7

I want to achieve something similar to the formula in this image

expected_result

I'm new to chemfig package and I used mol2chemfig webtool to obtain the basic molecule structure and then I modified it manually in order to insert circled and squared entries and the arrow.

This is the code so far:

\documentclass[tikz]{standalone}
\newcommand*\circled[1]{\tikz[baseline=(char.base)]{
            \node[shape=circle,draw,inner sep=0.5pt] (char) {#1};}}
\newcommand*\squared[1]{\tikz[baseline=(char.base)]{
            \node[shape=rectangle,draw,inner sep=2pt] (char) {#1};}}

\usepackage{chemformula}
\usepackage{mol2chemfig}
% bond styling
\setcrambond{2.5pt}{0.4pt}{1.0pt}
\setbondoffset{1pt}
\setdoublesep{2pt}
\setatomsep{16pt}
% print atoms with smaller font and in sans-serif
\renewcommand{\printatom}[1]%
{\fontsize{8pt}{10pt}\selectfont{\ensuremath{\mathsf{#1}}}}%
\begin{document}
\schemestart
\chemname{
\chemfig{
               O% 3
        =[:330]C% 2
                  (
             -[:30]\mcfright{O}{^{\mcfminus}}% 4
                  )
    -[:270,,,2]HC% 1
                  (
       -[:270,,2,1]CH_3% 5
                  )
         -[,,2]O% 6
              -P% 7
                  (
             =[:90]O% 8
                  )
                  (
        -[:270,,,1]OH% 10
                  )
        -[,,,1]OH% 9
}}{fosfoenolpiruvato}
\+
\chemname{
\chemfig{
           \circled{P}% 3
    -[:270]\circled{P}% 2
    -[:270]O% 1
    -[:270]\squared{Rib}% 4
         --\squared{Adenine}% 5
}}{ADP}
\arrow{->[\ch{Mg^2+},\ch{K+}][piruvato chinasi]}
\chemname{
\chemfig{
               O% 3
        =[:330]C% 2
                  (
             -[:30]\mcfright{O}{^{\mcfminus}}% 4
                  )
    -[:270,,,2]HC% 1
                  (
       -[:270,,2,1]CH_3% 5
                  )
         =[,,2]O% 6
}}{piruvato}
\+
\chemname{
\chemfig{
          -\squared{Adenine}% 4
    -[:180]\squared{Rib}% 3
     -[:90]O% 1
     -[:90]\circled{P}%% 2
     -[:90]\circled{P}%% 5
     -[:90]P% 6
              (
         -[:90]\mcfright{O}{^{\mcfminus}}% 7
              )
              (
    -[:180,,,2]^{\mcfminus}O% 8
              )
          =O% 9
}}{ATP}
\schemestop
\end{document}

And this is the result:

first_try

The things that I hope to achieve are:

  • Have the entire equation centered vertically
  • In the 2nd and 4th structures the circles and rectangles are not connected in the right way, i.e. the straight lines don't connect well with the circles and the rectangles
  • The arrow should be longer, or at least the string piruvato chinasi should be placed in two lines (but neither \\ nor \par works)
  • Put in evidence with a box filled with a chosen color a part of the 1st and 4th molecule.

The only requirements are:

  • It should be done with chemfig
  • it should be compatible with PDFLaTeX

Note that in order to compile the code you must download the package mol2chemfig.sty

8

You can achieve the vertical alignment by naming certain nodes with the @{...} syntax and using them as base. Naming nodes also allows you to shade parts of the diagram. I also made the arrow longer. To make your snipped compile, I had to download mol2chemfig.sty. Note that I removed the commands \squared and \circled in favor of a solution that does not nest tikzpictures. Nesting tikzpictures is risky, there is always a risk that at given point something breaks in such a way that it cannot be repaired easily. That's why I'd like to argue that it is better to avoid it.

enter image description here

\documentclass[tikz]{standalone}
\usetikzlibrary{fit}
\usepackage{chemformula}
\usepackage{mol2chemfig}
% bond styling
\setcrambond{2.5pt}{0.4pt}{1.0pt}
\setbondoffset{1pt}
\setdoublesep{2pt}
\setatomsep{16pt}
% print atoms with smaller font and in sans-serif
\renewcommand{\printatom}[1]%
{\fontsize{8pt}{10pt}\selectfont{\ensuremath{\mathsf{#1}}}}%
\begin{document}
\setarrowdefault{0,1.2}
\schemestart[][base]
\chemname{
\chemfig[baseline=(HC1.base)]{ % <- added base
               @{O1}O% 3
        =[:330]C% 2
                  (
             -[:30]@{O2}\mcfright{O}{^{\mcfminus}}% 4
                  )
    -[:270,,,2]@{HC1}HC% 1 % <- added @{HC1}
                  (
       -[:270,,2,1]CH_3% 5 
                  )
         -[,,2]O% 6
              -P% 7
                  (
             =[:90]@{O1}O% 8
                  )
                  (
        -[:270,,,1]@{OH1}OH% 10
                  )
        -[,,,1]O@{OH2}H% 9
}}{fosfoenolpiruvato}
\+
\chemname{
\chemfig[baseline=(P1.base)]{ %<-
           @{P4}{P\strut}% 3
    -[:270]@{P1}{P\strut}% 2 %<-
    -[:270]@{O6}{O}% 1
    -[:270]@{R1}{Rib}% 4
         --@{A1}{Adenine}% 5
}}{ADP}
\arrow(.mid east--.mid west){->[\ch{Mg^2+},\ch{K+}][\begin{tabular}{c}
piruvato\\ chinasi
\end{tabular}]}
\chemname{
\chemfig[baseline=(HC2.base)]{
               O% 3
        =[:330]C% 2
                  (
             -[:30]\mcfright{O}{^{\mcfminus}}% 4
                  )
    -[:270,,,2]@{HC2}HC% 1
                  (
       -[:270,,2,1]CH_3% 5
                  )
         =[,,2]O% 6
}}{piruvato}
\+
\chemname{
\chemfig[baseline=(P2.base)]{
          -[:180]@{A2}{Adenine}% 4
    -[:180,2]@{R2}{Rib}% 3
     -[:90]O% 1
     -[:90]@{P2}{P\strut}%% 2
     -[:90]@{P5}{P\strut}%% 5
     -[:90]@{P3}P% 6
              (
         -[:90]\mcfright{O}@{O3}{^{\mcfminus}}% 7
              )
              (
    -[:180,,,2]@{O4}^{\mcfminus}O% 8
              )
          =@{O5}O% 9
}}{ATP}
\chemmove{
\node[inner sep=2pt,fill=red,fill opacity=0.2,fit=(OH1) (OH2) (O1)]{};
\node[inner sep=2pt,fill=red,fill opacity=0.2,fit=(P3) (O3) (O4) (O5)]{};
\node[inner sep=1pt,draw,fit=(A1)]{};
\node[inner sep=1pt,draw,fit=(R1)] (R1box){};
\node[inner sep=1pt,draw,fit=(A2)]{};
\node[inner sep=1pt,draw,fit=(R2)]{};
\foreach \X in {1,2,4,5}
{\node[draw,circle,fit=(P\X)]{};}
\draw[thin,-] ([yshift=-1mm]O6.center) -- (R1box);
\draw[thin,-] ([yshift=1.5mm]O6.center) -- (P1);
}
\schemestop
\end{document}
  • Sorry. I forgot to notify that one should download mol2chemfig.sty in order to compile. – gvgramazio Apr 22 '18 at 17:11
  • There is something wrong in nesting tikzpicture? – gvgramazio Apr 22 '18 at 17:12
  • You solved all my troubles exept one: makes the connection with circled and squared atoms better. Thanks. – gvgramazio Apr 22 '18 at 17:14
  • @giusva Sorry, I was offline. I will try to fix it, but this might mean that I will change the way the boxes and circles are drawn. As I mentioned, you are nesting tikzpictures here, and this can have uncontrollable side effects. So I will try to find a safer solution. Yet this may take a short while. – user121799 Apr 22 '18 at 17:50
  • No problem. You already cover almost all my needs. So you suggest to never nest tikzpictures? I never heard of this before. I used this way of drawing boxes and circles because I already using them in other things. A safer solution will sure be appreciated. – gvgramazio Apr 22 '18 at 18:02

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