http://www.ccl.net/cca/text-processing/tex/chemtex/chap6a.shtml
CCL chap6a.tex
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\centerline{CHAPTER VI}
\vspace{\len mm}
\centerline{THE COMPLETE SYSTEM OF MACROS --- ITS DESIGN}
\centerline{AND ITS USE}
\vspace{\len mm}
\centerline{1. GENERAL DESIGN CRITERIA}
\vspace{\len mm}
LaTeX code can be written to typeset a structure diagram for any
chemical compound in such a way that the diagram conforms to
accepted practices in chemistry publications.  The purpose
of the macros in this thesis is to reduce the amount of
low-level, bond-by-bond coding necessary to typeset a particular
structure.  The problem of designing a generally useful system
of macros for this purpose has to be seen in the context
of the large number of possible structures: More than 7 million
chemical compounds are registered with the Chemical Abstracts
Service, including 60,000 different ring systems, and
The fragments to be typeset by the macros in this thesis were
selected such that they could be helpful in producing the
more common types of structures.  The arguments of each macro
in turn were selected with the goal of making the respective
fragment as flexible as possible, such that the more common
known structures of this type can be typeset by a particular
macro.  The selection criteria were informal, using the
expert knowledge'' of the writer. --- Where a related
approach to displaying chemical structure diagrams was taken
in previous work, a similar selection of fragments was made
(Zimmerman 84)(Bendall 80,85). Both authors are chemists and
present a collection of fragments without any attempt to
justify their choices.

For more flexibility, the user of the system of macros
presented in this thesis can effect many structural
variations by defining an outer picture (see chapter V)
and placing supplemental lines and atomic symbols into
it in addition to the fragment(s) produced by the macros.
It is estimated that the \newpage
\noindent macros can provide shortcuts
to the drawing of more than 50\% of the structures shown
in the widely used textbook by Solomons (Solomons 84).

The next section lists the individual macros in this system,
each with a typical generic structure and directions for
the use of all arguments.  Specific selection criteria for
the fragment as such and the arguments are mentioned in
many cases.  The fragments are listed in the traditional
categories of organic chemistry: acyclic structures,
alicyclic structures (rings where all ring members are
carbon atoms), and heterocyclic structures.  The number
of arguments is given in brackets behind the macro name.

\vspace{\len mm}
\centerline{2. MACROS OF THE SYSTEM}
\vspace{\len mm}
\noindent A. \underline{Macros for Acyclic Fragments}

\vspace{\len mm}
\indent i. \underline{Macro $\backslash$cbranch[9]}. \ This macro
typesets structural fragments with vertical branches:
\pht=700

$\cbranch{R^{1}}{S}{R^{3}}{S}{Z}{S}{R^{7}}{S}{R^{9}}$

\begin{description}
\item[{\rm \ \ \ \ \ \ Arguments 1, 3, 7, 9: }] The substituent formulas for
${\rm R^1}$, ${\rm R^3}$, ${\rm R^7}$, and
${\rm R^9}$.
\item[{\rm \ \ \ \ \ \ Argument 2: }] The bond between ${\rm R^1}$ and Z,
S'' for a single bond and D''for a double
bond. No action is taken for any other value of
the argument.
\item[{\rm \ \ \ \ \ \ Argument 4: }] The bond between ${\rm R^3}$ and Z,
S'' for a single bond and D'' for a double
bond. When the argument is Q'', no bond is
drawn and ${\rm R^3}$ is moved next to Z.
\item[{\rm \ \ \ \ \ \ Argument 5: }] The center atom(s), Z. When the argument is
a string of more than one character, argument~6
should not be S'' or D,'' and argument~7
should be an empty set.
\newpage
\item[{\rm \ \ \ \ \ \ Argument 6: }] The bond between Z and ${\rm R^7}$,
S'' for a single bond and D'' for a double
bond. No action is taken for any other value
of the argument.
\item[{\rm \ \ \ \ \ \ Argument 8:} ] The bond between Z and ${\rm R^9}$,
S'' for a single bond and D'' for a double
bond. No action is taken for any other value
of the argument.
\end{description}

\vspace{\len mm}
\indent ii. \underline{Macro $\backslash$tbranch[7]}. \
This macro typesets structural fragments with vertical branches
similar to \verb+\+cbranch. The main reason for including
\verb+\+tbranch is to show the use of the LaTeX tabbing
mechanism for printing structural fragments.
Macro \verb+\+cbranch is the preferred macro for structures
of this type.  In contrast to the other macros, \verb+\+tbranch
provides the math mode for the substituent formulas in the
macro code. Therefore substituent formula arguments do not
have to be enclosed by \$symbols. $\tbranch{R^1}{S}{R^3-}{Z-}{S}{R^6}{13}$ \begin{description} \item[{\rm \ \ \ \ \ \ Arguments 1 and 6: }] The substituent formulas for${\rm R^1}$and${\rm R^6}$. \item[{\rm \ \ \ \ \ \ Argument 2: }] The bond between${\rm R^1}$and Z, S'' for a single bond and D'' for a double bond. No action is taken for any other value of the argument. \item[{\rm \ \ \ \ \ \ Argument 3: }] Atom symbols and bonds to the left of Z. Single bonds have to be typed in as hyphens, double bonds as equal signs. \item[{\rm \ \ \ \ \ \ Argument 4: }] The center atom Z and any bonds and atom symbols to its right. Single bonds have to be typed in as hyphens, double bonds as equal signs. \item[{\rm \ \ \ \ \ \ Argument 5: }] The bond between Z and${\rm R^6}$, S'' for a single bond and D'' for a double bond. No action is taken for any other value of the argument. \newpage \item[{\rm \ \ \ \ \ \ Argument 7: }] An integer number which is interpreted as printer points of negative space between lines. The correct number for a document with double spacing is 13. \end{description} \vspace{\len mm} \indent iii. \underline{Macro$\backslash $ethene[4]}. \ This macro typesets an ethene fragment with four variable substituents: $\ethene{R^1}{R^2}{R^3}{R^4}$ Arguments 1 -- 4 are the substituent formulas represented by${\rm R^1}$,${\rm R^2}$,${\rm R^3}$, and${\rm R^4}$. \vspace{\len mm} \indent iv. \underline{Macro$\backslash $upethene[4]}. \ This macro is similar to \verb+\+ethene, but it draws the ethene double bond vertically: $\upethene{R^1}{R^2}{R^3}{R^4}$ The arguments have the same meaning as they do for \verb+\+ethene. \vspace{\len mm} \indent v. \underline{Macro$\backslash $cright[7]}. \ This macro typesets the following fragment which is often used for carboxylic acids and their derivatives: $\cright{R^1}{S}{Z}{S}{R^5}{S}{R^7}$ \begin{description} \item[{\rm \ \ \ \ \ \ Arguments 1,5,7:}] The substituent formulas${\rm R^1}$,${\rm R^5}$, and${\rm R^7}$. \newpage \item[{\rm \ \ \ \ \ \ Argument 2:}] The bond between${\rm R^1}$and Z, S'' for a single bond and D'' for a double bond. For an argument of Q'', no bond is drawn and${\rm R^1}$is moved next to Z. \item[{\rm \ \ \ \ \ \ Argument 3:}] The center atom(s) Z. \item[{\rm \ \ \ \ \ \ Argument 4:}] The bond between Z and${\rm R^5}$, S'' for a single bond and D'' for a double bond. \ri . \item[{\rm \ \ \ \ \ \ Argument 6:}] The bond between Z and${\rm R^7}$, S'' for a single bond and D'' for a double bond. \ri . \end{description} \vspace{\len mm} \indent vi. \underline{Macro$\backslash $cleft[7]}. \ This macro typesets a fragment similar to the one produced by \verb+\+cright, but opening to the left: $\cleft{R^1}{S}{Z}{S}{R^5}{S}{R^7}$ \begin{description} \item[{\rm \ \ \ \ \ \ Arguments 1, 5, 7:}] The substituent formulas${\rm R^1}$,${\rm R^5}$, and${\rm R^7}$. \item[{\rm \ \ \ \ \ \ Argument 2:}] The bond between${\rm R^1}$and Z, S'' for a single bond and D'' for a double bond. \ri . \item[{\rm \ \ \ \ \ \ Argument 3:}] The center atom(s) Z. When the argument is a string of more than one character, argument~6 should not be S'' or D'', and argument~7 should be an empty set. \item[{\rm \ \ \ \ \ \ Argument 4:}] The bond between${\rm R^5}$and Z, S'' for a single bond and D'' for a double bond. \ri . \item[{\rm \ \ \ \ \ \ Argument 6:}] The bond between Z and${\rm R^7}$, S''for a single bond and D'' for a double bond. \ri . \end{description} \vspace{\len mm} \newpage \indent vii. \underline{Macro$\backslash $chemup[7]}. \ This macro typesets the following fragment which can be used for small molecules with trigonal geometry: $\chemup{R^1}{S}{Z}{S}{R^5}{S}{R^7}$ \begin{description} \item[{\rm \ \ \ \ \ \ Arguments 1, 5, 7:}] The substituent formulas${\rm R^1}$,${\rm R^5}$, and${\rm R^7}$. \item[{\rm \ \ \ \ \ \ Argument 2:}] The bond between${\rm R^1}$and Z, S'' for a single bond and D'' for a double bond. \ri . \item[{\rm \ \ \ \ \ \ Argument 3:}] The center atom Z. \item[{\rm \ \ \ \ \ \ Argument 4:}] The bond between Z and${\rm R^5}$, S'' for a single bond and D'' for a double bond. \ri . \item[{\rm \ \ \ \ \ \ Argument 6:}] The bond between Z and${\rm R^7}$, S'' for a single bond and D'' for a double bond. \ri . \end{description} \vspace{\len mm} \indent viii. \underline{Macro$\backslash $cdown[7]}. \ This macro typesets a fragment similar to the one produced by \verb+\+chemup, but opening downwards: $\cdown{R^1}{S}{Z}{S}{R^5}{S}{R^7}$ The arguments have the same meaning as they do for \verb+\+chemup. \vspace{\len mm} \newpage \indent ix. \underline{Macro$\backslash $csquare[5]}. \ This macro typesets a fragment that is sometimes used when all four substituents on a center atom have to be shown explicitly: $\csquare{R^1}{R^2}{Z}{R^4}{R^5}$ \begin{description} \item[{\rm \ \ \ \ \ \ Arguments 1, 2, 3, 4:}] The substituent formulas${\rm R^1}$,${\rm R^2}$,${\rm R^4}$, and${\rm R^5}$. \item[{\rm \ \ \ \ \ \ Argument 3:}] The center atom Z. \end{description} \vspace{\len mm} \indent x. \underline{Macro$\backslash $ccirc[4]}. \ This macro typesets a fragment used to show the actual configuration at a tetrahedral atom. The tetrahedral atom itself is not shown and is assumed to be in the middle of the sphere represented by the circle. The bonds typeset as heavier lines and intersecting the circle are directed out of the plane of the paper, towards the viewer. $\ccirc{R^1}{R^2}{R^3}{R^4}$ The arguments 1 -- 4 are the substituent formulas${\rm R^1}$,${\rm R^2}$,${\rm R^3}$, and${\rm R^4}\$.

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