chemfig and lego-style molecule construction

Question

Many biochemical molecules, such as nucleic acids for example, are composed by nature in a hierarchical fashion from a limited number of building blocks. It would be nice to replicate this approach when typesetting these molecules. In the case of DNA and RNA, a natural approach would be:

1. Define separate structures for ribose, phosphate and the bases (A,C,G,T,U)
2. Derive deoxyribose from ribose
3. Create nucleosides by combining ribose or deoxyribose with each of the bases
4. Write DNA and RNA molecules as alternations of nucleosides and phosphate.

The chemfig package provides a \definesubmol command that allows for the definition of sub-molecules, which can then be substituted into other molecules. However, the package does not provide a built-in mechanism for making the results of such substitutions available as new sub-molecules. So, the question is how to define a command with the following behavior:

% "\derivesubmol" defines the new #1 submol, obtained by replacing all the
%  occurrences of "#3" by "#4" in the code of #2 submol

% arguments: #1 = new submol name, #2 = old submol name,
%            #3 = old substring, #4 = new substring
\newcommand*\derivesubmol[4]{% ...

This description is taken from the code that the package author of chemfig has provided to me by email. An example of his code in action is provided in the answer that I supply below.

To indicate that this question is, indeed, a question, let me add: ???

Answer 1

This answer was provided to me by Christian Tellechea in private correspondence; I post it here for the benefit of other people who may be interested.

\documentclass{minimal}
\usepackage{chemfig,xstring}
\makeatletter

% "\derivesubmol" defines the new #1 submol, obtained by replacing all the
%  occurrences of "#3" by "#4" in the code of #2 submol

% arguments: #1 = new submol name, #2 = old submol name,
%            #3 = old substring, #4 = new substring
\newcommand*\derivesubmol[4]{%
    \saveexpandmode\saveexploremode\expandarg\exploregroups
    \csname @\ifcat\relax\noexpand#2first\else second\fi oftwo\endcsname
        {\expandafter\StrSubstitute\@car#2\@nil}
        {\expandafter\StrSubstitute\csname CF@@#2\endcsname}
    {\@empty#3}{\@empty#4}[\temp@]%
    \csname @\ifcat\relax\noexpand#1first\else second\fi oftwo\endcsname
        {\expandafter\let\@car#1\@nil}
        {\expandafter\let\csname CF@@#1\endcsname}\temp@
    \restoreexpandmode\restoreexploremode
}
\makeatother

\setatomsep{2.5em}
\setcrambond{2pt}{}{}

\definesubmol{rt1}{-[2]rt1}
\definesubmol{rt2}{-[6,.6]rt2}

\definesubmol{ribose}{%
    -[:-90,2]%
        (%
            -[:25,1.176]O%
            -[:-25,1.176]%
        )%
    <[:-45,0.8]%
        (%
          -[0,,,,line width=2pt,shorten <=-.5pt,shorten >=-.5pt]%
              (!{rt2})%
          >[:45,0.8]%
              (!{rt1})%
         )%
}

\definesubmol{phosphate}{-[6,.6]O-[6,1.5]P(-[4,.8]HO)(=[6,0.8]O)-[,1.5]O}

\definesubmol{adenine}{N*5([::-18]-*6(-N=-N=(-NH_2)-)=-N=-)}

\definesubmol{uracil}{N*6(-(=O)-NH-(=O)-=-)}

\def\drawhline{\medbreak\hrulefill\medbreak}
\begin{document}

\chemfig{!{ribose}} \quad\quad The ribose template

\drawhline%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\derivesubmol{deoxyribose}{ribose}{(!{rt2})}{}% replace "(!{rt2})" by nothing
\chemfig{!{deoxyribose}} \quad\quad In deoxyribose, substituent rt2 is replaced by nothing

\drawhline

\derivesubmol{deoxyadenosine}{deoxyribose}{!{rt1}}{-[2,0.8]!{adenine}}
\chemfig{!{deoxyadenosine}} \quad\quad \parbox{4in}{Deoxyadenosine is derived from deoxyribose by substituting rt1 with adenine}

\drawhline%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% other method: locally redefine "rt1" submol and display "deoxyribose"
\begingroup
    \derivesubmol{rt1}{rt1}{rt1}{!{adenine}}
    \chemfig{!{deoxyribose}}
\endgroup
%
\quad\quad \parbox{4in}{Local redefinition of the rt 1 substituent in deoxyribose works, too}


\drawhline%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\derivesubmol{deoxyuridine}{deoxyribose}{!{rt1}}{-[2]!{uracil}}
\chemfig{
         !{deoxyuridine}
         !{phosphate}
         !{deoxyadenosine}
         !{phosphate}
         !{deoxyuridine}
        }
%
\quad\quad \parbox{2.5in}{Using the previously derived dU and dA templates, we can now easily write a DNA molecule}
\end{document}

The figure shows the result of the last \chemfig command:

Needless to say that I'm extremely happy with this solution. In case someone isn't, the chemfig package allows them to tweak all aspects of the structures with little effort. I recommend it highly.

Answer 2

It's not entirely clear what you mean, but the following seems a bit easier to use. Please note that I'm not a chemist and it's ages ago since I studied chemistry (at secondary school level).

\documentclass{minimal}
\usepackage{chemfig}   

\setatomsep{2.0em}
\setcrambond{2.0pt}{}{}
\setbondoffset{0.5pt}  

\definesubmol{OH}[HO]{OH} % let OH groups figure out which way to point

\definesubmol{phosphonate}{%
                 P          
     (=[::90,0.7]O)         
    (-[::-90,0.7]!{OH})     
       -[::0,0.7]!{OH}      
}                           

\definesubmol{sub1}{A}
\definesubmol{sub6}{B}

\definesubmol{fructose}{
      {}?[a]            
         (-[:90,0.6]    
          -[:30,0.7]O   
          -[:0,0.7]!{sub1}
         )
      <[:225,0.8]
         (-[:-90,0.6]OH)
         (-[:180,0.5,,,draw=none]          % note the devlishly clever trick
          -[:90,1.26,,,draw=none]O?[a]?[b] % to position the oxigen in the ring
         )
      -[:180,1,,,line width=2pt]
         (-[:90,0.6]OH)
      >[:135,0.8]?[b]
      -[:90,0.6]
      -[:150,0.7]O
      -[:180,0.7]!{sub6}
}

\begin{document}

\tikzset{sub1/.code=\redefinesubmol{sub1}{#1},
         sub6/.code=\redefinesubmol{sub6}{#1}}

\begin{tikzpicture}[x=0.8in,y=0.8in]
    \node[anchor=south west] at (0,2) {\chemfig{!{fructose}}};
    \begin{scope}[sub1=H,sub6=H]
        \node[anchor=south west,sub1=H,sub6=H] at (2.5,2) {\chemfig{!{fructose}}};
    \end{scope}
    \begin{scope}[sub1=!{phosphonate},sub6=H]
        \node[anchor=south west] at (5,2) {\chemfig{!{fructose}}};
    \end{scope}
    \begin{scope}[sub1=H,sub6=!{phosphonate}]
        \node[anchor=south west] at (0,0) {\chemfig{!{fructose}}};
    \end{scope}
    \begin{scope}[sub1=!{phosphonate},sub6=!{phosphonate}]
        \node[anchor=south west] at (2.5,0) {\chemfig{!{fructose}}};
    \end{scope}
\end{tikzpicture}

\end{document}

Of course you can also use the options sub1 and sub6 in the node options.

Perhaps you could explain again what you want? (Sorry about the ignorance.)