\subsection{Displaying atom numbers}

% well this is a steaming pile. What do I do with this? A better use of displaying atom numbers is in connection with cross bonds. Let's go for those, then. 


If we look closely at the second doxorubicin graphic above, we notice that some bonds aren't quite straight but are veering slightly off course. In order to fix that up manually, we would need to correlate the atoms in the generated \texttt{.tex} file with the graphic. To do so, we display their numbers with the \lstinline!--atom-numbers! or \lstinline!-n! option:

\lstinputlisting{doxo-numbered.sh}

which gives

\cfpic{doxo-numbered.tex}

Let's say we want to straighten out the double bonds that point to atom no.\ 9 and no.\ 10. We delve into the previously generated, unnumbered version of the file and locate the atoms (only a fragment of the file is shown):

\lstinputlisting[firstline=37,lastline=48]{doxo-stripped.tex}

We see that the bond angles slightly deviate from multiples of 90 degrees in both cases. Indeed, slightly inaccurate angles are seen all over the file; fixing them all would be tedious. Instead, we can simply ask \mcf to recalculate the coordinates for us.


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