OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Molecular Moldeling/Molecular Docking

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using for example scoring functions. Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Given the biological and pharmaceutical significance of molecular docking, considerable efforts have been directed towards improving the methods used to predict docking. Molecular docking can be categorized into two main kinds as following: Rigid-flexible docking (also rigid docking) is the molecular docking which allows only ligand (donor or small molecule) to change its orientation (depending on its torsional degree of freedom) during docking calculation. Flexible-flexible docking (also flexible docking), in addition to rigid docking, macromolecule (protein enzyme) also change its orientation, especially around active site.

## Molecular Docking Based Theory

Docking is based on equilibrium equation as following:
Binding energy indicates how good macromolecule and ligand can bind each other. Thus, even more negative binding energy, even more strength in binding between two molecules takes place. To succeed this case, K$_b$ should be great or K$_d$ should be low.

## Scoring Function

Scoring functions are the answer to the first question, “How to calculate the interactions?” They can tell “how good” a ligand of specific conformation can bind to a receptor. Since the interaction between a ligand and a receptor is a “function of their conformations”, researchers have ideas of trying to “approximate the function” as closely as they can. The approximating functions constructed are called “scoring functions” which can be classified into two main group.
The first group of functions contains scoring schemes based on physical interaction terms, such as Van der Waals interactions or hydrogen bonding. The binding interaction is calculated by the Lennard-Jones pair potential.
# Structural Biochemistry/Molecular Modeling/Molecular Docking
## Overview

In studying enzyme catalysis, an important factor to understand is how the substrate and enzyme interact with each other. The affinity of the substrate to the enzyme is a deciding factor to whether or not the binding in the active site occurs. There are many things that affect the affinity of the substrate to the enzyme. The surface, complementarily, flexibility and non-covalent charges are all important factors. Another influencing factor includes the orientation of the molecule. Molecular modeling is a technique used in computational chemistry, computational biology and material science to mimic the behavior of molecules to further understand its systems and how they bind to each other. A type of molecular modeling is docking. Molecular docking is a method that predicts the preferred orientation of a molecule when it binds to another molecule. It uses computers to create a 3D image of two molecules and shows how they fit together. Knowing the preferred orientation that a molecule has for another can help predict the strength of binding affinity that a substrate will have for an enzyme. A common application that molecular modeling is used for is drug design. When creating a new drug for a certain disease, molecular docking can be used to predict the binding affinity that the new drug has on the targeted protein. However, there are certain errors that can occur in relying mainly on this approach. For example, while molecular modeling can predict the preferred orientation that a drug may have for a protein, it is not able to effectively account for conformational changes that may occur. But despite this, molecular docking is still a very important technique that helps us further understand the molecular processes that occurs within the molecular level.
# Structural Biochemistry/Motor Systems
## Overview

Sensory systems provide the initial inputs to cognitive processes, and motor systems deliver the physical behavioral output that carries out movements. All body movements are generated by the stimulation of skeletal muscle fibers by the lower motor neurons- neurons whose cell bodies are located in the brain stem and spinal cord. The activation of lower motor neurons is coordinated by local circuits consisting of inter neurons, also located in the spinal cord and brainstem. Complex reflecxes and rhythmic locomotor movements can be generated and sustained by the coordinated activation of such local circuits in the absence of inputs from higher motor centers. At higher levels of the motor system, upper motor neurons in the cerebral cortex and brainstem provide descending control of local circuitry in the spinal cord and brain stem. The other two parts, the cerebellum and basal ganglia, modulate the activity of upper motor neurons in order to make online corrections in response to perturbations in ongoing movements and to help initiate goal directed movements.

## Reference

Levinthal, Charles, "Drugs, Behavior, and Modern Society", Pearson Education, Inc., 2008 Purves, Dale, "Principles of Cognitive Neuroscience", Sinauer Associates, Inc., 2008
# The Legend of Zelda: Oracle of Seasons/Walkthrough

As you will see in the opening sequence, the Triforce calls Link to Hyrule Castle and warps him to the land of Holodrum. The game starts out with Link waking up in an open field. He will soon meet a dancer named Din (the oracle of seasons). Suddenly after dancing with Din, General Onox will kidnap Din.

## Guide structure

Oracle of Seasons can be subdivided into eight main chapter (plus introduction and final chapter). Each chapter is characterized by a dungeon. Anyway, the name of each dungeon appears only once in the game, after the hero found it. On the other hand, during his quest to find the dungeon entrance, Link will be told many times the name of the corresponding surface area instead.
Therefore, it is much more useful to specify not just the dungeon name, but also the name of the area where it is located.
| Holodrum area | Dungeon name | Page |
| North Horon | Gnarled Root Dungeon | North Horon and Gnarled Root Dungeon |
| Woods of Winter | Snake's Remains | Woods of Winter and Snake's Remains |
| Spool Swamp | Poison Moth's Lair | Spool Swamp and Poison Moth's Lair |
| Mount Cucco | Dancing Dragon Dungeon | Mount Cucco and Dancing Dragon Dungeon |
| Eyeglass Lake | Unicorn's Cave | Eyeglass Lake and Unicorn's Cave |
| Tarm Ruins | Ancient Ruins | Tarm Ruins and Ancient Ruins |
| Graveyard | Explorer's Crypt | Graveyard and Explorer's Crypt |
| Temple Remains | Sword and Shield Maze | Temple Remains and Sword & Shield Dungeon |

### Linked games

Two different linked games can be played:
* Oracle of Seasons first, Oracle of Ages then: all information specific to this option is written in the page Secrets to and from Labrynna
* Oracle of Ages first, Oracle of Seasons then: all information specific to this option is written in sidebars in the main guide.
The extra final dungeon, identical in both versions, is described in the page Room of Rites
# The Legend of Zelda: The Minish Cap/Characters/Minish

In The Legend of Zelda: The Minish Cap, the Minish (known as Picori for the Hylian) are the thumb-sized people living in Hyrule.
They came from another world, through a portal that only opens every 100 years, and they are the ones hiding items in tall grass, under rocks and so on. They do this to make people happy.
# The Legend of Zelda: The Minish Cap

This is a Wikibook on the Game Boy Advance game, The Legend of Zelda: The Minish Cap.

## Table of contents

* Characters
** Ezlo
** Minish
* Weapons and items
** Kinstone
# The Legend of Zelda: The Minish Cap/Items/Kinstone

Kinstones are special artifacts first introduced in The Legend of Zelda: The Minish Cap which Link can find throughout his quest. They are kept in bags called Kinstone Bag. You receive the bag for free after you completed the first dungeon. Kinstones are generally green, blue or red although they can be gold if they are '"fused" with the wall.

## Fusing Kinstones

By pressing L, it allows the player to "fuse Kinstones" with non-player characters (NPCs) in the game. Two kinstones with complementary shapes be combined to form a coin. If the player can find the NPCs who possess a kinstone complementary to his, he can perform Kinstone Fusion, which causes special events to happen. For example, fusing Kinstones can reveal a secret passageway in a different area, or make a treasure chest appear.
# The Legend of Zelda: The Minish Cap/Characters/Ezlo

Ezlo is a character from the The Minish Cap He is Primarily a Craftsman of the Minish race but was turned into a Duck like hat by the Wind Mage Vaati. He serves as a Guide throughout the Game and helps Link with Various Tasks.

## Storyline

Ezlo is first encountered by Link being attacked by two octorocks inside the Minish Woods. Upon saving him Ezlo decides to accompany Link on his quest. Because he is unable to move very fast, having no legs, throughout the adventure he rides on top of Link's head like a hat.
Later in the game, it is revealed that Ezlo was once a highly skilled Minish Craftsman who created a magical cap with the power to grant wishes. However, his young apprentice (Vaati) stole the cap and used it to turn himself into a powerful sorcerer and transform Ezlo into his hat-like form.
At the end of the Game Ezlo is transformed back to normal and gives Link a new hat as a parting gift.

## Abilities

As a Minish he was able to create a magical cap that granted wishes, but he can do very little in his hat form.
Upon finding a Minish portal (A disguised object that allows one to change size) Ezlo is able to transform Link to the size of a Minish to let him explore areas where only someone the size of a bug can. Ezlo is very knowledgeable and is able to aid Link with information on the various places around Hyrule. He can also be used as a parachute when Link Jumps into a Whirlwind.
He is also one of the few Picori that can speak Hylian without use of the Jabber Nut.

## External links

* Ezlo at Zelda Wiki, a Zelda centric Wiki on Fandom.
* Ezlo at Zelda Dungeon.
# The Zope 3 Book

This book is about Zope 3, a Python framework for web application development. Zope 3 was developed by the Zope community with the leadership of Jim Fulton, the creator of original Zope. Zope 3 consists of a number of small frameworks and libraries written in Python programming language and it is usable in pieces or in whole. These frameworks and libraries can be put together to build any kind of web application. Most of the Zope 3 packages are built on top of a component architecture which helps to separate presentation code from the problem domain code and to create reusable components.
The goal for this project is to create a complete, free, open-content, well-organized book for Zope 3. The target audience of this book are Python programmers looking for developing web applications. However, the book doesn't assume you are familiar with any other web framework. This book will require prior knowledge Python programming language and at least some exposure to the basics of HTML, CSS and JavaScript.

## Table of Contents

* Introduction
* Getting Started
* Interfaces
* Component Architecture
* Unit Testing
* Content Components
* Functional Testing
* Resources
* Browser Views
* Skins and Layers
* Advanced Views
* Basic Security
* Schemas
* Forms
* Authentication
* Annotations
* Traversers
* Events
* Catalogs and Indices

## Appendices

* Setuptools and eggs
* Buildout
* Virtualenv

## Appendices

* Resources
* Glossary
# The Zope 3 Book/Buildout
## What is Buildout ?

From the buildout.zope.org site: Buildout is a system for managing development buildouts. While often identified as a Zope project, and indeed licensed under the ZPL by Zope creator Jim Fulton, buildout is useful for configurations beyond Zope, and even, in rare cases, a few that have nothing to do with Python.
# The Zope 3 Book/Preface

This book is about Zope 3, a Python framework for web application development. Zope 3 was developed by the Zope community with the leadership of Jim Fulton, the creator of original Zope. Zope 3 consists of a number of small frameworks and libraries written in Python programming language and it is usable in pieces or in whole. These frameworks and libraries can be put together to build any kind of web application. Most of the Zope 3 packages are built on top of a component architecture which helps to separate presentation code from the problem domain code and to create reusable components.
The goal for this project is to create a complete, free, open-content, well-organized book for Zope 3. The target audience of this book are Python programmers looking for developing web applications. However, the book doesn't assume you are familiar with any other web framework. This book will require prior knowledge Python programming language and at least some exposure to the basics of HTML, CSS and JavaScript.
# The animals speak/A lemur is born

(Greater bamboo lemur, Prolemus simus)

### The very little bamboo lemur

He was born on May 15, 2017.
# Wings 3D/Useful links

The homepage of Wings3D
The Wings3D forum
Subject:Blender 3D
Bay Raitt and Greg Minters's article "Digital Sculpture Techniques"
# Real Analysis/Compact Sets

Definition of compact set If any set has a open cover and containing finite subcover than it is compact

## Definition

Let (X, d) be a metric space and let A ⊆ X. We say that A is compact if for every open cover {U$_λ$}$_{λ∈Λ}$ there is a finite collection U$_{λ1}$, …,U$_{λk}$ so that $\textstyle A\subseteq \bigcup _{i=1}^{k}U_{\lambda _{i}}$. In other words a set is compact if and only if every open cover has a finite subcover. There is also a sequential definition of compact set. A set A in the metric space X is called compact if every sequence in that set have a convergent subsequence.

## Theorem

Let A be a compact set in $R^{n}$ with usual metric, then A is closed and bounded.

## Theorem (Heine-Borel)

If $\textstyle X=\mathbb {R} ^{n}$, with the usual metric, then every closed and bounded subset of X is compact.
# Real Analysis/Bibliography

| ←Landau notation | Real Analysis Bibliography | Index→ |
This Wikibook is written by Wikibookians who were inspired by other books. The list is provided below.
* J. K. Hunter and B. Nachtergaele (2001) Applied Analysis World Scientific Publishing, Singapore
* W. Rudin (1953) Principles of mathematical analysis. 3ed. McGraw-Hill Inc. New York
* David A. Sprecher (1970) Elements of Real Analysis Dover Publications, Mineola, New York
* R.G. Bartle, D.R. Sherbert, (2000) Introduction to Real Analysis 3ed. John Wiley & Sons
* M. Longo, V. Valori, The Comparison Test — Not Just for Nonnegative Series, Mathematics Magazine, Volume 79, Number 3, June 2006, pp. 205-210(6)
* Spivak, Michael (2008). Calculus (4th ed.). PMB 377, 1302 Waugh Drive, Houston, Texas: Publish or Perish, Inc. ISBN 978-0-914098-91-1.{{cite book}}: CS1 maint: location (link)
# Real Analysis/Connected Sets

Intuitively, the concept of connectedness is a way to describe whether sets are "all in one piece" or composed of "separate pieces". For motivation of the definition, any interval in $\mathbb {R}$ should be connected, but a set $A$ consisting of two disjoint closed intervals $[a,b]$ and $[c,d]$ should not be connected.
    Definition A set in $A$ in $\mathbb {R} ^{n}$ is connected if it is not a subset of the disjoint union of two open sets, both of which it intersects.
    Alternative Definition A set $X$ is called disconnected if there exists a continuous, surjective function $f:X\to \{0,1\}$, such a function is called a disconnection. If no such function exists then we say $X$ is connected.
    Examples The set $[0,2]$ cannot be covered by two open, disjoint intervals; for example, the open sets $(-1,1)$ and $(1,2)$ do not cover $[0,2]$ because the point $x=1$ is not in their union. Thus $[0,2]$ is connected.
    However, the set $\{0,2\}$ can be covered by the union of $(-1,1)$ and $(1,3)$, so $\{0,2\}$ is not connected.

## Path-Connected

A similar concept is path-connectedness.
    Definition A set is path-connected if any two points can be connected with a path without exiting the set.
A useful example is $\mathbb {R} ^{2}\setminus \{(0,0)\}$. Any two points a and b can be connected by simply drawing a path that goes around the origin instead of right through it; thus this set is path-connected. However, $\mathbb {R} \setminus \{0\}$ is not path-connected, because for $a=-3$ and $b=3$, there is no path to connect a and b without going through $x=0$.
As should be obvious at this point, in the real line regular connectedness and path-connectedness are equivalent; however, this does not hold true for $\mathbb {R} ^{n}$ with $n>1$. When this does not hold, path-connectivity implies connectivity; that is, every path-connected set is connected.

## Simply Connected

Another important topic related to connectedness is that of a simply connected set. This is an even stronger condition that path-connected.
    Definition A set $A$ is simply-connected if any loop completely contained in $A$ can be shrunk down to a point without leaving $A$.
An example of a Simply-Connected set is any open ball in $\mathbb {R} ^{n}$. However, the previous path-connected set $\mathbb {R} ^{2}\setminus \{(0,0)\}$ is not simply connected, because for any loop p around the origin, if we shrink p down to a single point we have to leave the set at $(0,0)$.
# Real Analysis/Arc Length

| ←Total Variation | Real Analysis Arc Length | Exponential Function→ |
Suppose we have a parametric curve in three dimensions, $f(t)=(x_{1}(t),x_{2}(t),x_{3}(t))$. Of course, it would be required that all three functions be continuous. This essentially defines a curve, since it is a continuous image of the real numbers onto the real 3-space.
Now, we can define the arc length of this curve over an interval. Say the interval is [a,b]. Now divide [a,b] into partitions, $a=a_{0}<a_{1}<a_{2}<a_{3}<...<a_{n}=b$, and call this partition P. Take the sum of the distances $|f(a_{n})-f(a_{n-1})|$, to get $\sum _{i=1}^{n}{\sqrt {\sum _{j=1}^{3}(x_{j}(a_{i})-x_{j}(a_{i-1}))^{2}}}$, and call this sum L(P). Now, take the supremum of the lengths, $\sup\{L(P)\in R|P$ is a partition$\$. If this number is finite, we call it a rectifiable curve.
Now we establish a sufficient and necessary condition for a curve in 3-space to be rectifiable (note: this can easily be extended to an n-space through an analogous argument).
Theorem: A continuous curve in three dimensions is rectifiable if and only if all of its component functions are functions of bounded variation. Proof:
Theorem: If a curve f(x) in 3-space is continuously differentiable in all 3 components, then it is rectifiable and the length from f(a) to f(b) is $\int _{a}^{b}|f'(x)|dx$. Proof:
# Real Analysis/Authors
## Authors

Martín Smith-Martínez SPat A Hypercube SharingNotes
# Role Playing Games/Printable version

The current, editable version of this book is available in Wikibooks, the open-content textbooks collection, at
https://en.wikibooks.org/wiki/Role_Playing_Games

# Overview
## Introduction

This Wikibook aims to offer a general overview of Role Playing games, also simply known as RPGs for short. If you are looking for new games to play, or which system to choose, then this is not the Wikibook for you. However if you are interested in learning what an RPG is for the first time, or are an RPG veteran looking for more info on the genre, this is the Wikibook for you! Most of this will be about video games, but there are parts about Text Adventures, Dungeons and Dragons, and more.

## About the Author

In case you are wondering of my "Web name" you can refer to me as MyFatSon (strange, isn't it).

# Introduction

This is an introduction to all RPGs (Role Playing games). What is an RPG? and why they are so fun? Well, an RPG is a genre of book, game, or anything else that you play a ROLE in. RPGs are probably the most common genres in the video game industry, and definitely the most recognized.

# Types of RPGs
## Settings

One common way of differentiating RPG is by setting. Common settings are Science Fiction, Contemporary, Historical, Fantasy, or some mixture of these.
For example, Mass Effect and Cyberpunk 2020 are science fiction series. The Fallout series is primarily science fiction, with light touches of Fantasy. A game like Shadowrun is nearly half science fiction and half fantasy.
Some games take place in a setting which is either meant to mirror the real world, or at least be similar to it, such as The Escapist or to a lesser extent Heavy Rain. A game like Vampire: The Masquerade uses both a contemporary setting and a fantasy setting, and integrates separation between the two into gameplay.
Some fantasy RPGs include a typical game of Dungeons and Dragons. This genre also includes Dragon Age and The Elder Scrolls, among other series.
Next to discuss is Text Adventures.
# Roman Culture

* Geography, Environment and Demographics (including census and, birth / death rates).
* Law & Government (provinces, popular reception of government, citizenship, monarchy to empire, crime & punishment, gangs, oratory)
* Early Republic
* Military (wars: Punic: Battle of Cannae, civil; Hannibal and The Second Punic War; navy; legions: Marian Reforms & Recruitment; equipment: personal, war machines; Military Strategy and Tactics, Roman Army; Roman Navy Ships, Military Organization and Leadership, Octavian's Civil War)
* Life Course (age groups, appropriate activities, etc.)
* Domestic Life (textiles, Jewelry, familial organization, sleeping, eating, Dining, working)
* Agriculture (farming, livestock, domestication)
* Economy (economic status, occupations, trade, Coinage, business regulations, poverty v. wealth, mines)
* Education (schools, teachers, students, books, curricula).
* Entertainment (Gladiators & Chariot racing, Spartacus, Game Venues, gambling)
* Religion (Roman Religion and Ritual, calendar holidays, Dionysus, Constantine and early Christianity, sacrifices, public cults, augury & magic, funerals)
* Philosophy (stoics).
* Mythology (heroes (Achilles), Roman Myths (Origin myths, Jupiter, Mars, Venus, Juno).
** Images of Aeneas
** Images of Minerva
** Images of Bacchus
* Literature (poetry, plays, prose)
* Art & Architecture (temples, famous craftspeople, styles, Pompeiian paintings, The Roman House, baths, necropolis, graffiti, Greek & Etruscan influence)
* Technology (Medicine, aqueducts, roads, arches, cement, city-planning, metallurgy, sewage, glass, heating/cooling, lighting, writing & Musical Instruments of Rome)
* Sex & Gender (prostitution, women; Mother; Homosexuality)
* Slavery
* Non-Romans (alliances, enemies, Carthage, Latin & Italian relations, languages spoken, Greece, Eturia)
* Illustri Viri
** Marcus Tullius Cicero
* Modern Reception (ruins)