[Tex/LaTex] Chemistry molecular structure drawing programs

mhchemtikz-pgf

I am looking for chemical molecular drawing packages.

There is mhchem which basically sets up a structure for including externally generated molecular structures.

Also Chemfig, which is the closest to a user friendly solution and uses pgf.

The vast majority of chemists would use ISISDraw or other program which has the advantage of being able to name the structure based on IUPAC rules. There is also the brookhaven Protein database which has a file format for large proteins.

My question is: Are there any packages that can convert ISISDraw (or similar molecular drawing packages) file formats to pgf or any packages that are closer to ISISDraw than Chemfig

Best Answer

The short answer is 'no' at the present time. Products such as ISISDraw/Accelrys Draw or ChemDraw produce binary files, which cannot be read directly by TeX. So any conversion would either require a separate tool or reading a text file format, such as ChemDraw's XML format.

By far the most popular file format for journal submission is ChemDraw's .cdx format, which is publicly documented. Thus perhaps the most sensible approach to creating a tool for the conversion would be to read .cdx files.

Related Solutions

[Tex/LaTex] Drawing 3d crystal lattice with molecular layer in tikz

I tried to exclude complex bits of code and maths. This is the brute force attack.

\documentclass{article}
\usepackage{tikz}
%\usetikzlibrary{calc,fadings,decorations.pathreplacing}

\tikzset{My Line Style/.style={ultra thick, blue, fill=yellow!10, fill opacity=0.5,join=round}}

\begin{document}
\begin{tikzpicture}[rotate around x=5] 
    \foreach \x in {0,1,2,3,4,5,6}{% 
      \foreach \z in {0,1,2,3,4,5,6}{%      
      \shade[ball color=gray] (\x,0,\z) circle(0.5);
      }
    }
    \foreach \x in {0.5,1.5,2.5,3.5,4.5,5.5}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0,1,2,3,4,5,6}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{2*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0.5,1.5,2.5,3.5,4.5,5.5}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{3*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0,1,2,3,4,5,6}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{4*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0.5,1.5,2.5,3.5,4.5,5.5}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{5*sqrt(0.74)},\z) circle(0.5);
      }
    }
    \foreach \x in {0,1,2,3,4,5,6}{%
      \foreach \z in {0,1,2,3,4,5,6}{%
      \shade[ball color=gray] (\x,{6*sqrt(0.74)},\z) circle(0.5);
      }
    }

    \draw [My Line Style] (6,{4*sqrt(0.74)},6) -- (4,{4*sqrt(0.74)},6) -- (4,{6*sqrt(0.74)},6) -- 
                          (6,{6*sqrt(0.74)},6) -- cycle;
    \draw [My Line Style] (4,{6*sqrt(0.74)},6) -- (4,{6*sqrt(0.74)},4) -- (6,{6*sqrt(0.74)},4) --
                          (6,{6*sqrt(0.74)},6) -- cycle;
    \draw [My Line Style] (6,{4*sqrt(0.74)},6) -- (6,{4*sqrt(0.74)},4) -- (6,{6*sqrt(0.74)},4) --
                          (6,{6*sqrt(0.74)},6) -- cycle;
\end{tikzpicture}
\end{document}

enter image description here

[Tex/LaTex] Using the mhchem and chemfig packages in conjunction

Bundling my comments into an answer:

I wrote »There is no way to make chemfigs bonds all the same length. Quoting part II section 4 Length of a bond of chemfig's manual:«

Rather than speaking of length of a bond, we should use the term interatomic spacing. If effect, only the interatomic spacing is adjustable with \setatomsep as we have seen on page 6. Once this parameter is set, the length of a bond depends on the content of atoms and, to a lesser extent, the angle the bond makes with the horizontal. It should be obvious that two “slimmer” atoms will have larger edge separations than two which are larger.

While this was true at the time I wrote my comment meanwhile there has been an update to chemfig. Since version 1.1 the following is possible:

When a star follows the macro \chemfig*, the bonds have a fixed length and therefore, the distance between center to center atoms becomes variable. The macro \enablefixedbondlength makes this behavior valid for all macros (starred or not) while \disablefixedbondlength goes back to the default behavior. [...] In rings, even with starred \chemfig*, the default behaviour is restored in order to draw regular polygons.
Regarding your second point part III section 4 Vertical alignment has some information. It will not be immediately helpful, though, I guess. Nonetheless it is important information. The solution for the formula in your question is simple, though: write your formula in a different way:
```
\chemfig{CH_3-C(=[6]O)-CH3}
```
Keep in mind that the first atom in a formula determines the baseline of the whole formula.
As for your third point I recommend reading the blog post “Exploring ChemFig: Customising appearance” of our own @JosephWright which explains a method of how to use mhchem's \cf inside chemfig's \printatom. The crucial part is a redefinition of \CF@node@content
```
\makeatletter
\def\CF@node@content{%
  \expandafter\expandafter\expandafter
    \printatom\expandafter\expandafter\expandafter
      {\csname atom@\number\CF@cnt@atomnumber\endcsname}%
    \ensuremath{\CF@node@strut}%
}
\makeatother
```
which then allows \renewcommand*{\printatom}[1]{{\sffamily\cf{#1}}} for example.

Best Answer

Related Solutions

[Tex/LaTex] Drawing 3d crystal lattice with molecular layer in tikz

[Tex/LaTex] Using the mhchem and chemfig packages in conjunction

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