TeX - LaTeX Asked on June 30, 2021
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_sanitizecatcodeendcsname}%
expandafterchemfigdoexpandafter{chemfiginputtemp}{#1}%
}%
% create new command for tikzpicture call
newcommandcallchemfigsymbol[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
defchemfigscale{1}
% define the color
defchemfigcolor{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}
The "MWE" in the question is neither minimal nor working. Here is a real MWE, which shows that the issue has nothing to do with mol2chemfig:
documentclass{standalone}
usepackage{mol2chemfig}
begin{document}
chemfig{
H% 2
-[:270]C% 1
(
-[:200]H% 4
)
(
<[:310]H% 5
)
<:[:350]H% 3
}
bigskip
chemfig{
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{document}
Correct answer by Michael Palmer on June 30, 2021
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