Merge pull request #17 from ljvmiranda921/update-readme

Update readme using LaTeX assets

.gitignore

@@ -3,6 +3,13 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# TeX files
+*.aux
+*.fdb_latexmk
+*.fls
+*.pdf
+*.synctex.gz
+
 # Ipython notebooks
 .ipynb_checkpoints
 

README.md

@@ -49,7 +49,7 @@ Given a sequence of *H* and *P* molecules, find a configuration with the
 highest number of adjacent **H-H** pairs. Your base score is determined by
 the number of **H-H** pairs you can create.
 
-<img src="/assets/pfolding_problem.svg" width="700">
+<img src="./assets/overview.png" width="600">
 
 
 ### Folding Rules
@@ -64,7 +64,7 @@ protein conformation. For our purposes, here it is in its simplest form:
 3. Assigning a molecule to an occupied space will incur a penalty.
 4. Trapping yourself and running out of moves will give you a heavy deduction.
 
-<img src="/assets/pfolding_rules.svg" width="700">
+<img src="./assets/rules.png" width="700">
 
 ## Basic Usage
 

assets/figures/actions_adjacent.tex

@@ -0,0 +1,31 @@
+% ==================================================
+% Asset file for gym-lattice
+% Author: Lester James V. Miranda
+
+\begin{tikzpicture}[
+ latticegrid/.style={very thin,gray!40,step=10mm},
+ container/.style={draw,white,minimum width=30mm, minimum height=24mm},
+ hydrophobic/.style={circle,fill=black,text=white},
+ polar/.style={circle,fill=white,text=black},
+ unknown/.style={circle,red,thick,text=red,dashed},
+ new/.style={circle,thick,text=black,dashed},
+ hbonds/.style={very thick,red},
+ bonds/.style={->,thick,black}
+]
+
+% Draw grid
+\node[container] (lattice) {};
+\draw[latticegrid] (lattice.south west) grid (lattice.north east);
+
+% Draw molecules
+\draw[hydrophobic] ($(lattice.center)+(0,0)$) circle (4mm) node (s0) {H};
+\draw[hydrophobic] ($(lattice.center)+(-10mm,0mm)$) circle (4mm) node (s1) {H};
+\draw[polar] ($(lattice.center)+(-10mm,10mm)$) circle (4mm) node (s2) {P};
+\draw[bonds] (s0) -- (s1);
+\draw[bonds] (s1) -- (s2);
+
+% Draw new and unknown
+\draw[new] ($(lattice.center)+(0mm,10mm)$) circle (4mm) node (legal) {\checkmark};
+\draw[unknown] ($(lattice.center)+(10mm,-10mm)$) circle (4mm) node (unk) {X};
+
+\end{tikzpicture}

assets/figures/actions_collision.tex

@@ -0,0 +1,41 @@
+% ==================================================
+% Asset file for gym-lattice
+% Author: Lester James V. Miranda
+
+\begin{tikzpicture}[
+ latticegrid/.style={very thin,gray!40,step=10mm},
+ container/.style={draw,white,minimum width=30mm, minimum height=24mm},
+ hydrophobic/.style={circle,fill=black,text=white},
+ polar/.style={circle,fill=white,text=black},
+ unknown/.style={circle,red,thick,text=black,dashed},
+ new/.style={circle,thick,text=black,dashed},
+ hbonds/.style={very thick,red},
+ bonds/.style={->,thick,black},
+ collision/.style={->,very thick, red}
+]
+
+% Draw grid
+\node[container] (lattice) {};
+\draw[latticegrid] (lattice.south west) grid (lattice.north east);
+
+% Draw molecules
+\draw[hydrophobic] ($(lattice.center)+(0,0)$) circle (4mm) node (s0) {H};
+\draw[hydrophobic] ($(lattice.center)+(-10mm,0mm)$) circle (4mm) node (s1) {H};
+\draw[polar] ($(lattice.center)+(-10mm,10mm)$) circle (4mm) node (s3) {P};
+\draw[hydrophobic] ($(lattice.center)+(0mm,10mm)$) circle (4mm) node (s4) {H};
+\draw[polar] ($(lattice.center)+(10mm,10mm)$) circle (4mm) node (s5) {P};
+\draw[polar] ($(lattice.center)+(10mm,0mm)$) circle (4mm) node (s6) {P};
+
+% Bonds
+\draw[bonds] (s0) -- (s1);
+\draw[bonds] (s1) -- (s3);
+\draw[bonds] (s3) -- (s4);
+\draw[bonds] (s4) -- (s5);
+\draw[bonds] (s5) -- (s6);
+\draw[hbonds] (s0) -- (s4);
+
+% Draw Collision
+\draw[collision] (s6) -- (s0) node[below=0.50 and -0.6] {Collision!};
+
+\end{tikzpicture}
+

assets/figures/actions_ldur.tex

@@ -0,0 +1,29 @@
+% ==================================================
+% Asset file for gym-lattice
+% Author: Lester James V. Miranda
+
+\begin{tikzpicture}[
+ latticegrid/.style={very thin,gray!40,step=10mm},
+ container/.style={draw,white,minimum width=30mm, minimum height=24mm},
+ hydrophobic/.style={circle,fill=black,text=white},
+ polar/.style={circle,fill=white,text=black},
+ unknown/.style={circle,red,thick,text=black,dashed},
+ new/.style={circle,thick,text=black,dashed},
+ hbonds/.style={very thick,red},
+ bonds/.style={->,thick,black}
+]
+
+% Draw grid
+\node[container] (lattice) {};
+\draw[latticegrid] (lattice.south west) grid (lattice.north east);
+
+% Draw molecules
+\draw[hydrophobic] ($(lattice.center)+(0,0)$) circle (4mm) node (h0) {H};
+
+% Possible actions
+\draw[new] ($(lattice.center)+(10mm,0mm)$) circle (4mm) node (h0) {\checkmark};
+\draw[new] ($(lattice.center)+(-10mm,0mm)$) circle (4mm) node (h0) {\checkmark};
+\draw[new] ($(lattice.center)+(0mm,10mm)$) circle (4mm) node (h0) {\checkmark};
+\draw[new] ($(lattice.center)+(0mm,-10mm)$) circle (4mm) node (h0) {\checkmark};
+
+\end{tikzpicture}

assets/figures/actions_trap.tex

@@ -0,0 +1,43 @@
+% ==================================================
+% Asset file for gym-lattice
+% Author: Lester James V. Miranda
+
+\begin{tikzpicture}[
+ latticegrid/.style={very thin,gray!40,step=10mm},
+ container/.style={draw,white,minimum width=30mm, minimum height=24mm},
+ hydrophobic/.style={circle,fill=black,text=white},
+ polar/.style={circle,fill=white,text=black},
+ unknown/.style={circle,red,thick,text=black,dashed},
+ new/.style={circle,thick,text=black,dashed},
+ hbonds/.style={very thick,red},
+ bonds/.style={->,thick,black},
+ collision/.style={->,very thick, red}
+]
+
+% Draw grid
+\node[container] (lattice) {};
+\draw[latticegrid] (lattice.south west) grid (lattice.north east);
+
+% Draw molecules
+\draw[hydrophobic] ($(lattice.center)+(-10mm,-10mm)$) circle (4mm) node (s0) {H};
+\draw[hydrophobic] ($(lattice.center)+(-10mm,0mm)$) circle (4mm) node (s1) {H};
+\draw[polar] ($(lattice.center)+(-10mm,10mm)$) circle (4mm) node (s2) {P};
+\draw[hydrophobic] ($(lattice.center)+(0mm,10mm)$) circle (4mm) node (s3) {H};
+\draw[hydrophobic] ($(lattice.center)+(10mm,10mm)$) circle (4mm) node (s4) {H};
+\draw[hydrophobic] ($(lattice.center)+(10mm,0mm)$) circle (4mm) node (s5) {H};
+\draw[polar] ($(lattice.center)+(10mm,-10mm)$) circle (4mm) node (s6) {P};
+\draw[hydrophobic] ($(lattice.center)+(0mm,-10mm)$) circle (4mm) node (s7) {H};
+\draw[polar] ($(lattice.center)+(0mm,0mm)$) circle (4mm) node (s8) {P};
+
+% Bonds
+\draw[bonds] (s0) -- (s1);
+\draw[bonds] (s1) -- (s2);
+\draw[bonds] (s2) -- (s3);
+\draw[bonds] (s3) -- (s4);
+\draw[bonds] (s4) -- (s5);
+\draw[bonds] (s5) -- (s6);
+\draw[bonds] (s6) -- (s7);
+\draw[bonds] (s7) -- (s8);
+
+\end{tikzpicture}
+

assets/figures/demo_lattice.tex

@@ -0,0 +1,59 @@
+% ==================================================
+% Asset file for gym-lattice
+% Author: Lester James V. Miranda
+
+\begin{tikzpicture}[
+ node distance=20mm,
+ agent/.style={draw,rounded corners,thick,color=black,fill=white},
+ latticegrid/.style={very thin,gray!40,step=10mm},
+ container/.style={draw,white,minimum width=45mm, minimum height=45mm},
+ hydrophobic/.style={circle,fill=black,text=white},
+ polar/.style={circle,fill=white,text=black},
+ unknown/.style={circle,red,thick,text=black,dashed},
+ new/.style={circle,thick,text=black,dashed},
+ hbonds/.style={very thick,red},
+ bonds/.style={->,thick,black},
+ collision/.style={->,very thick, red}
+]
+
+
+% Draw grid
+\node[container,label={[align=center,yshift=0.6cm]
+ Find a configuration\\
+ with the highest number\\
+ of H-H pairs (\textcolor{red}{red} line)}] (lattice) {};
+\draw[latticegrid] (lattice.south west) grid (lattice.north east);
+
+% Draw molecules
+\draw[hydrophobic] ($(lattice.center)+(-10mm,10mm)$) circle (4mm) node (s1) {H};
+\draw[hydrophobic] ($(lattice.center)+(-10mm,0mm)$) circle (4mm) node (s2) {H};
+\draw[hydrophobic] ($(lattice.center)+(-10mm,-10mm)$) circle (4mm) node (s3) {H};
+\draw[polar] ($(lattice.center)+(0mm,-10mm)$) circle (4mm) node (s4) {P};
+\draw[hydrophobic] ($(lattice.center)+(0mm,0mm)$) circle (4mm) node (s5) {H};
+\draw[polar] ($(lattice.center)+(10mm,0mm)$) circle (4mm) node (s6) {P};
+\draw[polar] ($(lattice.center)+(10mm,10mm)$) circle (4mm) node (s7) {P};
+\draw[hydrophobic] ($(lattice.center)+(0mm,10mm)$) circle (4mm) node (s8) {H};
+\draw[hydrophobic] ($(lattice.center)+(0mm,20mm)$) circle (4mm) node (s9) {H};
+
+% Draw bonds
+\draw[bonds] (s1) -- (s2);
+\draw[bonds] (s2) -- (s3);
+\draw[bonds] (s3) -- (s4);
+\draw[bonds] (s4) -- (s5);
+\draw[bonds] (s5) -- (s6);
+\draw[bonds] (s6) -- (s7);
+\draw[bonds] (s7) -- (s8);
+\draw[bonds] (s8) -- (s9);
+\draw[hbonds] (s1) -- (s8);
+\draw[hbonds] (s2) -- (s5);
+\draw[hbonds] (s5) -- (s8);
+
+% Add a node
+\node[agent,text=black, align=center, label={[align=center,yshift=3.0cm]Given a protein sequence,}]
+ (textbox)[left= of lattice]{\Large $HHHPHPPHH$};
+
+% Draw bonds
+\draw[bonds] (textbox.east) -- (lattice.west);
+
+
+\end{tikzpicture}

assets/overview.tex

@@ -0,0 +1,30 @@
+% ==================================================
+% Asset file for gym-lattice
+% Author: Lester James V. Miranda
+%
+% To compile, simpy run:
+% >>> pdflatex -shell-escape rules.tex
+%
+% This creates both .pdf and .svg files that you can
+% see in the README.md
+
+\documentclass[preview,convert={outfile=\jobname.png,density=300}]{standalone}
+
+\usepackage{tikz}
+\usepackage{color}
+\usepackage{subfig}
+
+\renewcommand\familydefault{\sfdefault}
+
+\usetikzlibrary{
+ matrix,shapes,
+ arrows,positioning,
+ calc}
+
+\def\checkmark{
+ \tikz\fill[scale=0.4]
+ (0,.35) -- (.25,0) -- (1,.7) -- (.25,.15) -- cycle;}
+
+\begin{document}
+ \input{./figures/demo_lattice.tex}
+\end{document}