The package chemscheme, included in chemstyle, allows for temporary text "tags" in .eps files to be replaced with designated chemical compound enumerations (A, B, C, ...; 1, 2, 3, ... ; etc.). This relies on the psfrag package, which requires DVI output; thus, pdfTeX is not directly compatible. The documentation for chemstyle suggests using \usepackage[runs=2]{auto-pst-pdf}, which uses --shell-escape to convert the relabelled .eps figure to .pdf files. However, arXiv does not allow --shell-escape.

Is there a package alternative to chemscheme or a workaround that allows similar functionality in pdfTeX? Can .eps figure chemical compound relabelling be done without --shell-escape?

  • There is chemnum but it also uses psfrag so the actual replacement works the same way. – clemens Mar 19 '16 at 6:55
  • Unfortunately, chemnum uses the same mechanism to replace the image. I would like to think that there is way to implement compound labeling without --shell-escape (I've clarified the question), especially since the arXiv, to which many chemistry paper preprints are sent, does not allow --shell-escape – Bob Mar 20 '16 at 0:37
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    @Anthony OT here, but I'd question 'many' chemistry papers going to arXiv. Most chemistry publishers would view that as 'previous publication' and would not take such drafts. (My day job is as a chemistry lecturer) – Joseph Wright Apr 11 '16 at 8:06
  • One might imagine writing a search-replace routine for EPS files in TeX itself, which would allow renumbering 'in place' (though would be risky as any EPS containing binary data would be messed up). However, I don't think anyone has done that. You've then got the issue that this won't work with PDF-based graphics anyway (fitting in a search-replace with epstopdf sounds very tricky). I'm not sure there's an answer here beyond 'no' at present. – Joseph Wright Apr 11 '16 at 8:09
  • My mistake regarding the arXiv and chemistry. Many of the professors at my university with whom I am familiar send preprints to the arXiv, though perhaps I am overgeneralizing, given these are mostly physical chemists. (I am only an undergraduate.) Do you normally just use the default latex (non-pdf) for chemistry publications when you need chemical compound labeling? Also, would you like to include your "no" response as an answer, so I may close the question? – Bob Apr 11 '16 at 8:35

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