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chemfig 和乐高风格的分子结构

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chemfig 和乐高风格的分子结构

许多生化分子，例如核酸，都是由自然界中有限数量的构建块以层次化方式组成的。在排版这些分子时，最好能复制这种方法。对于 DNA 和 RNA，一种自然的方法是：

  1. 定义核糖、磷酸和碱基（A、C、G、T、U）的单独结构
  2. 从核糖中提取脱氧核糖
  3. 通过将核糖或脱氧核糖与每个碱基结合来创建核苷
  4. 将 DNA 和 RNA 分子写为核苷和磷酸的交替形式。

该chemfig软件包提供了一个\definesubmol命令，允许定义子分子，然后可以将其替换为其他分子。但是，该软件包没有提供内置机制来使此类替换的结果可用作新的子分子。因此，问题是如何定义具有以下行为的命令：

% "\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]{% ...

此描述取自软件包作者chemfig通过电子邮件提供给我的代码。我在下面提供的答案中提供了他的代码运行示例。

为了表明这个问题确实是一个问题，让我补充一点：???

答案1

这个答案是 Christian Tellechea 在私人通信中提供给我的；我把它发布在这里是为了让其他可能感兴趣的人受益。

\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}

图中显示的是最后一条命令的结果\chemfig：

在此处输入图片描述

不用说，我对这个解决方案非常满意。如果有人不满意，这个chemfig软件包可以让他们毫不费力地调整结构的各个方面。我强烈推荐它。

答案2

你的意思不太清楚，但下面的方法似乎更容易使用。请注意，我不是化学家，而且我学化学（中学阶段）已经是很久以前的事了。

\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}

当然你也可以使用选项中的选项sub1和。sub6node

也许你可以再解释一下你想要什么？（抱歉我的无知。）

答案3

我写了一个简短申请上述 Christian Tellechea 通过 @MichaelPalmer 提供的答案，添加所有核苷并制作双链图片。完整代码可以在这里找到这里。

    \documentclass[11pt]{standalone}
\usepackage{chemfig,xstring}    %Draw molecules with easy syntax
\usepackage{times}
\frenchspacing
\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]%
        (%
            -[::115,1.176]O%
            -[::-50,1.176]%
        )%
    <[::45,0.8]%
        (%
          -[::45,,,,line width=2pt,shorten <=-.5pt,shorten >=-.5pt]%
              (!{rt2})%
          >[::45,0.8]%
              (!{rt1})%
         )%
}

\definesubmol{phosphate}{-[::-45,.6]O-[::0,1.5]P(-[::-90,1]O{^-})(=[::0,0.8]O)-[::90,1.5]O}

\definesubmol{adenine}{N*5([::-18]-*6(-N=-N(<:[::-83,1.6,,,red])=(-N(-[::66]H)-[::-66]H<:[::-18,1.5,,,red])-)=-N=-)}
\definesubmol{adenineR}{N*5([::-18]-=N-*6(-(-N(-[::66]H<:[::-25,1.5,,,red])-[::-66]H)=N(<:[::-76,1.5,,,red])-=N-)=-)}

\definesubmol{guanine}{N*5([::-18]-*6(-N=(-N(-[::66]H<:[::-25,1.6,,,red])-[::-66]H)-N(-H<:[::-17,1.7,,,red])-(=O<:[::-75,1.7,,,red])-)=-N=-)}
\definesubmol{guanineR}{N*5([::-18]-=N-*6(-(=O<:[::45,1.5,,,red])-N(-H<:[::-16,1.5,,,red])-(-N(-[::66]H)-[::-66]H<:[::-9,1.5,,,red])=N-)=-)}

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

\definesubmol{cytosine}{N*6(-(=O<:[::50,1.7,,,red])-N(<:[::-73,1.6,,,red])=(-N(-[::66]H)-[::-66]H<:[::-3,1.5,,,red])-=-)}
\definesubmol{cytosineR}{N*6(-=-(-N(-[::66]H<:[::-19,1.7,,,red])-[::-66]H)=N(<:[::-72,1.6,,,red])-(=O<:[::-75,1.6,,,red])-)}

\definesubmol{thymine}{N*6(-(=O)-N(-H<:[::-10,1.6,,,red])-(=O<:[::-75,1.5,,,red])-(-H_3C)=-)}
\definesubmol{thymineR}{N*6(-=(-H_3C)-(=O<:[::32,1.6,,,red])-N(-H<:[::-33,1.7,,,red])-(=O)-)}



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

\derivesubmol{deoxyribose}{ribose}{(!{rt2})}{}% replace "(!{rt2})" by nothing
\derivesubmol{deoxyadenosine}{deoxyribose}{!{rt1}}{-[::65,0.8]!{adenine}}
\derivesubmol{deoxyguanosine}{deoxyribose}{!{rt1}}{-[::65,0.8]!{guanine}}
\derivesubmol{deoxyuridine}{deoxyribose}{!{rt1}}{-[::45,0.8]!{uracil}}
\derivesubmol{deoxycytidine}{deoxyribose}{!{rt1}}{-[::45,0.8]!{cytosine}}
\derivesubmol{thymidine}{deoxyribose}{!{rt1}}{-[::45,0.8]!{thymine}}

\derivesubmol{deoxyadenosineR}{deoxyribose}{!{rt1}}{-[::-35,0.8]!{adenineR}}
\derivesubmol{deoxyguanosineR}{deoxyribose}{!{rt1}}{-[::-35,0.8]!{guanineR}}
\derivesubmol{deoxycytidineR}{deoxyribose}{!{rt1}}{-[::-60,0.8]!{cytosineR}}
\derivesubmol{thymidineR}{deoxyribose}{!{rt1}}{-[::-50,0.8]!{thymineR}}

\begin{tikzpicture}
\scriptsize
\node at (1,3) {\chemfig{ [:-65]
         !{phosphate}!{deoxyadenosine}!{phosphate}!{deoxyguanosine}!{phosphate}!{thymidine}!{phosphate}!{deoxycytidine}}};
\node at (6.4,2.5) {\chemfig{ [:115]
         !{phosphate}!{deoxyguanosineR}!{phosphate}!{deoxyadenosineR}!{phosphate}!{deoxycytidineR}!{phosphate}!{thymidineR}}};   

\end{tikzpicture} 

\end{document}

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