This issue very well could be related to: this post
When \callchemfigsymbol{s_adenosyl_l_methionine.tex} is uncommented, an error is observed. When \callchemfigsymbol{methane_pseudo_3D_stereo.tex} is called, the mwe compiles.
What's the difference? My first guess is that the commands (e.g. \mcfabove, \mcfplus, and \phantom) in the more complex structural formula are not playing well with catchfile?
I am compiling on W10 with MiKTeX. The version of mol2chemfig I am using should be the latest.
Error message:
Runaway argument?
{
! Paragraph ended before \CF_chemfigb was complete.
<to be read again>
\par
l.190 ...hemfigsymbol{s_adenosyl_l_methionine.tex}
%
?
Here is the not so minimal working (fingers crossed) example:
\documentclass[english,border=1mm]{standalone}
\usepackage[T1]{fontenc}
\usepackage{chemfig}
\usepackage{tikz}
\usepackage{catchfile}
\usepackage{mol2chemfig}%
\tikzset{
% #1 = left, #2 = lower, #3 = right, #4 = upper
enlarge bounding box by/.style n args={4}{
execute at end picture={
\path ([shift={(-#1, -#2)}]current bounding box.south west) --
([shift={(#3, #4)}]current bounding box.north east);
}
}
}
% chemfigdo
\newcommand{\chemfigdo}[2]{\chemfig[#2]{#1}}%
% chemfiginput
\newcommand{\chemfiginput}[2][]{%
\CatchFileDef{\chemfiginputtemp}{#2}{\csname CF_sanitizecatcode\endcsname}%
\expandafter\chemfigdo\expandafter{\chemfiginputtemp}{#1}%
}%
% create new command for tikzpicture call
\newcommand\callchemfigsymbol[1]{%
\chemfiginput[
atom style={scale=\chemfigscale},
atom sep=\chemfigatomsep,
chemfig style={
enlarge bounding box by={\chemfigborder}{\chemfigborder}{\chemfigborder}{\chemfigborder},
baseline=(current bounding box.center),
color=\chemfigcolor,
line width=\chemfiglinewidth
}
]{#1}%
}
\begin{filecontents}{s_adenosyl_l_methionine.tex}
O% 6
=[:95.9]% 26
(
-[:35.9]O% 5
-[:335.9,0.62]H% 50
)
-[:155.9]% 24
(
<:[:95.9]N% 10
(
-[:155.9,0.62]H% 46
)
-[:35.9,0.62]H% 45
)
(
-[:155.9,0.62]H% 44
)
-[:215.9]% 21
(
-[:235.9,0.62]H% 39
)
(
-[:315.9,0.62]H% 40
)
-[:155.9]% 18
(
-[:55.9,0.62]H% 34
)
(
-[:135.9,0.62]H% 35
)
-[:215.9]\mcfabove{S}{_{\mcfplus}}% 1
(
-[:275.9]% 22
(
-[:275.9,0.62]H% 42
)
(
-[:5.9,0.62]H% 43
)
-[:185.9,0.62]H% 41
)
-[:155.9]% 17
(
-[:55.9,0.62]H% 32
)
(
-[:135.9,0.62]H% 33
)
>[:215.9]% 13
(
-[:332.9,0.62]H% 28
)
-[:269.9]O% 2
-[:197.9]% 16
(
-[:125.9]% 15
(
-[:53.9]% 14
(
-[:341.9]% -> 13
)
(
-[:44.9,0.62]H% 29
)
<:[:107.9]O% 3
-[:47.9,0.62]H% 36
)
(
-[:116.9,0.62]H% 30
)
<:[:179.9]O% 4
-[:119.9,0.62]H% 37
)
(
-[:314.9,0.62]H% 31
)
<[:251.9]N% 7
-[:197.8,0.994]% 19
=^[:150]N% 9
-[:210]% 27
(
-[:150,0.62]H% 47
)
=^[:270]N% 11
-[:330]% 25
(
-[:270]N% 12
(
-[:330,0.62]H% 49
)
-[:210,0.62]H% 48
)
=^[:30]% 23
(
-[:90]% -> 19
)
-[:342.2,0.994]N% 8
=^[:54,0.994]% 20
(
-[:126,0.994]\phantom{N}% -> 7
)
-[,0.62]H% 38
\end{filecontents}
\begin{filecontents}{methane_pseudo_3D_stereo.tex}
H% 2
-[:270]C% 1
(
-[:200]H% 4
)
(
<[:310]H% 5
)
<:[:350]H% 3
\end{filecontents}
% define the atom sep
\newlength{\chemfigatomsep}%
\setlength{\chemfigatomsep}{2.75em}%
% define the line width
\newlength{\chemfiglinewidth}%
\setlength{\chemfiglinewidth}{0.75pt}%
% define the scale
\def\chemfigscale{1}
% define the color
\def\chemfigcolor{blue!40!black}
% define separation length
\newlength{\chemfigborder}
\setlength{\chemfigborder}{1mm}
\begin{document}
%\callchemfigsymbol{s_adenosyl_l_methionine.tex}% when I uncomment this, I observe error
\callchemfigsymbol{methane_pseudo_3D_stereo.tex}% this works fine
\end{document}
\usepackage[latin9]{inputenc}because give me an error but your mwe compiles correctly. What OS, do you use and what is the your LaTeX distribuition (is it outdata?), please? Regards. – Sebastiano Aug 01 '20 at 11:45tabularenvironment. I'm likely ignorant of a more elegant implementation, any advice is appreciated. – John Chris Aug 01 '20 at 17:11%\callchemfigsymbol{s_adenosyl_l_methionine.tex}%this line? – John Chris Aug 01 '20 at 20:56