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 \len=4
 \newcommand{\ri}{No action is taken for any other value of
 the argument}
 
 \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
 innumerable additional structures are possible.
 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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Modified: Sun Apr 14 16:00:00 1991 GMT
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