Hot answers tagged chemfig
9
An example for this is given in the documentation of chemfig (part III section 12.5 Draw polymer element). There a macro
\makebraces(<dim up>,<dim down>){<subscript>}{<opening node name>}{<closing node name>}
is defined that exploits chemfig's @{<node name>,<pos>} syntax inside formulas to position delimiters on a ...
8
The chemmacros package offers s,p and sp-hybrid orbitals (based on TikZ), d orbitals are missing (for now). These are examples from the documentation:
\documentclass{article}
\usepackage{chemfig,chemmacros}
\begin{document}
\setbondoffset{0pt}
\chemsetup[orbital]{
overlay ,
opacity = .75 ,
p/scale = 1.6 ,
s/color = blue!50 ,
s/scale = 1.6
...
7
\centerline{ isn't really a latex command (it is in the latex format but just escaped from plain TeX). It makes a box \hsize wide but does not know about latex list structures and the indentation they introduce. So you line is too wide by 25pt which will be the left margin of the list item. Just remove \centerline and replace it with a ...
6
\chemabove and \chembelow may help :
\documentclass{article}
\usepackage{chemfig}
\newcommand*\circleatom[1]{\tikz\node[circle,draw,fill=green!30]{\printatom{#1}};}
\begin{document}
\setlewisdist{4pt}
\schemestart
\chemname{%
\chemfig{%
H_{2}
-[:-90]\lewis{0:,N}
-[:225]H_{2}C
-[:-45]C(=[:-90]O)
...
6
I'll answer under the assumption that you're the one who emailed me the other day about Missing bond type in chemical rendering packages? and to whom I suggested the following definition of the submol {Rsubst}:
\tikzset{
subst/.style={shorten <= 10pt,preaction={draw=white,line width=6pt}}
}
\definesubmol{subst}{-[,-1,,,draw=none]-[::-30,1.5,,,subst]}
...
5
There seems to be some problem with chemfig and easytable; loading chemfig after easytable solves the problem (I commented out the line loading the morehelp package, since my LaTeX system doesn't have it):
\documentclass[12pt,doublespacing,letterpaper]{report}
\usepackage{etex}
\usepackage{cite}
%\usepackage{morehelp}
\usepackage{setspace}
...
5
All of chemfig's bonds have optional arguments which accept the following input:
<bond symb>[<angle spec>,<length factor>,<dpt atom>,<arr atom>,<tikz spec>]
The third, <dpt atom>, and fourth ,<arr atom>, are the important ones here: they specify from which atom of a group of atoms the bond departs and at ...
5
I'm guessing the \circleatom is a copy of what I used here. I vaguely remembered having defined something like it before.
The middle of an -U> arrow is a node named Uarrow@arctangent. If you have only one such arrow you can use that fact to write something beneath it with \chemmove:
\documentclass{article}
\usepackage{chemfig}
...
5
You should use chemfig's \definesubmol instead of \newcommand:
\documentclass{article}
\usepackage{chemfig}
\definesubmol{\lmethyl}{C(-[2]H)(-[4]H)(-[6]H)}
\definesubmol{\rmethyl}{C(-[2]H)(-[6]H)-H}
\definesubmol{\tmethyl}{C(-[2]H)(-[4]H)-H}
\definesubmol{\bmethyl}{C(-[4]H)(-[6]H)-H}
\begin{document}
\chemfig{!\lmethyl-!\rmethyl}
\end{document}
5
We can set the opacity of the bonds we do want to hide to zero and make them visible again with \pgfkeysalso.
Sadly, I have not found a simple way to pass TikZ options to the nodes (the atoms like C and H_3) otherwise it would work like the same with visible on=<slides>.
I propose two solutions:
Redefinition of \printatom with checks a set of ...
5
You can use \noindent to remove the paragraph indentation which saves half the over-hang, and for the rest you can shrink the arrows a bit (I hope that doesn't change the meaning, my chemistry is a bit rusty)
\documentclass[12pt,twocolumn]{article}
\usepackage{chemfig}
\usetikzlibrary{decorations.pathmorphing}
\usepackage{lipsum}
\begin{document}
...
4
The use of \rlap and \llap seems much easier in this case since there is no need to copy and adapt a complex macro:
\def\leftparen{\llap{$\left(\strut\right.$\kern5pt }}
\def\rightparen{\rlap{$\kern5pt \left.\strut\right)_n$}}
\chemfig{
CH_2=[:-30]CH-[:30]C(=[:90]O)-[:-30]O
-[:30]\leftparen CH_2CH_2|\rightparen
...
4
I'm not aware of a truly general approach. I solve these kinds of bonds by using invisible bonds -[,,,,draw=none] for placing atoms or determining access points for other bonds.
Ferrocene and similar compounds are not quite easy with chemfig and my approach is even less general. So far the only way I know is to draw them from scratch (but then I do not need ...
4
The \chemname command takes an optional argument for vertical spacing:
\chemname[<dim>]{\chemfig{<code of the molecule>}}{<name>}
However, since your problem is a common one chemfig gives you the possibility to initialize the space. Quoting the manual:
In fact, to draw the <name> the command \chemname inserts 1.5ex + the ...
4
What you're looking for is the \definesubmol{name}{code} command.
You can insert a sub-molecule inside a chemfig command with !{name}.
\definesubmol{rmethyl}{C(-[0]H)(-[2]H)(-[6]H)}
\chemfig{R-!{rmethyl}}
There are some other things you can do with that command, such as defining different code depending on what direction the bond comes from (so H_3C and ...
4
You could place the arrow's label's contents in a \parbox:
\documentclass{article}
\usepackage{chemfig}
\begin{document}
\schemestart
A \arrow{->[\parbox{5cm}{\centering a\\b}][c]} B
\schemestop
\end{document}
or for convenience define a command:
\documentclass{article}
\usepackage{chemfig}
\makeatletter
...
4
You can load the TikZ-library arrows and use the arrow tips left to and right to. Here's a quick example:
\documentclass{article}
\usepackage{chemfig}
\setatomsep{1.8em}
\usetikzlibrary{arrows}
\begin{document}
\schemestart
\chemfig{Cl|@{Cl}\Lewis{0.,\strut}}
% a long invisible bond should suffice but this demonstrates
% that also scheme nodes can ...
3
Solution
Reordering the load order will solve this issue: Gonzalo's answer demonstrates this nicely.
Underlying cause
The underlying problem here is how the file easy.sty does its allocation of registers:
%
% define dimens for internal computation.
%
\@tempcnta=30\relax
\@whilenum\@tempcnta>\z@\do{%
\expandafter\global\expandafter\newdimen\csname ...
3
Here is a pure chemfig solution :
\documentclass{article}
\usepackage{chemfig}
\begin{document}
\definesubmol{eau}{O(-[::-45]H)-[::45]H}
\def\dist{.75}% set the distance between C+ and water
\chemfig{C^{+}(-[:180,\dist,,,draw=none]!{eau})(-[:60,\dist,,,draw=none]!{eau})-[:-60,\dist,,,draw=none]!{eau}}
\end{document}
3
Simply use the optional argument of \arrow:
\documentclass{article}
\usepackage{chemfig}
\begin{document}
\schemestart
A + B \arrow[-90] AB
\schemestop
\end{document}
Update responding to edit of the question:
You can combine the use of \subscheme with the invisible arrow type 0:
\documentclass{article}
\usepackage{chemfig}
\begin{document}
% ...
3
Here is an imperfect idea. The current angle of the arriving bond at an atom is available through \CF@current@angle. The proposal below uses it to compute the position of the lone pair.
\documentclass{article}
\usepackage{chemfig}
% this is far from perfect, the most obvious restriction is that it only allows
% to place _one_ electron pair.
\makeatletter
...
3
connections between two molecules
If the question is how to draw connections between two molecules created with separate calls of \chemfig then the answer is in principle an easy one. ChemFig's molecules are TikZ pictures, really, and the atoms are nodes in this sense. As such they can be named through ChemFig's @{<node name>} syntax and connected ...
3
I believe a better idea would be to define two submols:
the glucose, i.e. the submol, in a way that it starts from “4” and ends in “1”
a second one identical to the first but all angles mirrored
Then you can simply put one glucose after another in \chemfig{} to get the cellulose structure. No need for flipping and manual adjustment for vertical shifts. ...
3
I usually don't use \chemname and \chemsign within the \schemestart \schemestop “environment”. (But that may be personal preferences). Instead I often use invisible arrows with length zero for dividing compounds. Also, I'd choose more meaningful node names than the default c1, c2,... This way it's easier to see when you refer to a compound which one you ...
3
You can set the bond length at the begining of the ring:
\chemfig{A-*6([,0.5]------)}
gives a ring with half lengthed bonds.
EDIT: this work also with **n syntax.
For example
\chemfig{A-**6([,0.5]------)} \chemfig{A-**6(------)}
gives
3
Your code is missing an opening brace for the \parbox and a \fi in the arrow definition. After adding those I changed the definition of the arrow as follows:
\makeatletter
\definearrow4{s>}{%
\ifx\@empty#3\@empty
\expandafter\draw\expandafter[\CF@arrow@current@style,-CF@full]
\CF@arrow@start@node)--(\CF@arrow@end@node);%
\else
...
2
You may cheat a little with white color :-)
Try this, for example:
\parbox[c][.5\textheight][c]{\columnwidth}{%
\centering\mbox{}%
\def\test{white}%
\only<2>{\def\test{red}}%
\only<3->{\def\test{black}}%
\chemfig[][scale=0.5]{CH_3%6
-[::30]%5
-[::-60]%4
...
2
A better solution is to start the chemfig code of "L-glyceraldehyde" with the middle "H" and to start the one of pyruvate with the middle "C". Then, you don't need the \arrow{0} trick and you don't need to adjust the vertical position of \+
\documentclass{article}
\usepackage{chemfig}
\begin{document}
\schemestart
...
2
You could simply insert a second invisible arrow and maybe use the optional arguments of \+{<dim1>,<dim2>,<dim3>} (where <dim1> is a horizontal space before the plus <dim2> a horizontal space after the plus and <dim3> a vertical shift) to adjust the plus vertically
\documentclass{article}
\usepackage{chemfig}
...
2
chemfig does not provide curved arrows. It is possible to define something with \definearrow - the documentation gives an example. This is not comfortable to use and is only part of what your scheme has: combined curved arrows.
It is probably possible to define such arrows, too, but I don't believe that they're any more comfortable to use. I would try to ...
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