hi!
 
-My name is Navan Chauhan. I do lots of different things. Most of the bigger projects I am working on are currently private/unlisted. Although, all of them will be open-sourced, I don't want to publish them until I am happy with the version 1.0.
+My name is Navan Chauhan. This is my small corner on the internet. Most of the bigger projects I am working on are either currently private or unlisted. Any of the cool research work I am doing also cannot be published anytime soon :(
+
+I like solving problems, no matter what field they are in. I might be a programmer by trade, but I have done way too much work in the field of drug discovery lately. I did fall in love with Math during college, and I have a special liking for probability theory. 
+
+When not in front of a screen, I can be found injuring myself mountain biking (I hate road bikers /s), skiing, or homebrewing (WLP618 for all legal purposes).
 
 Landing page with other links, and projects: [https://hi.navan.dev](https://hi.navan.dev)
 
@@ -23,7 +27,7 @@ My GPG Fingerprint:
 ## Links
 
 * [GitHub: @navanchauhan](https://github.com/navanchauhan)
-* [Mirror: Personal Instance of Gitea](https://pi4.navan.dev/gitea)
+* [Mirror: Personal Instance of Gitea](https://pi4.navan.dev/gitea) (Moving the Gitea server to another host)
 * [GoatCounter: This Website's Analytics](https://navanchauhan.goatcounter.com)
 * [Twitter: @navanchauhan](https://github.com/navanchauhan)
 * [Mastodon: @navanchauhan@mastodon.social](https://mastodon.social/@navanchauhan)
diff --git a/Content/colophon/index.md b/Content/colophon/index.md
new file mode 100644
index 0000000..80904b2
--- /dev/null
+++ b/Content/colophon/index.md
@@ -0,0 +1,8 @@
+# Colophon
+
+This website is generated using a custom static site generator I wrote in Python. The theme is a port of [@mdo's Hyde](http://hyde.getpoole.com/), ported by the makers of [Zola](https://www.getzola.org/).
+
+All the Open Graph images are generated using Pillow and the Futura font. The math is taken care of by an extra I created for the python-markdown2 library that converts inline and block $\LaTeX$ into MathML.
+
+Since this website is currently using the `.dev` tld, there is no support for HTTP in most browsers (Since they use HSTS preloading). But if you ever find yourself on an IBM PC 5150 and need to use `hget`, that should work.
+
diff --git a/Content/index.md b/Content/index.md
index fb22d38..b85aa59 100644
--- a/Content/index.md
+++ b/Content/index.md
@@ -1 +1,6 @@
-# Navan Chauhan
+# Some Projects
+
+* [iGopherBrowser](https://web.navan.dev/iGopherBrowser): A modern Gopher client for iOS, macOS, and VisionOS. It is built on top of my [swift-gopher](https://github.com/swift-gopher) library. Available on the [App Store](https://apps.apple.com/in/app/igopherbrowser/id647463884)
+* [TimeSlicerX](https://timeslicerx.prudent.studio): A timeboxing app for iOS (and macOS) to schedule tasks around your calendar items. Everything is done on-device. Available on the [App Store](https://apps.apple.com/us/app/timeslicerx/id6447939029?uo=4)
+* [VaporwaveGenerator](https://github.com/navanchauhan/VaporwaveGenerator): A E S T H E T I C S 
+
diff --git a/Content/posts/2020-07-01-Install-rdkit-colab.md b/Content/posts/2020-07-01-Install-rdkit-colab.md
index ff5da1e..4a87bf1 100644
--- a/Content/posts/2020-07-01-Install-rdkit-colab.md
+++ b/Content/posts/2020-07-01-Install-rdkit-colab.md
@@ -6,6 +6,16 @@ tags: Tutorial, Code-Snippet, Colab
 
 # Installing RDKit on Google Colab
 
+**Update: March 2024** 
+
+`rdkit-pypi` has been deprecated in favour of `rdkit`
+
+You can simply run:
+
+```
+!pip install rdkit
+```
+
 **EDIT:** Try installing RDKit using pip
 
 ```
diff --git a/Content/posts/2024-02-26-control-element-under-another-element-html-css.md b/Content/posts/2024-02-26-control-element-under-another-element-html-css.md
new file mode 100644
index 0000000..cbdfe6a
--- /dev/null
+++ b/Content/posts/2024-02-26-control-element-under-another-element-html-css.md
@@ -0,0 +1,77 @@
+---
+date: 2024-02-26 11:57
+description: With CSS you can disable any interactions with an element and directly control the underlying element
+tags: HTML, CSS
+draft: false
+---
+
+# Interacting with underlying element in HTML
+
+I know that the title is a bit weird. I was trying to interact with a video under an iPhone Bezel Screen frame.
+
+```html
+<div class="row-span-2 md:col-span-1 rounded-xl border-2 border-slate-400/10 bg-neutral-100 p-4 dark:bg-neutral-900">
+    <div class="content flex flex-wrap content-center justify-center">
+        <img src="iphone-12-white.png" class="h-[60vh] z-10 absolute">
+        <!--<img src="screenshot2.jpeg" class="h-[57vh] mt-4 mr-1 rounded-[2rem]">-->
+        <video src="screenrec.mp4" class="h-[57vh] mt-4 mr-1 rounded-[2rem]" controls muted autoplay></video>
+    </div>
+</div>
+```
+
+![Video Under a Transparent Image](/assets/underlying/video-under-element.jpg)
+
+Turns out, you can disable pointer events!
+
+In Tailwind, it is as simple as adding `pointer-events-none` to the bezel screen.
+
+In CSS, this can be done by:
+
+```css
+.className {
+    pointer-events: none
+}
+```
+
+Let us try this in a simple example.
+
+## Example
+
+Here, we create a button and overlay a transparent box
+
+```html
+<div style="height: 200px; width: 300px; background-color: rgba(255, 0, 0, 0.4); z-index: 2; position: absolute;">
+A box with 200px height and 200px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px;" onclick="alert('You were able to click this button')">Try clicking me</button>
+```
+
+<hr>
+
+<div style="height: 200px; width: 300px; background-color: rgba(255, 0, 0, 0.4); z-index: 2; position: absolute;">
+A box with 200px height and 300px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px;" onclick="alert('You were able to click this button')">Try clicking me</button>
+<hr>
+
+As you can see, you cannot click the button because the red box comes in the way. We can fix this by adding `pointer-events: none` to the box. 
+
+```html
+<div style="height: 200px; width: 300px; background-color: rgba(0, 255, 0, 0.4); z-index: 2; position: absolute; pointer-events: none;">
+A box with 200px height and 300px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px" onclick="alert('You were able to click this button')">Try clicking me</button>
+</div>
+```
+
+<hr>
+
+<div style="height: 200px; width: 300px; background-color: rgba(0, 255, 0, 0.4); z-index: 2; position: absolute; pointer-events: none;">
+A box with 200px height and 300px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px" onclick="alert('You were able to click this button')">Try clicking me</button>
+</div>
+
+
+
+
diff --git a/Content/posts/2024-03-04-opencvjs-video-processing.md b/Content/posts/2024-03-04-opencvjs-video-processing.md
new file mode 100644
index 0000000..cf87fb1
--- /dev/null
+++ b/Content/posts/2024-03-04-opencvjs-video-processing.md
@@ -0,0 +1,12 @@
+---
+date: 2024-03-04 12:01
+description: Real time video processing with OpenCV.js in the browser
+tags: HTML, JS, OpenCV
+draft: true
+---
+
+# Video Processing W/ OpenCV.js
+
+Note: A really weird bug you might run into when you are trying to mess around 
+and reloading the page on iOS is that OpenCV just stops loading. This is a bug in
+WebKit.:
diff --git a/Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md b/Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md
new file mode 100644
index 0000000..15161f5
--- /dev/null
+++ b/Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md
@@ -0,0 +1,267 @@
+---
+date: 2024-03-15 13:16
+description: This goes through compiling Open Watcom 2 and creating simple hello-world exampls
+tags: DOS, x86, macOS
+draft: false
+---
+
+# Cross-Compiling Hello World for DOS on macOS
+
+Technically this should work for any platform that OpenWatcom 2 supports compiling binaries for. Some instructions are based on [a post at retrocoding.net](https://retrocoding.net/openwatcom-gateway-to-ancient-world-of-x86),
+ and [John Tsiombikas's post](http://nuclear.mutantstargoat.com/articles/retrocoding/dos01-setup/#hello-world-program)
+
+## Prerequisites
+
+You should already have XCode / Command Line Tools, and Homebrew installed. To compile Open Watcom for DOS you will need DOSBox (I use DOSBox-X).
+
+```bash
+brew install --cask dosbox-x
+```
+
+## Compiling Open Watcom v2
+
+*If this process is super annoying, I might make a custom homebrew tap to build and install Open Watcom*
+
+```bash
+git clone https://github.com/open-watcom/open-watcom-v2
+cp open-watcom-v2/setvars.sh custom_setvars.sh
+```
+
+Now, edit this `setvars.sh` file. My file looks like this:
+
+```bash
+#!/bin/zsh
+export OWROOT="/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2"
+export OWTOOLS=CLANG
+export OWDOCBUILD=0
+export OWGUINOBUILD=0
+export OWDISTRBUILD=0
+export OWDOSBOX="/Applications/dosbox-x.app/Contents/MacOS/dosbox-x"
+export OWOBJDIR=binbuildV01
+. "$OWROOT/cmnvars.sh"
+echo "OWROOT=$OWROOT"
+cd "$OWROOT"
+```
+
+Note, your `OWRTOOT` is definitely going to be in a different location.
+
+```bash
+source ./custom_setvars.sh
+./build.sh
+./build.sh rel
+```
+
+This will build, and then copy everything to the `rel` directory inside `open-watcom-v2` directory. Since I ran this on an Apple Silicon Mac, 
+ all the binaries for me are in the `armo64` directory. You can now move everything inside the rel folder to another location, or create a simple 
+ script to init all variables whenever you want.
+
+I like having a script called `exportVarsForDOS.sh` 
+
+```bash
+#!/bin/zsh
+
+export WATCOM=/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2/rel
+export PATH=$PATH:$WATCOM/armo64
+export EDDAT=$WATCOM/eddat
+
+# For DOS 8088/8086 development
+export INCLUDE=$WATCOM/h
+export LIB=$WATCOM/lib286 # You don't really need this
+```
+
+Then, when you need to load up these variables, you can simply run `source exportVarsForDOS.sh` or `. exportVarsForDOS.sh`
+
+## Hello World
+
+### Buliding without any Makefiles
+
+Create a new file called `example1.c`
+
+```c
+#include<stdio.h>
+
+int main() {
+    printf("Hello World!");
+    return 0;
+}
+```
+
+First we compile the code:
+
+```bash
+$ wcc example1.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+example1.c: 7 lines, included 818, 0 warnings, 0 errors
+Code size: 19
+```
+
+Then, link to make an executable:
+
+```bash
+$ wlink name example1.exe system dos file example1.o
+Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+loading object files
+searching libraries
+creating a DOS executable 
+```
+
+If you want to test this executable, jump to the section titled `Testing with DOSBox-X` below.
+
+### Simple Makefile
+
+```makefile
+obj = main.o hello.o
+bin = tizts.com
+
+CC = wcc
+CFLAGS = -0
+LD = wlink
+
+$(bin): $(obj)
+	$(LD) name $@ system dos file main.o file hello.o 
+
+.c.o:
+	$(CC) $(CFLAGS) $<
+
+clean:
+	rm $(obj) $(bin)
+```
+
+Where, `main.c`
+```c
+void hello(void);
+
+int main(void)
+{
+    hello();
+    return 0;
+}
+```
+
+and `hello.c`
+
+```c
+/* hello.c */
+#include <stdio.h>
+
+void hello(void)
+{
+    printf("Hello!");
+}
+```
+
+To compile into `tizts.com` simply run `wmake`
+
+```bash
+$ wmake
+➜  simple-cpp wmake
+Open Watcom Make Version 2.0 beta Mar 15 2024 13:10:16
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1988-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+	wcc -0 main.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+main.c(8): Warning! W138: No newline at end of file
+main.c: 8 lines, included 53, 1 warnings, 0 errors
+Code size: 12
+	wcc -0 hello.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+hello.c: 8 lines, included 818, 0 warnings, 0 errors
+Code size: 17
+	wlink name tizts.com system dos file main.o file hello.o
+Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+loading object files
+searching libraries
+creating a DOS executable
+```
+
+### Using CMake
+
+Create a file called `CMakeLists.txt`
+
+```CMake
+project(hello)
+
+set(SOURCES abc.c)
+
+add_executable(hello ${SOURCES})
+```
+
+Where, `abc.c` is:
+
+```c
+#include <stdio.h>
+
+int main() {
+    printf("Does this work?");
+    return 0;
+}
+```
+
+```bash
+mkdir build
+cd build
+```
+
+And build using CMake
+
+```
+cmake -DCMAKE_SYSTEM_NAME=DOS -DCMAKE_SYSTEM_PROCESSOR=I86 -DCMAKE_C_FLAGS="-0 -bt=dos -d0 -oaxt" -G "Watcom WMake" ../..
+```
+
+There you have it. Three different ways to compile a C program on a macOS device in 2024 that can run on an IBM PC 5150 (which was released in 1981!)
+
+## Testing with DOSBox-X
+
+```bash
+cp example1.exe ~/Downloads
+/Applications/dosbox-x.app/Contents/MacOS/dosbox-x
+```
+
+In DOSBox-X we now mount the `~/Downloads` folder as our `C:` drive
+
+```
+mount C ~/Downloads
+```
+
+Switch to the C drive
+
+```
+C:
+```
+
+Run the program:
+
+```
+example1
+```
+
+![Running our program in DOSBox-X](/assets/posts/dosbox/hello-world.png)
+
+*My DOSBox setup might look slightly different than yours...*
+
+
diff --git a/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md b/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md
new file mode 100644
index 0000000..6317175
--- /dev/null
+++ b/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md
@@ -0,0 +1,242 @@
+---
+date: 2024-03-21 12:46
+description: Predicting n-th degree polynomials using TensorFlow 2.x
+tags: Tutorial, Tensorflow, Colab
+---
+
+# Polynomial Regression Using TensorFlow 2.x
+
+I have a similar post titled [Polynomial Regression Using Tensorflow](/posts/2019-12-16-TensorFlow-Polynomial-Regression.html) that used `tensorflow.compat.v1` (Which still works as of TF 2.16). But, I thought it would be nicer to redo it with newer TF versions. 
+
+I will be skipping all the introductions about polynomial regression and jumping straight to the code. Personally, I prefer using `scikit-learn` for this task.
+
+## Position vs Salary Dataset
+
+Again, we will be using https://drive.google.com/file/d/1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9/view (Salary vs Position Dataset)
+
+If you are in a Python Notebook environment like Kaggle or Google Colaboratory, you can simply run:
+```Termcap
+!wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9' -O data.csv
+```
+
+## Code
+
+If you just want to copy-paste the code, scroll to the bottom for the entire snippet. Here I will try and walk through setting up code for a 3rd-degree (cubic) polynomial
+
+### Imports
+
+```python
+import pandas as pd
+import tensorflow as tf
+import matplotlib.pyplot as plt
+import numpy as np
+```
+
+### Reading the Dataset
+
+```python
+df = pd.read_csv("data.csv")
+```
+
+### Variables and Constants
+
+Here, we initialize the X and Y values as constants, since they are not going to change. The coefficients are defined as variables.
+
+```python
+X = tf.constant(df["Level"], dtype=tf.float32)
+Y = tf.constant(df["Salary"], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(4)]
+```
+
+Here, `X` and `Y` are the values from our dataset. We initialize the coefficients for the equations as small random values.
+
+These coefficients are evaluated by Tensorflow's `tf.math.poyval` function which returns the n-th order polynomial based on how many coefficients are passed. Since our list of coefficients contains 4 different variables, it will be evaluated as:
+
+```
+y = (x**3)*coefficients[3] + (x**2)*coefficients[2] + (x**1)*coefficients[1] (x**0)*coefficients[0]
+``` 
+
+Which is equivalent to the general cubic equation:
+
+<script src="https://cdn.jsdelivr.net/npm/mathjax@4.0.0-beta.4/tex-mml-chtml.js" id="MathJax-script"></script>
+<script src="https://cdn.jsdelivr.net/npm/mathjax@4.0.0-beta.4/input/tex/extensions/noerrors.js" charset="UTF-8"></script>
+
+$$
+y = ax^3 + bx^2 + cx + d
+$$
+
+### Optimizer Selection & Training
+
+```python
+optimizer = tf.keras.optimizers.Adam(learning_rate=0.3)
+num_epochs = 10_000
+
+for epoch in range(num_epochs):
+    with tf.GradientTape() as tape:
+        y_pred = tf.math.polyval(coefficients, X)
+        loss = tf.reduce_mean(tf.square(y - y_pred))
+    grads = tape.gradient(loss, coefficients)
+    optimizer.apply_gradients(zip(grads, coefficients))
+    if (epoch+1) % 1000 == 0:
+        print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}"
+```
+
+In TensorFlow 1, we would have been using `tf.Session` instead. 
+
+Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. 
+
+Our loss function is Mean Squared Error (MSE):
+
+$$
+= \frac{1}{n} \sum_{i=1}^{n}{(Y\_i - \hat{Y\_i})^2}
+$$
+
+Where <math xmlns="http://www.w3.org/1998/Math/MathML"><mover><msub><mi>Y</mi><mi>i</mi></msub><mo stretchy="false" style="math-style:normal;math-depth:0;">^</mo></mover></math> is the predicted value and <math xmlns="http://www.w3.org/1998/Math/MathML"><msub><mi>Y</mi><mi>i</mi></msub></math> is the actual value
+
+### Plotting Final Coefficients
+
+```python
+final_coefficients = [c.numpy() for c in coefficients]
+print("Final Coefficients:", final_coefficients)
+
+plt.plot(df["Level"], df["Salary"], label="Original Data")
+plt.plot(df["Level"],[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df["Level"]])
+plt.ylabel('Salary')
+plt.xlabel('Position')
+plt.title("Salary vs Position")
+plt.show()
+```
+
+
+## Code Snippet for a Polynomial of Degree N
+
+### Using Gradient Tape
+
+This should work regardless of the Keras backend version (2 or 3)
+
+```python
+import tensorflow as tf
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+df = pd.read_csv("data.csv")
+
+############################
+## Change Parameters Here ##
+############################
+x_column = "Level"         #
+y_column = "Salary"        #
+degree = 2                 #
+learning_rate = 0.3        #
+num_epochs = 25_000        #
+############################
+
+X = tf.constant(df[x_column], dtype=tf.float32)
+Y = tf.constant(df[y_column], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)]
+
+optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate)
+
+for epoch in range(num_epochs):
+    with tf.GradientTape() as tape:
+        y_pred = tf.math.polyval(coefficients, X)
+        loss = tf.reduce_mean(tf.square(Y - y_pred))
+    grads = tape.gradient(loss, coefficients)
+    optimizer.apply_gradients(zip(grads, coefficients))
+    if (epoch+1) % 1000 == 0:
+        print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}")
+
+final_coefficients = [c.numpy() for c in coefficients]
+print("Final Coefficients:", final_coefficients)
+
+print("Final Equation:", end=" ")
+for i in range(degree+1):
+  print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n")
+
+plt.plot(X, Y, label="Original Data")
+plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]]), label="Our Poynomial"
+plt.ylabel(y_column)
+plt.xlabel(x_column)
+plt.title(f"{x_column} vs {y_column}")
+plt.legend()
+plt.show()
+```
+
+### Without Gradient Tape
+
+This relies on the Optimizer's `minimize` function and uses the `var_list` parameter to update the variables.
+
+This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend.
+
+```python
+import tensorflow as tf
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+df = pd.read_csv("data.csv")
+
+############################
+## Change Parameters Here ##
+############################
+x_column = "Level"         #
+y_column = "Salary"        #
+degree = 2                 #
+learning_rate = 0.3        #
+num_epochs = 25_000        #
+############################
+
+X = tf.constant(df[x_column], dtype=tf.float32)
+Y = tf.constant(df[y_column], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)]
+
+optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate)
+
+def loss_function():
+  pred_y = tf.math.polyval(coefficients, X)
+  return tf.reduce_mean(tf.square(pred_y - Y))
+
+for epoch in range(num_epochs):
+    optimizer.minimize(loss_function, var_list=coefficients)
+    if (epoch+1) % 1000 == 0:
+        current_loss = loss_function().numpy()
+        print(f"Epoch {epoch+1}: Training Loss: {current_loss}")
+
+final_coefficients = coefficients.numpy()
+print("Final Coefficients:", final_coefficients)
+
+print("Final Equation:", end=" ")
+for i in range(degree+1):
+  print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n")
+
+plt.plot(X, Y, label="Original Data")
+plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]], label="Our Polynomial")
+plt.ylabel(y_column)
+plt.xlabel(x_column)
+plt.legend()
+plt.title(f"{x_column} vs {y_column}")
+plt.show()
+```
+
+
+As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset.
+
+## Further Programming
+
+How would you modify this code to use another type of nonlinear regression? Say, 
+
+$$ y = ab^x $$
+
+Hint: Your loss calculation would be similar to:
+
+```python
+bx = tf.pow(coefficients[1], X)
+pred_y = tf.math.multiply(coefficients[0], bx)
+loss = tf.reduce_mean(tf.square(pred_y - Y))
+```
+
+
diff --git a/Content/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.md b/Content/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.md
new file mode 100644
index 0000000..0435a6c
--- /dev/null
+++ b/Content/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.md
@@ -0,0 +1,55 @@
+---
+date: 2024-03-26 15:36
+description: Quick derivation of the quadratic equation by completing the square 
+tags: mathematics 
+---
+
+# Quadratic Formula Derivation
+
+The standard form of a quadratic equation is:
+
+$$
+ax^2 + bx + c = 0
+$$
+
+Here, $a, b, c \in \mathbb{R}$, and $a \neq 0$
+
+We begin by first dividing both sides by the coefficient $a$
+
+$$
+\implies x^2 + \frac{b}{a}x + \frac{c}{a} = 0
+$$
+
+We can rearrange the equation:
+
+$$
+x^2 + \frac{b}{a}x = - \frac{c}{a}
+$$
+
+We can then use the method of completing the square. ([Maths is Fun](https://www.mathsisfun.com/algebra/completing-square.html) has a really good explanation for this technique)
+
+$$
+x^2 + \frac{b}{a}x + (\frac{b}{2a})^2 = \frac{-c}{a} + (\frac{b}{2a})^2
+$$
+
+On our LHS, we can clearly recognize that it is the expanded form of $(x + d)^2$ i.e $x^2 + 2x\cdot d + d^2$
+
+$$
+\implies (x + \frac{b}{2a})^2 = \frac{-c}{a} + \frac{b^2}{4a^2} = \frac{-4ac + b^2}{4a^2}
+$$
+
+Taking the square root of both sides
+
+$$
+\begin{align*}
+x + \frac{b}{2a} &= \frac{\sqrt{-4ac + b^2}}{2a} \\
+x &= \frac{\pm \sqrt{-4ac + b^2} - b}{2a} \\
+&= \frac{-b \pm \sqrt{b^2 - 4ac}}{2a}
+\end{align*}
+$$
+
+This gives you the world famous quadratic formula:
+
+$$
+x = \frac{-b \pm \sqrt{b^2 - 4ac}}{2a}
+$$
diff --git a/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md b/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md
new file mode 100644
index 0000000..f43f15c
--- /dev/null
+++ b/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md
@@ -0,0 +1,379 @@
+---
+date: 2024-03-28 20:12
+description: Fixing ADFRsuite on M1/MX chip Macs - CLI Tools
+tags: macOS, Cheminformatics
+---
+
+# Fixing ADFRSuite for Apple Silicon
+
+We are going to be running everything through Rosetta 2. I am confident that if I had access to the original source code, I could find a way to run everything natively. 
+
+These are the following issues that we will be fixing in this part:
+
+* “python2.7” cannot be opened because the developer cannot be verified.
+* OpenBabel Error
+* Segmentation fault while running the [redocking tutorial](https://ccsb.scripps.edu/adcp/tutorial-redocking/)
+
+For the sake of simplicity, I am assuming that I am running all these commands in the folder `~/Developer/scrippstuff/`
+
+## Installing Rosetta 2
+
+We are going to run all of these steps in the terminal
+
+```bash
+/usr/sbin/softwareupdate --install-rosetta --agree-to-license
+```
+
+### Install Homebrew for x86
+
+Both versions of homebrew (x86 and arm64) can peacefully coexist on your system.
+
+From now on, every command should be run in a terminal session that starts with this as the first command:
+
+```bash
+arch -x86_64 zsh
+```
+
+Now, we can install homebrew:
+
+```bash
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+```
+
+Here is my output:
+
+``` bash
+➜  scrippstuff uname -a
+Darwin Navans-MacBook-Pro.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:31:00 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6020 x86_64
+➜  scrippstuff /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+==> Checking for `sudo` access (which may request your password)...
+Password:
+==> This script will install:
+/usr/local/bin/brew
+/usr/local/share/doc/homebrew
+/usr/local/share/man/man1/brew.1
+/usr/local/share/zsh/site-functions/_brew
+/usr/local/etc/bash_completion.d/brew
+/usr/local/Homebrew
+==> The following new directories will be created:
+/usr/local/Cellar
+/usr/local/Caskroom
+
+Press RETURN/ENTER to continue or any other key to abort:
+==> /usr/bin/sudo /bin/mkdir -p /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /bin/chmod ug=rwx /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/sbin/chown navanchauhan /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/bin/chgrp admin /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan:admin /usr/local/Homebrew
+==> /usr/bin/sudo /bin/mkdir -p /Users/navanchauhan/Library/Caches/Homebrew
+==> /usr/bin/sudo /bin/chmod g+rwx /Users/navanchauhan/Library/Caches/Homebrew
+==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan /Users/navanchauhan/Library/Caches/Homebrew
+==> Downloading and installing Homebrew...
+remote: Enumerating objects: 47, done.
+remote: Counting objects: 100% (47/47), done.
+remote: Compressing objects: 100% (19/19), done.
+remote: Total 47 (delta 28), reused 47 (delta 28), pack-reused 0
+Unpacking objects: 100% (47/47), 6.11 KiB | 223.00 KiB/s, done.
+From https://github.com/Homebrew/brew
+ + 18ebdd8c8f...67a096fcbb tapioca-compiler-for-tty-rbi -> origin/tapioca-compiler-for-tty-rbi  (forced update)
+Switched to and reset branch 'stable'
+==> Updating Homebrew...
+==> Installation successful!
+
+==> Homebrew has enabled anonymous aggregate formulae and cask analytics.
+Read the analytics documentation (and how to opt-out) here:
+  https://docs.brew.sh/Analytics
+No analytics data has been sent yet (nor will any be during this install run).
+
+==> Homebrew is run entirely by unpaid volunteers. Please consider donating:
+  https://github.com/Homebrew/brew#donations
+
+==> Next steps:
+- Run these two commands in your terminal to add Homebrew to your PATH:
+    (echo; echo 'eval "$(/usr/local/bin/brew shellenv)"') >> /Users/navanchauhan/.zprofile
+    eval "$(/usr/local/bin/brew shellenv)"
+- Run brew help to get started
+- Further documentation:
+    https://docs.brew.sh
+```
+
+At this point, you don't need to edit your `zshrc` or `zsh_profile`.
+
+### Install pyenv
+
+The reason we are installing pyenv is because it is easier to build Python 2.7.18 from scratch than messing around with codesigning and quarantine bs on macOS.
+
+```bash
+➜  scrippstuff brew install pyenv
+==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36
+############################################################################################################################################################### 100.0%
+==> Fetching dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
+############################################################################################################################################################### 100.0%
+==> Fetching m4
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
+############################################################################################################################################################### 100.0%
+==> Fetching autoconf
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
+############################################################################################################################################################### 100.0%
+==> Fetching ca-certificates
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
+############################################################################################################################################################### 100.0%
+==> Fetching openssl@3
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
+############################################################################################################################################################### 100.0%
+==> Fetching pkg-config
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
+############################################################################################################################################################### 100.0%
+==> Fetching readline
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4
+############################################################################################################################################################### 100.0%
+==> Fetching pyenv
+==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba
+############################################################################################################################################################### 100.0%
+==> Installing dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline
+==> Installing pyenv dependency: m4
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json
+==> Pouring m4--1.4.19.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/m4/1.4.19: 13 files, 739.9KB
+==> Installing pyenv dependency: autoconf
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json
+==> Pouring autoconf--2.72.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/autoconf/2.72: 71 files, 3.6MB
+==> Installing pyenv dependency: ca-certificates
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json
+==> Pouring ca-certificates--2024-03-11.all.bottle.tar.gz
+==> Regenerating CA certificate bundle from keychain, this may take a while...
+🍺  /usr/local/Cellar/ca-certificates/2024-03-11: 3 files, 229.6KB
+==> Installing pyenv dependency: openssl@3
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json
+==> Pouring openssl@3--3.2.1.sonoma.bottle.1.tar.gz
+🍺  /usr/local/Cellar/openssl@3/3.2.1: 6,874 files, 32.5MB
+==> Installing pyenv dependency: pkg-config
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json
+==> Pouring pkg-config--0.29.2_3.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/pkg-config/0.29.2_3: 11 files, 656.4KB
+==> Installing pyenv dependency: readline
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json
+==> Pouring readline--8.2.10.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/readline/8.2.10: 50 files, 1.7MB
+==> Installing pyenv
+==> Pouring pyenv--2.3.36.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/pyenv/2.3.36: 1,158 files, 3.4MB
+==> Running `brew cleanup pyenv`...
+Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
+Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
+```
+
+And, build the last version of Python 2.7
+
+```bash
+➜  scrippstuff PYENV_ROOT="~/Developer/scrippstuff" pyenv install 2.7.18
+python-build: use openssl from homebrew
+python-build: use readline from homebrew
+Downloading Python-2.7.18.tar.xz...
+-> https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz
+Installing Python-2.7.18...
+patching file configure
+patching file configure.ac
+patching file setup.py
+patching file 'Mac/Tools/pythonw.c'
+patching file setup.py
+patching file 'Doc/library/ctypes.rst'
+patching file 'Lib/test/test_str.py'
+patching file 'Lib/test/test_unicode.py'
+patching file 'Modules/_ctypes/_ctypes.c'
+patching file 'Modules/_ctypes/callproc.c'
+patching file 'Modules/_ctypes/ctypes.h'
+patching file 'Modules/_ctypes/callproc.c'
+patching file setup.py
+patching file 'Mac/Modules/qt/setup.py'
+patching file setup.py
+python-build: use readline from homebrew
+python-build: use zlib from xcode sdk
+Installed Python-2.7.18 to /Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18
+```
+
+Test the new installation:
+
+```bash
+➜  scrippstuff ~/Developer/scrippstuff/\~/Developer/scrippstuff/versions/2.7.18/bin/python2.7
+Python 2.7.18 (default, Mar 28 2024, 20:47:13)
+[GCC Apple LLVM 15.0.0 (clang-1500.1.0.2.5)] on darwin
+Type "help", "copyright", "credits" or "license" for more information.
+>>> from random import randint
+>>> randint(0,10)
+6
+>>> exit()
+```
+
+Now, we can compress this newly created Python version into a `tar.gz` file to replace the one provided in ADFRsuite_x86_64Darwin_1.0.tar.gz. Don't forget the `.` at the end
+
+```bash
+➜  scrippstuff tar -C ./\~/Developer/scrippstuff/versions/2.7.18 -czf new.tar.gz .
+```
+
+## Install ADFRsuite
+
+If you don't already have the tarball, you can download it by:
+
+```bash
+$ curl -o adfr.tar.gz https://ccsb.scripps.edu/adfr/download/1033/
+```
+
+Uncompress it
+
+```bash
+$ tar -xvzf adfr.tar.gz
+```
+
+Replace the provided Python archive with the one we created:
+
+```bash
+$ cd ADFRsuite_x86_64Darwin_1.0
+$ mv new.tar.gz Python2.7.tar.gz
+```
+
+Note: For some reason simply copying it doesn't work and you need to use `mv`
+
+Just to not mess with anything else, I will be installing everything in a folder called `clean_install`
+
+```bash
+$ mkdir clean_install
+$ ./install.sh -d clean_install
+...
+ ADFRsuite installation complete.
+To run agfr, agfrgui, adfr, autosite, about, pythonsh scripts located at:
+/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin
+add  /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin to the path environment variable in .cshrc or .bashrc:
+.cshrc:
+set path = (/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin $path)
+
+.bashrc:
+export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH
+```
+
+Now, to test `agfr`, first run the command (replacing `navanchauhan` with yout username)
+
+```bash
+$ export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH
+$ agfr
+➜  ADFRsuite_x86_64Darwin_1.0 agfr
+==============================
+*** Open Babel Error  in openLib
+  /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so did not load properly.
+ Error: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so, 0x0009): Library not loaded: /opt/X11/lib/libcairo.2.dylib
+  Referenced from: <24174F3E-2670-79AC-4F26-F8B49774194A> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so
+  Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/usr/local/lib/libcairo.2.dylib' (no such file), '/usr/lib/libcairo.2.dylib' (no such file, not in dyld cache)
+==============================
+```
+
+
+## Fixing `Open Babel Error`
+
+```bash
+$ brew install cairo
+```
+
+## Completing the re-docking tutorial
+
+### Dowbloading the dataset
+
+```bash
+$ curl -o tutorial-data.zip https://ccsb.scripps.edu/adcp/download/1063/
+$ unzip tutorial-data.zip
+$ cd ADCP_tutorial_data/3Q47
+```
+
+### Conversion to PDBQT
+
+```bash
+$ reduce 3Q47_rec.pdb > 3Q47_recH.pdb
+$ reduce 3Q47_pep.pdb > 3Q47_pepH.pdb
+```
+
+### Preparing Receptor
+
+```
+$ prepare_receptor -r 3Q47_recH.pdb
+$ prepare_ligand -l 3Q47_pepH.pdb
+```
+
+### Generate Target File
+
+```bash
+$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+➜  3Q47 agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+Traceback (most recent call last):
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py", line 36, in <module>
+    from ADFR.utils.runAGFR import runAGFR
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py", line 41, in <module>
+    from ADFR.utils.maps import flexResStr2flexRes
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py", line 35, in <module>
+    from ADFRcc.adfr import GridMap
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py", line 34, in <module>
+    from ADFRcc.adfr import Parameters
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py", line 43, in <module>
+    import ADFRcc.adfrcc as CPP
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 28, in <module>
+    _adfrcc = swig_import_helper()
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 24, in swig_import_helper
+    _mod = imp.load_module('_adfrcc', fp, pathname, description)
+ImportError: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so, 0x0002): Library not loaded: /Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib
+  Referenced from: <424BF61E-BF0F-351E-B546-E82EBBD8FBF5> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so
+  Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache)
+➜  3Q47
+```
+
+Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the `libgomp.1.dylib`. I haven't tested using a newer version of GCC to make it work. Building GCC 8 yourself is absolutely painful. We are going to use a copy generated by the homebrew team.
+
+```bash
+$ cd ../../
+$ pwd
+/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0
+$ curl -L -H "Authorization: Bearer QQ==" -o gcc8amd64.tar.gz https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2
+$ tar -xzf gcc8amd64.tar.gz
+$ cp -r gcc@8/8.5.0/lib/gcc/8/* clean_install/lib/
+```
+
+Now, we should be able to go back and run the target generation command:
+
+```bash
+$ cd ADCP_tutorial_data/3Q47
+$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+#################################################################
+# If you used AGFR in your work, please cite:                   #
+#                                                               #
+# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #
+# M.F. Sanner                                                   #
+# AutoDockFR: Advances in Protein-Ligand Docking with           #
+...
+```
+
+### Docking Peptide
+
+```bash
+$ adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb
+```
+
+There you have it. Running ADCP on the newest macOS version against all odds.
+
+I haven't yet looked into fixing/patching `agfrgui` as I don't use the software. But, if someone reallllly needs to run it on Apple Silicon, I am happy to take a look at monkeypatching it.
+
+In case years down the line the prebuilt version of GCC 8 is not available, let me know so I can replace the link with my mirror.