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\documentstyle[12pt]{report}
\nofiles
\def\LATEX{\LaTeX}
\let\TEX = \TeX
\setcounter{totalnumber}{5}
\setcounter{topnumber}{3}
\setcounter{bottomnumber}{3}
\setlength{\oddsidemargin}{3.9cm} %real measurement 1.5in
\setlength{\textwidth}{5.7in} %right margin is now 1in
\setlength{\topmargin}{1cm}
\setlength{\headheight}{.6cm}
\setlength{\textheight}{8.5in}
\setlength{\parindent}{1cm}
\renewcommand{\baselinestretch}{1.5}
\raggedbottom
\input{init.tex}
\input{hetisix.tex}
\input{hetifive.tex}
\input{furanose.tex}
\input{pyranose.tex}
\input{purine.tex}
\input{six.tex}
\input{fparts.tex}
\input{cleft.tex}
\input{cto.tex}
\begin {document}
\setcounter{page}{35}
\setcounter{chapter}{5}
\textfont1=\tenrm
\initial
\len=4
\centerline{CHAPTER V}
\vspace{\len mm}
\centerline{COMBINING STRUCTURES FROM SEVERAL MACROS}
\vspace{\len mm}
\centerline{1. GENERAL CONSIDERATIONS FOR COMBINING STRUCTURES}
\centerline{IN THIS SYSTEM}
\vspace{\len mm}
Many individual
structure diagrams can be typeset using just one of the macros
together with condensed, one-line formulas; but often it will be
necessary to combine the ring structure or the branched fragment
from one macro with a structure part from another. To do this,
the separate parts have to be precisely aligned horizontally and
vertically. The typesetting of chemical equations containing
structure diagrams also requires such alignments and is therefore
included in this chapter.
For the system of macros described here, alignment consists of moving
each of the structure fragments as a whole, either within its
picture box or together with the box.
In each structure diagram there are many different points to which
other fragments can be attached. Similarly, one and the same
structure can be aligned in different ways with others to produce
a chemical equation. For these reasons, it was not considered
feasible to develop a symbolic language for alignment, such as
``attach(sixring) at(1) to(fivering) at(4).'' Instead, this
system lets the user manipulate the placement of the structures
at a lower level by using some of the numerical coordinates from
the macros. While it may be considered a disadvantage that the
user has to extract information from the macros, this method also
puts a lot more control into the hands of the user. The type of
user anticipated for this system will probably prefer this
mechanism to an overdose of user-friendliness. Outright manipulation
of coordinates is also well suited for the textual method of
structure input employed in this system, since it helps the user
to visualize the result.
The information that is needed from a macro
to form a new structure \linebreak from fragments is the coordinate
pair for the point of attachment in each fragment. A part of
the code for the sixring and the relevant part of the structure
is shown in figure 5.1 to illustrate briefly how these
coordinate pairs are obtained:
If a fragment is to be attached directly to a ring position,
for example to position 1, the coordinate pair is found in
the unconditional part of the code as the origin of the bondline
beginning at position 1. (The code for the bond is located by
finding the respective line comment.) The coordinate pair in
this case would be (342,200). --- A fragment can also be attached
to the end of a bond extending from the ring. These bonds are
optional and part of the conditional code. The optional bond
extending from position 1 is located through the comment
``substituent on 1.'' The x-coordinate at the end of this bond
is $342 + 128 = 470$, since the length of the bond given in
the code, 128 units, is the projection on the x-axis.
The y increment from ring position 1 to the end of the bond
is obtained from the slope of the line and the x increment
of 128: ${\rm \Delta x(3\mbox{/}5)=77}$.
Thus, the y-coordinate at the end of the bond is
$200 + 77 = 277$ units. -- Appendix B lists the coordinates
of the more commonly used points of attachment for the
system of macros described here.
\setlength{\unitlength}{.2pt}
\begin{figure}[tb]
\hspace{5cm}
\begin{picture}(400,530)(0,-200)
\put(342,200) {\line(0,-1) {200}}
\put(342,0) {\line(-5,-3){171}}
\put(171,303) {\line(5,-3) {171}}
\put(342,200) {\line(5,3) {128}}
\thinlines
\put(342,200) {\vector(1,0){128}}
\put(470,200) {\vector(-1,0){128}}
\put(470,200) {\vector(0,1) {77}}
\put(470,277) {\vector(0,-1){77}}
\put(320,160) {{\scriptsize 1}}
\put(320,0) {{\scriptsize 2}}
\put(370,150) {{\scriptsize 128}}
\put(490,220) {{\scriptsize 77}}
\end{picture}
\begin{minipage}{14cm}
\begin{verbatim}
\begin{picture}(\pw,\pht)(-\xi,-\yi)
.....
\put(342,200) {\line(0,-1) {200}} % bond from 1 to 2
\ifx#1Q
\else\put(342,200){\line(5,3) {128}} % substituent on 1
\put(475,250){#1} \fi
.....
\end{picture}
\end{verbatim}
\end{minipage}
\caption{Finding coordinates of points of attachment}
\end{figure} %figure 5.1
\setlength{\unitlength}{.1pt}
Two conceptually different methods were used in this thesis
to combine structure fragments from different macros. ---
One method follows a suggestion in the LaTeX manual (Lamport 86,
p. 110) to put subpictures into an encompassing picture with
the \verb+\+put command: \\
\centerline{$\backslash $put(x,y)\{$\backslash $begin\{picture\}
$\ldots \backslash $end\{picture\} \ \ \}. }
The reference point (x,y) is the lower left corner of the
subpicture. When this technique is applied to the chemical
structure macros, the macro invocation constitutes the
subpicture. The user has to set up the encompassing picture
and determine the coordinates of the reference points from
the coordinates of the points of attachment between structure
fragments.
The second method is somewhat less versatile; but there are
applications for which it is preferable. In this method, the
individual picture boxes are put next to one another on one
line or on successive lines. The fragments in the separate
pictures are aligned by shifting the coordinate system, i. e.
by changing the \verb+\+xi and \verb+\+yi values in the
picture declaration, in one or more of the pictures.
Finally, for the alignment of structures in a chemical
equation, it is convenient to use a paragraph box
construction (\verb+\+parbox) in addition to coordinate
shifting. LaTeX centers a paragraph box vertically on the
current line which contains, in the case of the chemical
equation, textual items such as plus symbols, condensed
formulas, and reaction arrows.
Typical applications of all methods of combining structure
fragments will be described in the rest of this chapter.
\pagebreak
\vspace{\len mm}
\centerline{2. COMBINING FRAGMENTS TO FORM A NEW STRUCTURE}
\vspace{\len mm}
\noindent A. \underline{Attachment by the Subpicture Method}
A simple example for this technique of structure-building is
shown in figure 5.2, where two different heterocycles are
fitted together to produce the structure of nicotine.
The LaTeX code to be entered by the user for this structure
is given underneath the diagram.
\begin{figure}[h] % fig. 5.2
\hspace{5cm}
\begin{picture}(900,900)(0,0)
\put(0,0) {\hetisix{D}{Q}{}{Q}{Q}{Q}{D}{D}{N} }
\put(470,277) {\hetifive{$CH_{3}$}{Q}{Q}{Q}{Q}{S}{S}{S}{N} }
\put(135,330) {A}
\put(605,600) {B}
\end{picture}
\begin{minipage}{14 cm}
\begin{verbatim}
\begin{picture}(900,900)(0,0)
\put(0,0) {\hetisix{D}{Q}{}{Q}{Q}{Q}{D}{D}{N} }
\put(470,277) {\hetifive{$CH_{3}$}{Q}{Q}{Q}{Q}{S}{S}{S}{N}}
\end{picture}
\end{verbatim}
\end{minipage}
\caption{Nicotine structure with LaTeX code}
\end{figure}
The code in figure 5.2 illustrates how the user has to set up the
encompassing picture with the \verb+\+begin and \verb+\+end
statements and estimated values for the picture width and height,
both 900 units (about 3cm) in this example. Then the picture box
of the pyridine ring is placed at the origin of the outer picture.
Next, the points of attachment are found in the respective
macros as ${\rm x_{AB}=470}$, ${\rm y_{AB}=277}$ for pyridine
and ${\rm x_{BA}=0}$, ${\rm y_{BA}=0}$ for pyrrolidine.
The coordinates of the reference point in the outer picture
where the inner picture with the pyrrolidine ring has to be
placed then are \\
\centerline{${\rm x=x_{AB}-x_{BA}=470}$, \
${\rm y=y_{AB}-y_{BA}=277}$.}
It is assumed that the lower left corner of both subpictures has
the same coordinates, and this is the case when the macros
are used. When more than two ring structures are combined
one after the other, the calculation of the reference points
is appropriately extended.
Since the macros for the various acyclic branched fragments also
consist of picture boxes, these fragments can be used as
subpictures together with ring structures and with other
acyclic fragments. Thus the structure of thymol in figure 5.3
is produced from the \verb+\+sixring and the \verb+\+cdown
macros. Again, the coordinates for the point of reference for
the \verb+\+cdown picture are calculated from the points of
attachment:\\
\indent ${\rm x=x_{sixring}-x_{cdown}=\ \ 171-\ \ 33=\ \ 138}$\\
\indent ${\rm y=y_{sixring}-y_{cdown}=-103-220=-323}$.\\
Figure 5.4, the structure of penicillic acid, combines
three subpictures, one from the \verb+\+cleft macro and two
from the \verb+\+cbranch macro which draws vertical branches.
\begin{figure}[h] % fig. 5.3
\hspace{6cm}
\begin{picture}(500,1100)(0,-300)
\put(0,0) {\sixring{Q}{$OH$}{Q}{Q}{Q}{$CH_{3}$}{S}{S}{C} }
\put(138,-323) {\begin{picture}(\pw,\pht)(-\xi,-\yi)
\put(33,80) {\line(0,1) {140}}
\put(0,0) {$CH$}
\put(0,0) {\line(-5,-3){121}}
\put(80,0) {\line(5,-3) {121}}
\put(-430,-150){\makebox(300,87)[r]{$H_{3}C$}}
\put(210,-140) {$CH_{3}$}
\end{picture} }
\end{picture}
\begin{minipage}{14cm}
\begin{verbatim}
\begin{picture}(500,1100)(0,-300) % estimated dimensions
\put(0,0) {\sixring ... }
\put(138,-323){\cdown ... }
\end{picture}
\end{verbatim}
\end{minipage}
\caption{Combining ring structure and acyclic subpictures}
\end{figure}
% I did not use the cdown macro, because this chapter needs
% several macros and I did not want to run out of Tex memory.
% But I tried the structure out with the macro.
\yi=200
\begin{figure}[t] % fig. 5.4
\hspace{4.5cm}
\begin{picture}(900,600)(0,-100)
\put(-405,160) {\makebox(300,87)[r]{$H_{3}C$}}
\put(0,70) {\line(-1,1) {100}}
\put(-405,-185) {\makebox(300,87)[r]{$H_{2}C$}}
\put(-9,9) {\line(-1,-1) {100}}
\put(9,-9) {\line(-1,-1) {100}}
\put(0,0) {$C$}
\put(90,33) {\line(1,0) {140}}
\put(240,200) {$O$}
\multiput(267,85)(26,0){2} {\line(0,1){100}}
\put(240,0) {$C$}
\put(330,33) {\line(1,0) {140}}
\put(480,200) {$OCH_{3}$}
\put(520,85) {\line(0,1) {100}}
\put(480,0) {$C$}
\multiput(570,20)(0,26){2} {\line(1,0){140}}
\put(720,0) {$CHCOOH$}
\end{picture}
\caption{Combining acyclic subpictures}
\end{figure}
% Again I did not actually use the macros here, but
% I tried it out with them.
Many structures contain condensed formula fragments between
ring diagrams. The structure of the anesthetic piridocaine
is shown as an example in figure 5.5. In such a case one has
to estimate the average horizontal space per character and move
the second subpicture that much further to the right for each
character, including the subscripts, in the condensed formula
fragment. In the ten point size, in which the characters in
figure 5.5 are printed, the horizontal space per character
is 6.8 points or 68 of the picture units.
\pht=800
\begin{figure}[h] % fig. 5.5
\hspace{4.5cm}
\begin{picture}(1200,800)(0,0)
\put(0,0) {\sixring{$NH_{2}$}{$COOCH_{2}CH_{2}$}
{Q}{Q}{Q}{Q}{D}{D}{D} }
\put(1210,0) {\hetisix{$H$}{Q}{Q}{Q}{Q}{}{Q}{}{$N$} }
\end{picture}
\caption{Condensed formula fragment between rings}
\end{figure}
\reinit
Other special cases occur where a diagram would become
too crowded when the two fragments are put next to one
another. (This does not necessarily reflect steric hindrance
in the real, three-dimensional chemical structure.)
In such cases the user can design a longer bondline and
put it into the outer picture between two points of attachment
on macro-produced structure fragments. The structure of
sucrose, shown in figure 5.6, illustrates this technique.
For this structure, it was estimated that the x-offset
between the bonding oxygen on glucose and the fructose
ring should be at least 200 units to produce a diagram
that does not appear crowded. Using this x-offset and
a bonding angle of $45^{0}$ (the angle used in the pyranose
macro for glucose), the user can then easily calculate the
point of reference for the fructose subpicture.
\begin{figure}
\hspace{3.5cm}
\begin{picture}(1200,800)(0,-100)
\put(0,0) {\pyranose{$H$}{$O$}{}{$OH$}{$OH$}{}{}
{$HO$}{$HO$} }
\put(785,200) {\line(1,1){200}}
\put(985,100) {\furanose{}{$CH_{2}OH$}{$HO$}{}{}{$OH$}{Q}{$HO$} }
\end{picture}
\begin{minipage}{14cm}
\begin{verbatim}
\put(0,0) {\pyranose .... }
\put(785,200) {\line(1,1){200}} } % user-designed line
\put(985,100) {\furanose ... }
\end{verbatim}
\end{minipage}
\caption{User-designed connecting bond line}
\end{figure}
An important special case of combining structure fragments is
the generation of fused ring systems. In a fused ring system
more than one ring atom is shared between rings. ---
A simple method for producing such diagrams is to print the
shared bondlines from individual ring structures precisely
on top of each other. The bond lines have to have the same
lengths, which is true in this system of macros for the
five- and sixrings, the most frequently occurring ones.
The shared lines don't appear to be heavier in the printed
picture than other bond lines. Figure 5.7 shows the structure
diagram of quinoline produced by this method together with
the respective LaTeX code. These fused systems can of
course include substituents and multiple bond variations
at all positions where the original macros made them
possible. --- A relatively small number of single-ring
fragments can produce a large number of fused systems
in this way, among them the very common fused systems
of anthracene, phenanthrene, chrysene, indene, indol,
benzimidazole, quinoline, and acridine.
\begin{figure} % fig. 5.7
\hspace{6cm}
\begin{picture}(900,900)(0,0)
\put(0,0) {\sixring{Q}{Q}{Q}{Q}{Q}{Q}{S}{D}{D} }
\put(342,0) {\hetisix{D}{Q}{Q}{Q}{Q}{Q}{D}{D}{$N$}}
\end{picture}
\begin{minipage}{14cm}
\begin{verbatim}
\begin{picture}(900,900)(0,0)
\put(0,0) {\sixring{Q}{Q}{Q}{Q}{Q}{Q}{S}{D}{D} }
\put(342,0) {\hetisix{D}{Q}{Q}{Q}{Q}{Q}{D}{D}{N} }
\end{picture}
\end{verbatim}
\end{minipage}
\caption{Fusion of fully drawn rings}
\end{figure}
There are also some macros that draw fragments specifically
designed for fusing. The following fragments \\
\[ \fuseiv{Q}{Q}{Q}{Q}{Q}{Q}{Q}{Q}{Q} \hspace{2.6cm}
\fuseup{Q}{Q}{Q}{Q}{Q}{Q}{Q}{Q}{Q} \hspace{1.4cm}
\fuseiii{Q}{Q}{Q}{Q}{Q}{Q} \]
are produced by the \verb+\+fuseiv, \verb+\+fuseup, and
\verb+\+fuseiii macros. They can be attached to the five-
and sixrings as subpictures. These fragments have the
advantage that they can provide more options for double
bond locations than a full ring structure within the
constraint of nine arguments.
\vspace{\len mm}
\noindent B. \underline{Attachment by Shifting the Coordinate
System}
This method is easy to use when a complex structure can be
perceived as a series of fragments put next to one another
horizontally, although not necessarily on exactly the same
level. The structure of nicotine shown in figure 5.2
belongs to this category. As an alternative to the code
listed in figure 5.2, the following LaTeX statements can
be used to produce the nicotine diagram: \\
\indent \verb+\+pw = 470 \\
\indent \verb+\+hetisix $\ldots$ \\
\indent \verb+\+advance \verb+\+yi by 277 \\
\indent \verb+\+hetifive $\ldots$\ \ \ . \\
The first statement here sets the picture width \verb+\+pw
for the pyridine ring so that the rightside end of the
picture box is at the x-coordinate of the point of attachment.
Now LaTeX will put the next item on the line, in this case
the picture box with the pyrrolidine ring, flush next to
the pyridine box. When the structure is printed in a math
display environment (see chapter II) where no spacing between
items on a line is applied, there will be no space between
the picture boxes. When the structure is put into a figure
environment only, without math display, normal spacing
occurs as it would happen between words on a line.
The user then has to request negative horizontal space
between invoking the pyridine and the pyrrolidine macro
to correct for the spacing. A statement
\verb+\+hspace\{-11pt\} produced the right correction for the
typestyle of this document.
The statement \verb+\+advance \verb+\+yi by 277 causes the
coordinate-shifting in the pyrrolidine picture.
By increasing the y-coordinate, the pyrrolidine structure
is shifted upwards so that the points of attachment
of the two rings meet. In general, the coordinate shifts
$\,\Delta $xi and $\,\Delta $yi applied to the second or any
following picture are determined from the points of
attachment (${\rm x_{AB}}$,${\rm y_{AB}}$) and
(${\rm x_{BA}}$,${\rm y_{BA}}$)
(the terminology used for figure 5.2) as follows: \\
\centerline{${\rm \Delta xi=x_{BA} \mbox{,}\;
\Delta yi=y_{AB}-y_{BA} }$.}
For vertical attachment, connecting one fragment to the
lower end of another by coordinate shifting, the following
steps are necessary: The points of attachment of the
upper and the lower fragment are shifted to the bottom
and to the top of their respective picture boxes and
the x-coordinates of attachment are aligned. The new
\verb+\+xi and \verb+\+yi values are then \\
\indent $\backslash {\rm yi_{upper}=-y_{upper} }$ \\
\indent $\backslash {\rm xi_{lower}=x_{upper}-x_{lower} }$ \\
\indent $\backslash {\rm yi_{lower}=\backslash pht_{lower}-
y_{lower}+14}$(correction for vertical spacing). \\
\indent For the structure of adenosine shown in figure 5.8
the points of attachment on purine (at the bottom of
N-9) and on deoxyribose (at the top of the long bond)
have the coordinates (513,-130) and (448,380),
respectively. Thus the structure was produced by the code
given underneath the diagram.
The horizontal space is used here instead of the centering
option. The blank lines \newpage
\noindent after each ring structure code are
necessary to inform LaTeX that the next item should not
be printed on the same line.
\begin{figure}
\hspace{5cm} \yi=130
\purine{Q}{D}{Q}{D}{Q}{$NH_2$}{Q}{D}{Q}
\hspace{5cm} \xi=65 \yi=534
\furanose{N}{}{}{$OH$}{}{$OH$}{}{$HO$}
\begin{minipage}{14cm}
\begin{verbatim}
\hspace{5cm} \yi=130 \purine{ ... }
(blank line)
\hspace{5cm} \xi=65 \yi=534 \furanose{ ... }
(blank line)
\caption{ ... }
\end{verbatim}
\end{minipage}
\caption{Vertical attachment by coordinate shifting}
\end{figure}
\vspace{\len mm}
\centerline{3. ALIGNING STRUCTURES IN AN EQUATION}
\vspace{\len mm}
In a chemical equation containing structure diagrams the
various constituents of the equation have to be horizontally
aligned. The equation is typeset in LaTeX's horizontal mode
on one line, the current printline. Text items such as
condensed formulas and plus symbols are put on the line
as usual, their (imaginary) baseline determining the
position of the line. The structure diagrams, as drawn
by the macros, will not be vertically centered on the
current line. They are drawn in picture boxes which are
typeset on the line with the lower end of the (imaginary)
box at the baseline of the current line. The picture boxes
are positioned at this height without regard to the
coordinates declared for the lower left corner of the
box. To line up the vertical middle of the diagram in the
box with the text of the line, one would have to shift the
diagram downwards beyond the bottom of the declared picture.
While this can be done, it might result in a lack of space
under the equation, since LaTeX reserves space only according
to the declared dimensions of the picture. Paragraph boxes
on the other hand are normally centered on the vertical
center of the current line. Paragraph boxes containing
the macros are positioned somewhat differently, with
a point one third up from the bottom of the picture at
the base of the current line. Thus there is one third of
the declared picture below the base of the current line
which yields enough vertical space to set off the
equation from the succeeding text.
The equation in
figure 5.9 was typeset by putting each macro-drawn
diagram into a \verb+\+parbox. The y-coordinate of the
lower end of the pictures is -300 as usual, which puts
position 2 of the sixring and the CHOH part from the
\verb+\+cleft macro at the base of the current line.
The LaTeX code for the equation is shown underneath it
in the figure.
The y-coordinates of the structures and of the reaction
arrow, in this case drawn by a macro, could be
shifted individually as well to change the alignment.
The TeX control sequence \verb+\+to ($\to $) can be used
instead of the special reaction arrow for chemistry;
($\,\to $) is always centered on the line.
Getting good-looking horizontal spacings within the
equation usually requires some experimenting.
As previously mentioned, there is no inter-item
spacing in math mode. Therefore more explicit horizontal
space has to be added when chemical equations are
typeset in the math display environment.
\begin{figure}
\hspace{1.5cm}
\parbox{40pt}{\sixring{Q}{$R^{2}$}{Q}{Q}{Q}{Q}{S}{S}{C} }
\hspace{1cm} $+$ \hspace{1.5cm}
\parbox{40pt}{\cleft{$CH_{3}$}{S}{$CHOH$}{S}
{$CH_{3}$}{Q}{} }
\parbox{40pt}{\cto{BF_{3}}{60^{0}}{3} }
\hspace{3mm}
\parbox{40pt}{\sixring{$CH{(CH_3)}_2$}{$R^{2}$}{Q}{Q}{Q}{Q}{S}{S}{C} }
\begin{minipage}{14cm}
\begin{verbatim}
\hspace{1.5cm}
\parbox{40pt}{\sixring{Q}{$R^{2}$}{Q}{Q}{Q}{Q}{S}{S}{C} }
\hspace{1cm} $+$ \hspace{1.5cm}
\parbox{40pt}{\cleft{$CH_{3}$}{S}{$CHOH$}{S}
{$CH_{3}$}{Q}{} }
\parbox{40pt}{\cto{BF_{3}}{60_{0}}{3} }
\hspace{3mm}
\parbox{40pt}{\sixring{$CH{(CH_3)}_2$}{$R_{2}$}{Q}{Q}{Q}{Q}
{S}{S}{C} }
\end{verbatim}
\end{minipage}
\caption{Alignment in a chemical equation}
\end{figure}
\end{document}
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